diff --git a/doc/Manual.pdf b/doc/Manual.pdf index 3798dcd2e..0f5f3497d 100644 Binary files a/doc/Manual.pdf and b/doc/Manual.pdf differ diff --git a/doc/html/Manual.html b/doc/html/Manual.html index 1480a9f0f..ad381570b 100644 --- a/doc/html/Manual.html +++ b/doc/html/Manual.html @@ -1,440 +1,440 @@ LAMMPS-ICMS Documentation — LAMMPS documentation

LAMMPS-ICMS Documentation

-

28 Jul 2016 version

+

30 Jul 2016 version

Version info:

The LAMMPS “version” is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on this page of the WWW site. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of the first page of the manual (this page).

LAMMPS-ICMS is an experimental variant of LAMMPS with additional features made available for testing before they will be submitted for inclusion into the official LAMMPS tree. The source code is based on the official LAMMPS svn repository mirror at the Institute for Computational Molecular Science at Temple University and generally kept up-to-date as much as possible. Sometimes, e.g. when additional development work is needed to adapt the upstream changes into LAMMPS-ICMS it can take longer until synchronization; and occasionally, e.g. in case of the rewrite of the multi-threading support, the development will be halted except for important bugfixes until all features of LAMMPS-ICMS fully compatible with the upstream version or replaced by alternate implementations.

  • If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current version of upstream LAMMPS, but may be missing some new features in LAMMPS-ICMS.
  • If you browse the HTML doc pages included in your tarball, they describe the version you have, however, not all new features in LAMMPS-ICMS are documented immediately.
  • The PDF file on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don’t want it to be part of every patch.
  • There is also a Developer.pdf file in the doc directory, which describes the internal structure and algorithms of LAMMPS.

LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator.

LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL).

The primary developers of LAMMPS are Steve Plimpton, Aidan Thompson, and Paul Crozier who can be contacted at sjplimp,athomps,pscrozi at sandia.gov. The LAMMPS WWW Site at http://lammps.sandia.gov has more information about the code and its uses.

The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so we can improve the LAMMPS documentation.

Once you are familiar with LAMMPS, you may want to bookmark this page at Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands.

PDF file of the entire manual, generated by htmldoc

Indices and tables

\ No newline at end of file diff --git a/doc/html/_sources/Manual.txt b/doc/html/_sources/Manual.txt index d93d66dc2..84beb3023 100644 --- a/doc/html/_sources/Manual.txt +++ b/doc/html/_sources/Manual.txt @@ -1,105 +1,105 @@ .. raw:: html

LAMMPS Documentation ==================== -28 Jul 2016 version +30 Jul 2016 version ------------------- Version info: ------------- The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on `this page of the WWW site `_. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of the first page of the manual (this page). * If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current version of LAMMPS. * If you browse the HTML doc pages included in your tarball, they describe the version you have. * The `PDF file `_ on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don't want it to be part of every patch. * There is also a `Developer.pdf `_ file in the doc directory, which describes the internal structure and algorithms of LAMMPS. LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The primary developers of LAMMPS are `Steve Plimpton `_, Aidan Thompson, and Paul Crozier who can be contacted at sjplimp,athomps,pscrozi at sandia.gov. The `LAMMPS WWW Site `_ at http://lammps.sandia.gov has more information about the code and its uses. .. _bug: http://lammps.sandia.gov/bug.html .. _sjp: http://www.sandia.gov/~sjplimp ---------- The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so we can improve the LAMMPS documentation. Once you are familiar with LAMMPS, you may want to bookmark :ref:`this page ` at Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands. `PDF file `_ of the entire manual, generated by `htmldoc `_ .. toctree:: :maxdepth: 2 :numbered: Section_intro Section_start Section_commands Section_packages Section_accelerate Section_howto Section_example Section_perf Section_tools Section_modify Section_python Section_errors Section_history Indices and tables ================== * :ref:`genindex` * :ref:`search` .. raw:: html .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/compute_rigid_local.txt b/doc/html/_sources/compute_rigid_local.txt index 9c1ba55d4..b8755e5a3 100644 --- a/doc/html/_sources/compute_rigid_local.txt +++ b/doc/html/_sources/compute_rigid_local.txt @@ -1,177 +1,200 @@ .. index:: compute rigid/local compute rigid/local command =========================== Syntax """""" .. parsed-literal:: compute ID group-ID rigid/local rigidID input1 input2 ... * ID, group-ID are documented in :doc:`compute ` command * rigid/local = style name of this compute command * rigidID = ID of fix rigid/small command or one of its variants * input = one or more rigid body attributes +.. parsed-literal:: + + possible attributes = id, mol, mass, + x, y, z, xu, yu, zu, ix, iy, iz + vx, vy, vz, fx, fy, fz, + omegax, omegay, omegaz, + angmomx, angmomy, angmomz, + quatw, quati, quatj, quatk, + tqx, tqy, tqz, + inertiax, inertiay, inertiaz + id = atom ID of atom within body which owns body properties + mol = molecule ID used to define body in :doc:`fix rigid/small ` command + mass = total mass of body + x,y,z = center of mass coords of body + xu,yu,zu = unwrapped center of mass coords of body + ix,iy,iz = box image that the center of mass is in + vx,vy,vz = center of mass velocities + fx,fy,fz = force of center of mass + omegax,omegay,omegaz = angular velocity of body + angmomx,angmomy,angmomz = angular momentum of body + quatw,quati,quatj,quatk = quaternion components for body + tqx,tqy,tqz = torque on body + inertiax,inertiay,inertiaz = diagonalized moments of inertia of body Examples """""""" .. parsed-literal:: compute 1 all rigid/local myRigid mol x y z Description """"""""""" Define a computation that simply stores rigid body attributes for rigid bodies defined by the :doc:`fix rigid/small ` command or one of its NVE, NVT, NPT, NPH variants. The data is stored as local data so it can be accessed by other :ref:`output commands ` that process local data, such as the :doc:`compute reduce ` or :doc:`dump local ` commands. Note that this command only works with the :doc:`fix rigid/small ` command or its variants, not the fix rigid command and its variants. The ID of the :doc:`fix rigid/small ` command used to define rigid bodies must be specified as *rigidID*\ . The :doc:`fix rigid ` command is typically used to define a handful of (potentially very large) rigid bodies. It outputs similar per-body information as this command directly from the fix as global data; see the :doc:`fix rigid ` doc page for details The local data stored by this command is generated by looping over all the atoms owned on a processor. If the atom is not in the specified *group-ID* or is not part of a rigid body it is skipped. If it is not the atom within a body that is assigned to store the body information it is skipped (only one atom per body is so assigned). If it is the assigned atom, then the info for that body is output. This means that information for N bodies is generated. N may be less than the # of bodies defined by the fix rigid command, if the atoms in some bodies are not in the *group-ID*\ . .. note:: Which atom in a body owns the body info is determined internal to LAMMPS; it's the one nearest the geometric center of the body. Typically you should avoid this complication, by defining the group associated with this fix to include/exclude entire bodies. Note that as atoms and bodies migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. Here is an example of how to use this compute to dump rigid body info to a file: .. parsed-literal:: compute 1 all rigid/local myRigid mol x y z fx fy fz dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7] ---------- This section explains the rigid body attributes that can be specified. The *id* attribute is the atomID of the atom which owns the rigid body, which is assigned by the :doc:`fix rigid/small ` command. The *mol* attribute is the molecule ID of the rigid body. It should be the molecule ID which all of the atoms in the body belong to, since that is how the :doc:`fix rigid/small ` command defines its rigid bodies. The *mass* attribute is the total mass of the rigid body. There are two options for outputting the coordinates of the center of mass (COM) of the body. The *x*\ , *y*\ , *z* attributes write the COM "unscaled", in the appropriate distance :doc:`units ` (Angstroms, sigma, etc). Use *xu*\ , *yu*\ , *zu* if you want the COM "unwrapped" by the image flags for each atobody. Unwrapped means that if the body COM has passed thru a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box. The image flags for the body can be generated directly using the *ix*\ , *iy*\ , *iz* attributes. For periodic dimensions, they specify which image of the simulation box the COM is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as the rigid body COMs cross periodic boundaries during the simulation. The *vx*\ , *vy*\ , *vz*\ , *fx*\ , *fy*\ , *fz* attributes are components of the COM velocity and force on the COM of the body. The *omegax*\ , *omegay*\ , and *omegaz* attributes are the angular velocity componennts of the body around its COM. The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular momentum components of the body around its COM. The *quatw*\ , *quati*\ , *quatj*\ , and *quatk* attributes are the components of the 4-vector quaternion representing the orientation of the rigid body. See the :doc:`set ` command for an explanation of the quaternion vector. The *angmomx*\ , *angmomy*\ , and *angmomz* attributes are the angular momentum components of the body around its COM. The *tqx*\ , *tqy*\ , *tqz* attributes are components of the torque acting on the body around its COM. The *inertiax*\ , *inertiay*\ , *inertiaz* attributes are components of diagonalized inertia tensor for the body, i.e the 3 moments of inertia for the body around its principal axes, as computed internally by LAMMPS. ---------- **Output info:** This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the array is the number of rigid bodies. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See :ref:`this section ` for an overview of LAMMPS output options. The vector or array values will be in whatever :doc:`units ` the corresponding attribute is in: * id,mol = unitless * mass = mass units * x,y,z and xy,yu,zu = distance units * vx,vy,vz = velocity units * fx,fy,fz = force units * omegax,omegay,omegaz = radians/time units * angmomx,angmomy,angmomz = mass*distance^2/time units * quatw,quati,quatj,quatk = unitless * tqx,tqy,tqz = torque units * inertiax,inertiay,inertiaz = mass*distance^2 units Restrictions """""""""""" This compute is part of the RIGID package. It is only enabled if LAMMPS was built with that package. See the :ref:`Making LAMMPS ` section for more info. Related commands """""""""""""""" :doc:`dump local `, :doc:`compute reduce ` **Default:** none .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/manifolds.txt b/doc/html/_sources/manifolds.txt index 6b2486b8f..19e0a636a 100644 --- a/doc/html/_sources/manifolds.txt +++ b/doc/html/_sources/manifolds.txt @@ -1,45 +1,55 @@ -Description -""""""""""" +Manifolds (surfacse) +==================== -Below is a list of currently supported manifolds, their parameters and a short description of them. -The parameters listed here are in the same order as they should be passed to the relevant fixes. +**Overview:** + +This doc page is not about a LAMMPS input script command, but about +manifolds, which are generalized surfaces, as defined and used by the +USER-MANIFOLD package, to track particle motion on the manifolds. See +the src/USER-MANIFOLD/README file for more details about the package +and its commands. + +Below is a list of currently supported manifolds by the USER-MANIFOLD +package, their parameters and a short description of them. The +parameters listed here are in the same order as they should be passed +to the relevant fixes. +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | *manifold* | *parameters* | *equation* | *description* | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | cylinder | R | x^2 + y^2 - R^2 = 0 | Cylinder along z-axis, axis going through (0,0,0) | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | cylinder_dent | R l a | x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise | A cylinder with a dent around z = 0 | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | dumbbell | a A B c | -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 | A dumbbell | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | ellipsoid | a b c | (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 | An ellipsoid | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | plane | a b c x0 y0 z0 | a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 | A plane with normal (a,b,c) going through point (x0,y0,z0) | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | plane_wiggle | a w | z - a*sin(w*x) = 0 | A plane with a sinusoidal modulation on z along x. | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | sphere | R | x^2 + y^2 + z^2 - R^2 = 0 | A sphere of radius R | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | supersphere | R q | |x|^q + |y|^q + |z|^q - R^q = 0 | A supersphere of hyperradius R | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | spine | a, A, B, B2, c | -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | An approximation to a dendtritic spine | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | spine_two | a, A, B, B2, c | -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise | Another approximation to a dendtritic spine | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | thylakoid | wB LB lB | Various, see :ref:`(Paquay) ` | A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ | torus | R r | (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 | A torus with large radius R and small radius r, centered on (0,0,0) | | +---------------+----------------+----------------------------------------------------------------------------------------------------------------------------+------------------------------------------------------------------------------------------------------------------------------------+--+ .. _Paquay: **(Paquay)** Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published, preprint available at `arXiv:1411.3019 `_. .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/pair_modify.txt b/doc/html/_sources/pair_modify.txt index d52065356..7a01f9d57 100644 --- a/doc/html/_sources/pair_modify.txt +++ b/doc/html/_sources/pair_modify.txt @@ -1,292 +1,289 @@ .. index:: pair_modify pair_modify command =================== Syntax """""" .. parsed-literal:: pair_modify keyword values ... * one or more keyword/value pairs may be listed * keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner* or *tabinner/disp* or *tail* or *compute* .. parsed-literal:: *pair* values = sub-style N *special* which wt1 wt2 wt3 sub-style = sub-style of :doc:`pair hybrid ` N = which instance of sub-style (only if sub-style is used multiple times) *special* which wt1 wt2 wt3 = override *special_bonds* settings (optional) which = *lj/coul* or *lj* or *coul* w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive *mix* value = *geometric* or *arithmetic* or *sixthpower* *shift* value = *yes* or *no* *table* value = N 2^N = # of values in table *table/disp* value = N 2^N = # of values in table *tabinner* value = cutoff cutoff = inner cutoff at which to begin table (distance units) *tabinner/disp* value = cutoff cutoff = inner cutoff at which to begin table (distance units) *tail* value = *yes* or *no* *compute* value = *yes* or *no* Examples """""""" .. parsed-literal:: pair_modify shift yes mix geometric pair_modify tail yes pair_modify table 12 pair_modify pair lj/cut compute no pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 Description """"""""""" Modify the parameters of the currently defined pair style. Not all parameters are relevant to all pair styles. If used, the *pair* keyword must appear first in the list of keywords. It can only be used with the :doc:`hybrid and hybrid/overlay ` pair styles. It means that all the following parameters will only be modified for the specified sub-style. If the sub-style is defined multiple times, then an additional numeric argument *N* must also be specified, which is a number from 1 to M where M is the number of times the sub-style was listed in the :doc:`pair_style hybrid ` command. The extra number indicates which instance of the sub-style the remaining keywords will be applied to. Note that if the *pair* keyword is not used, and the pair style is *hybrid* or *hybrid/overlay*\ , then all the specified keywords will be applied to all sub-styles. The *special* keyword can only be used in conjunction with the *pair* keyword and must directly follow it. It allows to override the :doc:`special_bonds ` settings for the specified sub-style. More details are given below. The *mix* keyword affects pair coefficients for interactions between atoms of type I and J, when I != J and the coefficients are not explicitly set in the input script. Note that coefficients for I = J must be set explicitly, either in the input script via the "pair_coeff" command or in the "Pair Coeffs" section of the :doc:`data file `. For some pair styles it is not necessary to specify coefficients when I != J, since a "mixing" rule will create them from the I,I and J,J settings. The pair_modify *mix* value determines what formulas are used to compute the mixed coefficients. In each case, the cutoff distance is mixed the same way as sigma. Note that not all pair styles support mixing. Also, some mix options are not available for certain pair styles. See the doc page for individual pair styles for those restrictions. Note also that the :doc:`pair_coeff ` command also can be to directly set coefficients for a specific I != J pairing, in which case no mixing is performed. mix *geometric* .. parsed-literal:: epsilon_ij = sqrt(epsilon_i * epsilon_j) sigma_ij = sqrt(sigma_i * sigma_j) mix *arithmetic* .. parsed-literal:: epsilon_ij = sqrt(epsilon_i * epsilon_j) sigma_ij = (sigma_i + sigma_j) / 2 mix *sixthpower* .. parsed-literal:: epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) / (sigma_i^6 + sigma_j^6) sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) The *shift* keyword determines whether a Lennard-Jones potential is shifted at its cutoff to 0.0. If so, this adds an energy term to each pairwise interaction which will be included in the thermodynamic output, but does not affect pair forces or atom trajectories. See the doc page for individual pair styles to see which ones support this option. The *table* and *table/disp* keywords apply to pair styles with a long-range Coulombic term or long-range dispersion term respectively; see the doc page for individual styles to see which potentials support these options. If N is non-zero, a table of length 2^N is pre-computed for forces and energies, which can shrink their computational cost by up to a factor of 2. The table is indexed via a bit-mapping technique :ref:`(Wolff) ` and a linear interpolation is performed between adjacent table values. In our experiments with different table styles (lookup, linear, spline), this method typically gave the best performance in terms of speed and accuracy. The choice of table length is a tradeoff in accuracy versus speed. A larger N yields more accurate force computations, but requires more memory which can slow down the computation due to cache misses. A reasonable value of N is between 8 and 16. The default value of 12 (table of length 4096) gives approximately the same accuracy as the no-table (N = 0) option. For N = 0, forces and energies are computed directly, using a polynomial fit for the needed erfc() function evaluation, which is what earlier versions of LAMMPS did. Values greater than 16 typically slow down the simulation and will not improve accuracy; values from 1 to 8 give unreliable results. The *tabinner* and *tabinner/disp* keywords set an inner cutoff above which the pairwise computation is done by table lookup (if tables are invoked), for the corresponding Coulombic and dispersion tables discussed with the *table* and *table/disp* keywords. The smaller the cutoff is set, the less accurate the table becomes (for a given number of table values), which can require use of larger tables. The default cutoff value is sqrt(2.0) distance units which means nearly all pairwise interactions are computed via table lookup for simulations with "real" units, but some close pairs may be computed directly (non-table) for simulations with "lj" units. When the *tail* keyword is set to *yes*\ , certain pair styles will add a long-range VanderWaals tail "correction" to the energy and pressure. These corrections are bookkeeping terms which do not affect dynamics, unless a constant-pressure simulation is being performed. See the doc page for individual styles to see which support this option. These corrections are included in the calculation and printing of thermodynamic quantities (see the :doc:`thermo_style ` command). Their effect will also be included in constant NPT or NPH simulations where the pressure influences the simulation box dimensions (e.g. the :doc:`fix npt ` and :doc:`fix nph ` commands). The formulas used for the long-range corrections come from equation 5 of :ref:`(Sun) `. .. note:: The tail correction terms are computed at the beginning of each run, using the current atom counts of each atom type. If atoms are deleted (or lost) or created during a simulation, e.g. via the :doc:`fix gcmc ` command, the correction factors are not re-computed. If you expect the counts to change dramatically, you can break a run into a series of shorter runs so that the correction factors are re-computed more frequently. Several additional assumptions are inherent in using tail corrections, including the following: * The simulated system is a 3d bulk homogeneous liquid. This option should not be used for systems that are non-liquid, 2d, have a slab geometry (only 2d periodic), or inhomogeneous. * G(r), the radial distribution function (rdf), is unity beyond the cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an LJ fluid), and it is probably a good idea to verify this assumption by checking the rdf. The rdf is not exactly unity beyond the cutoff for each pair of interaction types, so the tail correction is necessarily an approximation. The tail corrections are computed at the beginning of each simulation run. If the number of atoms changes during the run, e.g. due to atoms leaving the simulation domain, or use of the :doc:`fix gcmc ` command, then the corrections are not updates to relect the changed atom count. If this is a large effect in your simulation, you should break the long run into several short runs, so that the correction factors are re-computed multiple times. * Thermophysical properties obtained from calculations with this option enabled will not be thermodynamically consistent with the truncated force-field that was used. In other words, atoms do not feel any LJ pair interactions beyond the cutoff, but the energy and pressure reported by the simulation include an estimated contribution from those interactions. The *compute* keyword allows pairwise computations to be turned off, even though a :doc:`pair_style ` is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for performing a :doc:`rerun ` simulation, when you only wish to compute partial forces that do not include the pairwise contribution. Two examples are as follows. First, this option allows you to perform a simulation with :doc:`pair_style hybrid ` with only a subset of the hybrid sub-styles enabled. Second, this option allows you to perform a simulation with only long-range interactions but no short-range pairwise interactions. Doing this by simply not defining a pair style will not work, because the :doc:`kspace_style ` command requires a Kspace-compatible pair style be defined. ---------- -Use of *special* keyword -^^^^^^^^^^^^^^^^^^^^^^^^ - The *special* keyword allows to override the 1-2, 1-3, and 1-4 exclusion settings for individual sub-styles of a :doc:`hybrid pair style `. It requires 4 arguments similar to the :doc:`special_bonds ` command, *which* and wt1,wt2,wt3. The *which* argument can be *lj* to change the Lennard-Jones settings, *coul* to change the Coulombic settings, or *lj/coul* to change both to the same set of 3 values. The wt1,wt2,wt3 values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, 1-3, and 1-4 bond topology neighbors, respectively. The *special* keyword can only be used in conjunction with the *pair* keyword and has to directly follow it. .. note:: The global settings specified by the :doc:`special_bonds ` command affect the construction of neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) exclude those pairs from the neighbor list entirely. Weights of 1.0 store the neighbor with no weighting applied. Thus only global values different from exactly 0.0 or 1.0 can be overridden and an error is generated if the requested setting is not compatible with the global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is usually a sufficient workaround in this case without causing a significant error. ---------- Restrictions """""""""""" none You cannot use *shift* yes with *tail* yes, since those are conflicting options. You cannot use *tail* yes with 2d simulations. Related commands """""""""""""""" :doc:`pair_style `, :doc:`pair_coeff `, :doc:`thermo_style ` Default """"""" The option defaults are mix = geometric, shift = no, table = 12, tabinner = sqrt(2.0), tail = no, and compute = yes. Note that some pair styles perform mixing, but only a certain style of mixing. See the doc pages for individual pair styles for details. ---------- .. _Wolff: **(Wolff)** Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). .. _Sun: **(Sun)** Sun, J Phys Chem B, 102, 7338-7364 (1998). .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/_sources/tutorial_github.txt b/doc/html/_sources/tutorial_github.txt index 37cb6ffb5..586ac009d 100644 --- a/doc/html/_sources/tutorial_github.txt +++ b/doc/html/_sources/tutorial_github.txt @@ -1,256 +1,248 @@ LAMMPS GitHub tutorial -********************** +====================== -written by Stefan Paquay -======================== +**written by Stefan Paquay** ---------- -This document briefly describes how to use GitHub to merge changes -into LAMMPS using GitHub. It assumes that you are familiar with +This document briefly describes how to use GitHub to merge changes you +make into LAMMPS, using GitHub. It assumes that you are familiar with git. You may want to have a look at the `Git book `_ to reacquaint yourself. ---------- -Making an account -***************** +**Making an account** First of all, you need a GitHub account. This is fairly simple, just go to `GitHub `_ and create an account by clicking the ``Sign up for GitHub'' button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password. ---------- -Forking the repository -********************** +**Forking the repository** To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to `LAMMPS on GitHub `_ and make sure branch is set to ``lammps-icms'', see the figure below. .. image:: JPG/tutorial_branch.png :align: center Now, click on fork in the top right corner: .. image:: JPG/tutorial_fork.png :align: center This will create your own fork of the LAMMPS repository. You can make changes in this fork and later file *pull requests* to allow the upstream repository to merge changes from your own fork into the one we just forked from. At the same time, you can set things up, so you can include changes from upstream into your repository. ---------- -Adding changes to your own fork -******************************* +**Adding changes to your own fork** Before adding changes, it is better to first create a new branch that will contain these changes, a so-called feature branch. -Feature branches -================ +**Feature branches** Since LAMMPS is such a big project and most user contributions come in small portions, the most ideal workflow for LAMMPS is the so-called ``Feature branch'' workflow. It is explained in great detail here: `feature branch workflow `_. The idea is that every new feature for LAMMPS gets its own branch. This way, it is fairly painless to incorporate new features into the upstream repository. I will explain briefly here how to do it. In this feature branch, I will add a USER-package. I assume that git is installed on the local machine and you know how to use a command line. First of all, you need to clone your own fork of LAMMPS: .. parsed-literal:: $ git clone https://github.com//lammps.git You can find the proper url to the right of the "HTTPS" block, see figure. .. image:: JPG/tutorial_https_block.png :align: center The above command copies (``clones'') the git repository to your local machine. You can use this local clone to make changes and test them without interfering with the repository on github. First, however, it is recommended to make a new branch for a particular feature you would like added to LAMMPS. In this example, I will try adding a new USER-package called USER-MANIFOLD. To create a new branch, run the following git command in your repository: .. parsed-literal:: $ git checkout -b add-user-manifold The name of this new branch is "add-user-manifold" in my case. Just name it after something that resembles the feature you want added to LAMMPS. Now that you've changed branches, you can edit the files as you see fit, add new files, and commit as much as you would like. Just remember that if halfway you decide to add another, unrelated feature, you should switch branches! After everything is done, add the files to the branch and commit them: .. parsed-literal:: $ git add src/USER-MANIFOLD examples/USER/manifold/ $ git add doc/fix_nv\ *t,e*\ _manifold_rattle.txt $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt After the files are added, the change should be comitted: .. parsed-literal:: $ git commit -m 'Added user-manifold package' The "-m" switch is used to add a message to the commit. Use this to indicate what type of change was commited. -Wisdom by Axel: ---------------- +**Wisdom by Axel** *"Do not use "git commit -a". the -a flag will automatically include *all* modified or new files. mercurial does that and it find it hugely annoying and often leading to accidental commits of files you don't want. use git add, git rm, git mv for adding, removing, renaming and then git commit to finalize the commit. personally, i find it very convenient to use the bundled gui for commits, i.e. git gui. typically, i will do git add and other operations, but then verify and review them with git gui. git gui also allows to do line-by-line unstaging and other convenient operations."* After the commit, the changes can be pushed to the same branch on GitHub: .. parsed-literal:: $ git push Git will ask you for your user name and password on GitHub if you have not configured anything. If you correctly type your user name and password, the change should be added to your fork on GitHub. If you want to make really sure you push to the right repository (which is good practice), you can provide it explicitly: .. parsed-literal:: $ git push origin or using an explicit URL: .. parsed-literal:: $ git push git@github.com:Pakketeretet2/lammps.git After that, you can file a new pull request based on this branch. GitHub will now look like this: .. image:: JPG/tutorial_pull_request_feature_branch1.png :align: center Make sure that the current branch is set to the correct one, which, in this case, is "add-user-manifold". Now click "New pull request". If done correctly, the only changes you will see are those that were made on this branch, so in my case, I will see nothing related to $\mathrm*pair\_dzugatov*.$ This will open up a new window that lists changes made to the repository. If you are just adding new files, there is not much to do, but I suppose merge conflicts are to be resolved here if there are changes in existing files. If all changes can automatically be merged, green text at the top will say so and you can click the "Create pull request" button, see image. .. image:: JPG/tutorial_pull_request2.png :align: center After this you have to specify a short title and a comment with details about your pull request. I guess here you write what your modifications do and why they should be incorporated upstream. After that, click the "Create pull request" button, see image below. .. image:: JPG/tutorial_pull_request3.png :align: center Now just write some nice comments, click "Comment", and that is it. It is now up to the maintainer(s) of the upstream repository to incorporate the changes into the repository and to close the pull request. .. image:: JPG/tutorial_pull_request4.png :align: center ---------- -Additional changes -****************** +**Additional changes** Before the pull request is accepted, any additional changes you push into your repository will automatically become part of the pull request. ---------- -After a merge -************* +**After a merge** When everything is fine the feature branch is merged into the LAMMPS repositories: .. image:: JPG/tutorial_merged.png :align: center Now one question remains: What to do with the feature branch that got merged into upstream? It is in principle safe to delete them from your own fork. This helps keep it a bit more tidy. Note that you first have to switch to another branch! .. parsed-literal:: $ git checkout lammps-icms $ git pull lammps-icms $ git branch -d add-user-manifold If you do not pull first, it is not really a problem but git will warn you at the next statement that you are deleting a local branch that was not yet fully merged into HEAD. This is because git does not yet know your branch just got merged into lammps-icms upstream. If you first delete and then pull, everything should still be fine. Finally, if you delete the branch locally, you might want to push this to your remote(s) as well: .. parsed-literal:: $ git push origin :add-user-manifold .. _lws: http://lammps.sandia.gov .. _ld: Manual.html .. _lc: Section_commands.html#comm diff --git a/doc/html/compute_rigid_local.html b/doc/html/compute_rigid_local.html index d2ddebee8..154d01a90 100644 --- a/doc/html/compute_rigid_local.html +++ b/doc/html/compute_rigid_local.html @@ -1,327 +1,350 @@ compute rigid/local command — LAMMPS documentation

compute rigid/local command

Syntax

compute ID group-ID rigid/local rigidID input1 input2 ...
  • ID, group-ID are documented in compute command
  • rigid/local = style name of this compute command
  • rigidID = ID of fix rigid/small command or one of its variants
  • input = one or more rigid body attributes
+
+possible attributes = id, mol, mass,
+                   x, y, z, xu, yu, zu, ix, iy, iz
+                   vx, vy, vz, fx, fy, fz,
+                      omegax, omegay, omegaz,
+                   angmomx, angmomy, angmomz,
+                   quatw, quati, quatj, quatk,
+                      tqx, tqy, tqz,
+                      inertiax, inertiay, inertiaz
+    id = atom ID of atom within body which owns body properties
+    mol = molecule ID used to define body in fix rigid/small command
+    mass = total mass of body
+    x,y,z = center of mass coords of body
+    xu,yu,zu = unwrapped center of mass coords of body
+    ix,iy,iz = box image that the center of mass is in
+    vx,vy,vz = center of mass velocities
+    fx,fy,fz = force of center of mass
+    omegax,omegay,omegaz = angular velocity of body
+    angmomx,angmomy,angmomz = angular momentum of body
+    quatw,quati,quatj,quatk = quaternion components for body
+    tqx,tqy,tqz = torque on body
+    inertiax,inertiay,inertiaz = diagonalized moments of inertia of body
+

Examples

compute 1 all rigid/local myRigid mol x y z

Description

Define a computation that simply stores rigid body attributes for rigid bodies defined by the fix rigid/small command or one of its NVE, NVT, NPT, NPH variants. The data is stored as local data so it can be accessed by other output commands that process local data, such as the compute reduce or dump local commands.

Note that this command only works with the fix rigid/small command or its variants, not the fix rigid command and its variants. The ID of the fix rigid/small command used to define rigid bodies must be specified as rigidID. The fix rigid command is typically used to define a handful of (potentially very large) rigid bodies. It outputs similar per-body information as this command directly from the fix as global data; see the fix rigid doc page for details

The local data stored by this command is generated by looping over all the atoms owned on a processor. If the atom is not in the specified group-ID or is not part of a rigid body it is skipped. If it is not the atom within a body that is assigned to store the body information it is skipped (only one atom per body is so assigned). If it is the assigned atom, then the info for that body is output. This means that information for N bodies is generated. N may be less than the # of bodies defined by the fix rigid command, if the atoms in some bodies are not in the group-ID.

Note

Which atom in a body owns the body info is determined internal to LAMMPS; it’s the one nearest the geometric center of the body. Typically you should avoid this complication, by defining the group associated with this fix to include/exclude entire bodies.

Note that as atoms and bodies migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next.

Here is an example of how to use this compute to dump rigid body info to a file:

compute 1 all rigid/local myRigid mol x y z fx fy fz
 dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]

This section explains the rigid body attributes that can be specified.

The id attribute is the atomID of the atom which owns the rigid body, which is assigned by the fix rigid/small command.

The mol attribute is the molecule ID of the rigid body. It should be the molecule ID which all of the atoms in the body belong to, since that is how the fix rigid/small command defines its rigid bodies.

The mass attribute is the total mass of the rigid body.

There are two options for outputting the coordinates of the center of mass (COM) of the body. The x, y, z attributes write the COM “unscaled”, in the appropriate distance units (Angstroms, sigma, etc). Use xu, yu, zu if you want the COM “unwrapped” by the image flags for each atobody. Unwrapped means that if the body COM has passed thru a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box.

The image flags for the body can be generated directly using the ix, iy, iz attributes. For periodic dimensions, they specify which image of the simulation box the COM is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as the rigid body COMs cross periodic boundaries during the simulation.

The vx, vy, vz, fx, fy, fz attributes are components of the COM velocity and force on the COM of the body.

The omegax, omegay, and omegaz attributes are the angular velocity componennts of the body around its COM.

The angmomx, angmomy, and angmomz attributes are the angular momentum components of the body around its COM.

The quatw, quati, quatj, and quatk attributes are the components of the 4-vector quaternion representing the orientation of the rigid body. See the set command for an explanation of the quaternion vector.

The angmomx, angmomy, and angmomz attributes are the angular momentum components of the body around its COM.

The tqx, tqy, tqz attributes are components of the torque acting on the body around its COM.

The inertiax, inertiay, inertiaz attributes are components of diagonalized inertia tensor for the body, i.e the 3 moments of inertia for the body around its principal axes, as computed internally by LAMMPS.

Output info:

This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the array is the number of rigid bodies. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See this section for an overview of LAMMPS output options.

The vector or array values will be in whatever units the corresponding attribute is in:

  • id,mol = unitless
  • mass = mass units
  • x,y,z and xy,yu,zu = distance units
  • vx,vy,vz = velocity units
  • fx,fy,fz = force units
  • omegax,omegay,omegaz = radians/time units
  • angmomx,angmomy,angmomz = mass*distance^2/time units
  • quatw,quati,quatj,quatk = unitless
  • tqx,tqy,tqz = torque units
  • inertiax,inertiay,inertiaz = mass*distance^2 units

Restrictions

This compute is part of the RIGID package. It is only enabled if LAMMPS was built with that package. See the Making LAMMPS section for more info.

\ No newline at end of file diff --git a/doc/html/manifolds.html b/doc/html/manifolds.html index aef95c505..73f57ef60 100644 --- a/doc/html/manifolds.html +++ b/doc/html/manifolds.html @@ -1,286 +1,294 @@ - Description — LAMMPS documentation + Manifolds (surfacse) — LAMMPS documentation
-
-

Description

-

Below is a list of currently supported manifolds, their parameters and a short description of them. -The parameters listed here are in the same order as they should be passed to the relevant fixes.

+
+

Manifolds (surfacse)

+

Overview:

+

This doc page is not about a LAMMPS input script command, but about +manifolds, which are generalized surfaces, as defined and used by the +USER-MANIFOLD package, to track particle motion on the manifolds. See +the src/USER-MANIFOLD/README file for more details about the package +and its commands.

+

Below is a list of currently supported manifolds by the USER-MANIFOLD +package, their parameters and a short description of them. The +parameters listed here are in the same order as they should be passed +to the relevant fixes.

manifold parameters equation description  
cylinder R x^2 + y^2 - R^2 = 0 Cylinder along z-axis, axis going through (0,0,0)  
cylinder_dent R l a x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise A cylinder with a dent around z = 0  
dumbbell a A B c -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 A dumbbell  
ellipsoid a b c (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 An ellipsoid  
plane a b c x0 y0 z0 a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 A plane with normal (a,b,c) going through point (x0,y0,z0)  
plane_wiggle a w z - a*sin(w*x) = 0 A plane with a sinusoidal modulation on z along x.  
sphere R x^2 + y^2 + z^2 - R^2 = 0 A sphere of radius R  
supersphere R q |x|^q + |y|^q + |z|^q - R^q = 0 A supersphere of hyperradius R  
spine a, A, B, B2, c -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise An approximation to a dendtritic spine  
spine_two a, A, B, B2, c -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise Another approximation to a dendtritic spine  
thylakoid wB LB lB Various, see (Paquay) A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB  
torus R r (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 A torus with large radius R and small radius r, centered on (0,0,0)  

(Paquay) Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published, preprint available at arXiv:1411.3019.

\ No newline at end of file diff --git a/doc/html/pair_modify.html b/doc/html/pair_modify.html index fe24147bb..b45eacca3 100644 --- a/doc/html/pair_modify.html +++ b/doc/html/pair_modify.html @@ -1,434 +1,431 @@ pair_modify command — LAMMPS documentation

pair_modify command

Syntax

pair_modify keyword values ...
  • one or more keyword/value pairs may be listed
  • keyword = pair or shift or mix or table or table/disp or tabinner or tabinner/disp or tail or compute
 pair values = sub-style N special which wt1 wt2 wt3
   sub-style = sub-style of pair hybrid
   N = which instance of sub-style (only if sub-style is used multiple times)
   special which wt1 wt2 wt3 = override special_bonds settings (optional)
   which = lj/coul or lj or coul
   w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive
 mix value = geometric or arithmetic or sixthpower
 shift value = yes or no
 table value = N
   2^N = # of values in table
 table/disp value = N
   2^N = # of values in table
 tabinner value = cutoff
   cutoff = inner cutoff at which to begin table (distance units)
 tabinner/disp value = cutoff
   cutoff = inner cutoff at which to begin table (distance units)
 tail value = yes or no
 compute value = yes or no

Examples

pair_modify shift yes mix geometric
 pair_modify tail yes
 pair_modify table 12
 pair_modify pair lj/cut compute no
 pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0

Description

Modify the parameters of the currently defined pair style. Not all parameters are relevant to all pair styles.

If used, the pair keyword must appear first in the list of keywords. It can only be used with the hybrid and hybrid/overlay pair styles. It means that all the following parameters will only be modified for the specified sub-style. If the sub-style is defined multiple times, then an additional numeric argument N must also be specified, which is a number from 1 to M where M is the number of times the sub-style was listed in the pair_style hybrid command. The extra number indicates which instance of the sub-style the remaining keywords will be applied to. Note that if the pair keyword is not used, and the pair style is hybrid or hybrid/overlay, then all the specified keywords will be applied to all sub-styles.

The special keyword can only be used in conjunction with the pair keyword and must directly follow it. It allows to override the special_bonds settings for the specified sub-style. More details are given below.

The mix keyword affects pair coefficients for interactions between atoms of type I and J, when I != J and the coefficients are not explicitly set in the input script. Note that coefficients for I = J must be set explicitly, either in the input script via the “pair_coeff” command or in the “Pair Coeffs” section of the data file. For some pair styles it is not necessary to specify coefficients when I != J, since a “mixing” rule will create them from the I,I and J,J settings. The pair_modify mix value determines what formulas are used to compute the mixed coefficients. In each case, the cutoff distance is mixed the same way as sigma.

Note that not all pair styles support mixing. Also, some mix options are not available for certain pair styles. See the doc page for individual pair styles for those restrictions. Note also that the pair_coeff command also can be to directly set coefficients for a specific I != J pairing, in which case no mixing is performed.

mix geometric

epsilon_ij = sqrt(epsilon_i * epsilon_j)
 sigma_ij = sqrt(sigma_i * sigma_j)

mix arithmetic

epsilon_ij = sqrt(epsilon_i * epsilon_j)
 sigma_ij = (sigma_i + sigma_j) / 2

mix sixthpower

epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) /
              (sigma_i^6 + sigma_j^6)
 sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6)

The shift keyword determines whether a Lennard-Jones potential is shifted at its cutoff to 0.0. If so, this adds an energy term to each pairwise interaction which will be included in the thermodynamic output, but does not affect pair forces or atom trajectories. See the doc page for individual pair styles to see which ones support this option.

The table and table/disp keywords apply to pair styles with a long-range Coulombic term or long-range dispersion term respectively; see the doc page for individual styles to see which potentials support these options. If N is non-zero, a table of length 2^N is pre-computed for forces and energies, which can shrink their computational cost by up to a factor of 2. The table is indexed via a -bit-mapping technique (Wolff) and a linear interpolation is +bit-mapping technique (Wolff) and a linear interpolation is performed between adjacent table values. In our experiments with different table styles (lookup, linear, spline), this method typically gave the best performance in terms of speed and accuracy.

The choice of table length is a tradeoff in accuracy versus speed. A larger N yields more accurate force computations, but requires more memory which can slow down the computation due to cache misses. A reasonable value of N is between 8 and 16. The default value of 12 (table of length 4096) gives approximately the same accuracy as the no-table (N = 0) option. For N = 0, forces and energies are computed directly, using a polynomial fit for the needed erfc() function evaluation, which is what earlier versions of LAMMPS did. Values greater than 16 typically slow down the simulation and will not improve accuracy; values from 1 to 8 give unreliable results.

The tabinner and tabinner/disp keywords set an inner cutoff above which the pairwise computation is done by table lookup (if tables are invoked), for the corresponding Coulombic and dispersion tables discussed with the table and table/disp keywords. The smaller the cutoff is set, the less accurate the table becomes (for a given number of table values), which can require use of larger tables. The default cutoff value is sqrt(2.0) distance units which means nearly all pairwise interactions are computed via table lookup for simulations with “real” units, but some close pairs may be computed directly (non-table) for simulations with “lj” units.

When the tail keyword is set to yes, certain pair styles will add a long-range VanderWaals tail “correction” to the energy and pressure. These corrections are bookkeeping terms which do not affect dynamics, unless a constant-pressure simulation is being performed. See the doc page for individual styles to see which support this option. These corrections are included in the calculation and printing of thermodynamic quantities (see the thermo_style command). Their effect will also be included in constant NPT or NPH simulations where the pressure influences the simulation box dimensions (e.g. the fix npt and fix nph commands). The formulas used for the long-range corrections come from equation 5 of (Sun).

Note

The tail correction terms are computed at the beginning of each run, using the current atom counts of each atom type. If atoms are deleted (or lost) or created during a simulation, e.g. via the fix gcmc command, the correction factors are not re-computed. If you expect the counts to change dramatically, you can break a run into a series of shorter runs so that the correction factors are re-computed more frequently.

Several additional assumptions are inherent in using tail corrections, including the following:

  • The simulated system is a 3d bulk homogeneous liquid. This option should not be used for systems that are non-liquid, 2d, have a slab geometry (only 2d periodic), or inhomogeneous.
  • G(r), the radial distribution function (rdf), is unity beyond the cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an LJ fluid), and it is probably a good idea to verify this assumption by checking the rdf. The rdf is not exactly unity beyond the cutoff for each pair of interaction types, so the tail correction is necessarily an approximation.

The tail corrections are computed at the beginning of each simulation run. If the number of atoms changes during the run, e.g. due to atoms leaving the simulation domain, or use of the fix gcmc command, then the corrections are not updates to relect the changed atom count. If this is a large effect in your simulation, you should break the long run into several short runs, so that the correction factors are re-computed multiple times.

  • Thermophysical properties obtained from calculations with this option enabled will not be thermodynamically consistent with the truncated force-field that was used. In other words, atoms do not feel any LJ pair interactions beyond the cutoff, but the energy and pressure reported by the simulation include an estimated contribution from those interactions.

The compute keyword allows pairwise computations to be turned off, even though a pair_style is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for performing a rerun simulation, when you only wish to compute partial forces that do not include the pairwise contribution.

Two examples are as follows. First, this option allows you to perform a simulation with pair_style hybrid with only a subset of the hybrid sub-styles enabled. Second, this option allows you to perform a simulation with only long-range interactions but no short-range pairwise interactions. Doing this by simply not defining a pair style will not work, because the kspace_style command requires a Kspace-compatible pair style be defined.

-
-

Use of special keyword

The special keyword allows to override the 1-2, 1-3, and 1-4 exclusion settings for individual sub-styles of a hybrid pair style. It requires 4 arguments similar to the special_bonds command, which and wt1,wt2,wt3. The which argument can be lj to change the Lennard-Jones settings, coul to change the Coulombic settings, or lj/coul to change both to the same set of 3 values. The wt1,wt2,wt3 values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, 1-3, and 1-4 bond topology neighbors, respectively. The special keyword can only be used in conjunction with the pair keyword and has to directly follow it.

Note

The global settings specified by the special_bonds command affect the construction of neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) exclude those pairs from the neighbor list entirely. Weights of 1.0 store the neighbor with no weighting applied. Thus only global values different from exactly 0.0 or 1.0 can be overridden and an error is generated if the requested setting is not compatible with the global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is usually a sufficient workaround in this case without causing a significant error.

-

Restrictions

none

You cannot use shift yes with tail yes, since those are conflicting options. You cannot use tail yes with 2d simulations.

Default

The option defaults are mix = geometric, shift = no, table = 12, tabinner = sqrt(2.0), tail = no, and compute = yes.

Note that some pair styles perform mixing, but only a certain style of mixing. See the doc pages for individual pair styles for details.

(Wolff) Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999).

(Sun) Sun, J Phys Chem B, 102, 7338-7364 (1998).

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0,495,519,524],"var":[3,11,12,178,358,376,508,524],"void":[4,6,7,8,41,181,225,244,500],"while":[1,3,9,11,12,13,17,74,75,115,152,161,176,189,203,208,217,229,231,235,247,248,253,254,255,257,263,271,294,307,308,312,314,318,348,378,386,393,399,410,416,458,459,480,482,485,492,495,506,511,518],__main__:495,__pthread_key_cr:12,_boundingbox:204,_compute_group_group:154,_compute_heat_flux:154,_compute_t:8,_j1m1m1:152,_j2m2m2:152,_manifold_rattl:519,_pair_lj:9,_serial:12,_wirnsberg:238,a10:360,a123:360,a12:460,a2m:[6,99],a_0:[257,347,399],a_0_real:257,a_1:347,a_2:347,a_3:347,a_4:347,a_c:407,a_cc:407,a_f:482,a_ij:399,a_pi:399,a_sigma:399,a_ss:407,aat:185,aatom1:[68,126],aatom2:[68,126],aatom3:[68,126],ab_23_cd:360,abbrevi:12,abc:[3,12,360,495,524],aberdeen:[88,89,240,322],abf:230,abf_integr:13,abi:208,abil:[3,229,271,304,317,418],abl:[3,8,9,11,12,39,94,203,208,228,237,245,287,343,350,393,495,524,528],ablat:347,abort:512,about:[0,1,3,6,8,9,11,12,13,15,16,39,41,42,63,65,82,119,126,127,130,172,178,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,235,236,237,238,239,243,244,245,246,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,267,270,276,280,281,282,283,284,285,286,287,288,289,290,293,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,319,320,321,331,332,333,335,336,338,339,340,341,342,343,344,345,346,347,349,350,351,352,354,355,356,357,358,375,378,385,386,388,393,398,404,409,426,455,459,488,495,498,499,504,505,507,512,516,519,524,527,529],abov:[1,2,6,7,8,10,11,12,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,34,35,37,40,41,42,43,44,45,46,47,48,49,50,51,53,54,56,59,65,66,71,74,75,76,77,80,81,94,95,97,98,99,103,104,106,107,123,125,127,130,152,153,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,176,177,178,180,181,184,185,186,187,188,189,190,191,192,193,195,196,197,199,203,204,205,206,207,210,211,212,213,214,219,220,222,223,225,228,229,231,232,237,241,244,246,250,252,254,255,256,260,270,271,276,300,303,305,310,316,317,318,323,331,335,338,339,340,341,358,360,361,362,363,364,365,366,367,368,370,372,378,380,383,387,388,392,393,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,448,449,450,451,453,455,456,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,491,492,493,494,495,497,498,499,500,501,504,505,506,507,508,511,512,515,518,519,524,525,528,529],abscissa:[450,451,478,479],absenc:214,absent:518,absolut:[3,207,217,230,231,235,318,323,337,377,378,386,423,431,498],absorb:347,absoult:378,abstol:318,ac3:177,academ:246,acc:342,acceler:0,accelri:[6,13],accept:[7,12,95,176,178,207,228,231,246,318,342,403,435,505,512,519],acceptanc:217,acceptor:425,access:[0,3,6,7,8,9,11,12,15,38,40,58,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,93,96,97,98,99,100,101,102,103,105,106,109,110,111,113,114,115,116,117,118,119,121,122,123,124,125,126,128,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,173,174,175,176,177,200,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,230,231,232,233,236,237,238,239,243,244,245,246,247,248,249,250,251,252,254,256,257,258,259,260,261,262,263,264,265,267,268,269,270,271,276,280,281,282,283,284,285,286,287,288,289,290,293,297,298,299,301,302,303,304,305,306,307,308,309,310,311,313,314,315,316,317,319,320,321,323,328,331,332,333,334,335,336,337,338,339,340,341,343,344,345,346,347,349,350,351,352,353,354,355,356,357,373,377,393,395,421,423,425,426,443,458,459,468,494,495,498,503,515,516,524],accident:519,accidenti:370,accler:[9,12],accommod:215,accomod:271,accompani:8,accomplish:[15,231,258,288],accord:[6,66,75,88,133,139,142,160,206,217,226,227,242,257,271,287,299,307,323,325,344,345,347,352,353,355,356,357,389,418,423,434,437,456,463,465,466,468,470,471,473,474,475,511,524],accordingli:[11,112,156,157,171,176,182,389,440,441,475],account:[3,6,95,130,160,176,177,186,198,220,222,236,238,251,252,254,271,277,278,279,291,292,294,296,298,302,308,317,319,321,331,333,334,335,338,339,340,343,347,350,366,387,409,414,423,431,435,440,441,443,446,466,494,511],accuml:[3,317,343,350],accumul:[6,8,14,75,88,154,210,220,221,254,317,323,349,375,393,503,523],accur:[1,3,6,9,14,16,37,41,56,161,225,269,312,317,318,321,335,343,350,356,358,378,399,418,422,423,448,460,476,478,479,480,482,511,516,524],accuraci:[1,3,6,12,41,202,203,207,225,238,248,271,309,321,348,358,377,378,385,395,418,448,450,451,458,459,478,479,486,506,511,516,518,524,528],accuractli:516,ach:377,achiev:[1,3,6,9,10,15,16,17,28,41,225,238,246,248,271,272,287,299,300,307,377,426,506],achiv:17,acid:9,ackland1:416,ackland2:416,ackland:2,acknowledg:0,acml:12,aco:524,acolor:[206,207],acoust:299,acquir:[3,6,60,63,64,181,182,227,229,231,271,454,490,502,518],across:[1,2,3,6,9,12,13,14,41,59,63,68,71,73,75,84,102,119,126,128,166,180,182,219,222,225,236,250,317,318,319,324,343,347,350,356,360,388,393,492,497,500,501,505,514,516],act:[3,6,73,119,129,163,235,249,252,253,254,255,257,260,270,317,328,342,344,345,347,356,357,358,386,401,412,422,423,425,460,475],acta:[130,177,394],actinid:[9,446],action:[2,6,11,12,75,247,252,345,518],activ:[5,8,11,12,13,15,55,61,95,176,230,247,251,254,260,266,270,297,317,318,326,346,375,439,476,506,518,521,524],active:[266,491],actual:[1,3,6,8,12,56,64,134,161,203,204,207,211,212,224,226,227,235,254,255,294,298,303,304,312,315,323,335,338,339,340,342,348,357,358,377,389,422,424,429,434,440,441,475,494,495,506,507,515,524],actualli:337,adam:[377,378],adapt:[2,3,6,9,95,172,210],adapti:298,adaptiv:[9,230,395],add:[0,1,3,5,6,7,8,9,11,12,13,14,15,16,17,18,40,42,75,95,99,112,125,128,129,131,176,178,179,203,204,205,206,210,211,212,213,214,216,218,219,220,222,223,227,230,235,237,238,244,248,249,250,252,254,256,257,261,269,270,271,272,273,274,275,276,277,278,279,291,292,294,295,296,298,306,316,317,320,321,331,332,334,338,340,341,345,346,347,349,351,352,356,358,378,380,385,387,395,400,402,405,409,418,426,431,443,448,449,453,459,461,495,497,498,503,505,507,509,516,518,519],add_molecul:216,add_speci:216,add_to_nodeset:216,added:[498,519],addforc:[2,3,210],adding:[8,213,237,316],addit:[1,2,3,4,6,7,8,9,12,13,14,15,16,17,19,21,28,32,36,37,39,40,41,42,44,50,55,56,65,118,119,124,154,178,179,181,182,186,191,197,198,199,200,201,206,207,208,210,213,221,224,225,229,230,235,237,238,241,242,246,248,249,250,254,257,271,272,273,274,275,276,277,278,279,289,291,292,294,295,296,298,306,317,320,321,322,324,348,351,352,356,362,368,371,373,378,380,388,390,393,394,395,399,400,402,404,406,408,409,412,414,415,416,417,418,419,423,424,426,427,428,430,431,439,441,442,443,444,445,446,448,450,451,452,453,456,458,459,461,466,467,476,477,478,479,480,481,482,485,489,492,497,498,499,504,505,506,509,511,518,519,520,522,524,527,528,529],addition:[0,4,6,8,11],additionali:204,addres:9,address:[7,8,11,206,253,519],addtorqu:2,adequ:[263,335,348,377,388,506],adher:28,adhikari:257,adiabat:0,adiam:[206,207],adjac:[39,176,178,238,388,448,478,479,480,511,512],adjiman:447,adjust:[2,3,6,15,16,41,61,130,140,156,157,158,161,162,165,166,171,172,177,182,203,206,219,225,229,231,251,254,258,262,267,268,271,272,276,294,298,301,303,304,307,308,309,310,315,317,318,326,335,339,343,348,350,351,352,354,355,357,377,378,386,388,393,395,415,440,441,466,482,507,525],adjust_radiu:326,adjust_radius_factor:326,admiss:276,adof:[158,219],adopt:[316,518],adp:[2,3,7],adri:[9,313,458,459],adust:172,advanc:[3,15,251,399,492,503],advantag:[1,6,8,11,17,39,40,41,225,393,417,506,511],advect:[3,6,335],advertis:8,advis:[318,388,457,516],afer:3,affect:[1,6,10,14,16,40,62,63,75,96,128,153,162,176,182,206,207,212,219,220,222,223,226,227,228,229,231,232,238,244,250,252,254,260,266,268,272,273,274,275,277,278,279,285,291,292,294,296,317,319,333,347,357,370,377,384,385,386,388,389,390,393,418,440,441,448,494,495,497,499,500,502,505,507,516],affin:[15,16,17,231,393,408],affiniti:393,afile:248,aforement:17,afresh:[305,505,524],afshar:413,after:[2,3,5,6,8,11,12,14,20,21,32,39,40,41,44,50,59,60,61,63,65,75,156,157,158,159,160,161,162,165,166,167,168,170,171,178,179,181,182,185,186,191,197,202,203,204,205,206,207,208,210,211,212,216,217,219,220,225,226,227,228,229,231,235,246,257,258,259,260,261,267,268,269,271,277,278,279,285,291,292,294,296,299,303,307,315,317,318,321,330,332,336,338,339,340,342,343,344,345,346,350,352,354,358,361,362,368,376,383,384,386,387,389,391,392,393,394,395,399,406,408,416,417,418,419,420,426,427,428,439,440,441,443,444,445,446,450,451,452,456,458,459,466,467,476,477,479,480,481,482,485,492,494,496,497,498,499,500,502,503,505,507,509,511,514,515,516,518],afterrun:505,afterward:3,afterword:41,ag1:177,ag2:177,again:[6,11,12,16,64,152,158,164,172,203,207,231,238,250,303,361,376,388,440,441,492,494,495,497,499,504,511,513,524,527],against:[11,12,13,66,232,388,458,459],aggreg:[6,12,68,71,73,84,102,119,126,250,267,315,317,333,492,525],aggress:[238,250,511],agilio:[9,13],agre:[3,8,199,386,395,428,459],agreement:[5,7],ahd:425,ahead:354,aidan:[0,5,7,9,13,380],aij:13,aim:6,airebo:[2,3,7,226,227,314],ajaramil:[7,9,13],aka:206,akohlmei:[7,9,13,208,251],aktulga:[7,9,310,459],al2o3:466,al2o3_001:[130,319],al3:177,ala:[257,466],alain:9,alat:[298,443],albe:[456,480,482],albeit:316,albert:9,alchem:[95,172],alcohol:350,alcu:[394,399],alcu_eam:456,alderton:412,alejandr:[271,272],alessandro:13,algebra:446,algorithm:[0,1,6,7,8,9,41,63,207,210,216,225,228,231,238,250,257,259,260,285,300,308,317,321,322,342,343,347,350,355,384,385,386,390,393,414,418,441,446,463,465,492,494,511],alia:[9,15],alias:[1,378],aliceblu:207,align:[6,9,12,28,41,75,180,199,225,252,380,497,500,518],alkali:418,all:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,32,36,38,39,40,41,42,44,50,54,55,57,58,59,61,62,63,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,171,172,173,174,175,176,177,178,179,180,181,182,184,186,191,197,198,199,200,203,204,205,206,207,208,210,211,212,213,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,234,235,236,237,238,239,240,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,263,264,266,267,269,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,289,290,291,292,293,294,295,296,297,298,299,300,302,303,304,305,306,307,308,309,310,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,330,331,332,334,335,336,337,338,339,342,343,344,345,346,347,348,349,350,352,353,354,355,356,357,358,359,360,361,362,366,371,373,375,376,377,378,379,380,383,386,387,388,389,390,392,393,394,395,396,398,399,400,402,403,404,405,406,408,409,412,413,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,435,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,488,489,490,491,492,494,495,496,497,498,499,500,501,502,504,505,506,507,508,509,510,511,512,514,515,516,518,519,523,524,525,527,528,529],allen:[28,95,412,422],allentildeslei:95,allign:3,allindex:359,alloc:[3,5,6,8,9,11,12,62,244,349,387,389,393,454,459,497,505],allocat:3,alloi:[2,3,12,13,394,399,409],allosw:75,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,21,36,38,39,40,41,55,57,58,59,60,61,63,64,65,81,100,117,119,154,156,157,158,171,176,177,178,180,186,198,199,200,202,203,204,206,207,208,210,211,213,214,215,216,217,219,220,221,222,223,224,225,227,228,229,230,231,232,233,236,237,244,246,247,248,249,251,252,254,257,260,261,266,268,271,272,289,298,302,303,304,305,306,307,309,311,316,317,318,319,320,321,323,325,326,330,331,332,333,334,335,342,343,344,345,347,348,349,350,351,352,356,358,360,362,371,373,377,378,380,386,387,388,389,392,393,395,396,399,400,401,402,403,404,409,416,418,423,424,425,426,431,435,440,441,446,448,456,459,460,463,465,466,475,483,486,488,490,492,495,497,499,500,501,502,503,504,507,509,510,511,514,515,519,524,525],almost:[2,3,12,15,62,252,307,347,378,390,393,475],alo:409,alon:[6,7,228,313,458,459,495],alond:13,along:[6,8,12,28,40,74,75,95,130,176,177,178,202,203,206,219,228,238,252,257,258,262,263,268,270,307,317,321,323,327,331,333,342,346,347,353,356,358,380,382,384,385,386,388,409,412,423,426,429,431,435,443,458,459,478,479,497,500,507,508,524],alonso:[444,445],alpha:[6,12,51,211,257,307,308,312,386,394,397,400,409,413,414,416,417,419,420,425,430,431,443,449,455,481,483,515,518],alpha_c:439,alpha_i:467,alpha_lj:439,alphabet:[2,3,21,36,44,55,65,186,198,210,362,371,387,406,476,497],alphanumer:[3,65,210,306,314,360,387,524],alreadi:[3,7,8,9,12,16,17,42,57,178,179,181,205,215,219,225,227,231,261,305,307,335,358,359,387,388,413,424,426,433,441,475,486,489,493,497,498,502,507,523,524],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,21,28,35,36,37,39,40,41,42,44,54,55,56,60,61,63,65,69,74,75,76,77,79,81,86,87,88,89,95,97,98,100,103,113,114,115,116,117,118,120,121,123,125,127,128,131,152,153,154,155,156,157,158,159,160,161,162,164,165,166,167,168,170,171,172,173,174,175,178,179,180,181,182,184,186,198,199,201,202,203,204,205,206,207,208,210,211,212,213,215,218,219,220,221,222,223,224,225,226,227,228,229,231,232,237,240,241,242,244,245,246,247,248,250,251,254,255,256,257,266,268,269,271,272,273,274,275,276,277,278,279,284,288,289,291,292,294,295,296,298,299,300,302,303,304,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,327,328,331,333,335,338,339,340,341,342,346,347,348,349,351,353,356,358,359,360,362,368,371,375,377,378,380,381,383,386,387,388,389,390,392,393,399,403,404,406,410,411,412,413,416,417,418,422,423,425,426,427,435,439,440,443,446,448,452,454,455,456,457,459,460,461,463,470,471,473,474,476,477,478,479,480,481,482,483,485,492,494,495,496,497,498,499,500,501,502,504,505,506,507,509,510,511,512,515,516,517,518,519,520,522,523,524,525,527,529],alter:[3,6,8,9,11,12,41,61,155,156,157,158,159,161,164,165,166,167,170,171,178,182,203,204,206,208,211,212,219,226,227,228,229,231,270,271,312,315,317,320,328,335,343,350,357,385,388,426,497,502,504,507,524,525,529],altern:[1,6,8,9,11,12,15,16,17,99,178,203,210,220,231,240,251,255,271,306,317,318,342,343,350,363,367,377,385,386,394,395,409,414,416,417,419,428,431,439,443,444,445,452,456,457,467,477,480,482,485,495,497,498,510,512,515],alternat:[386,518],although:[15,28,42,199,260,271,304,308,317,342,376,504,518,529],aluminum:489,alwai:[0,6,11,12,15,16,17,54,59,65,75,176,207,219,220,221,223,227,230,246,248,252,309,312,317,335,352,356,357,361,377,378,384,386,387,389,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497,498,502,507,509,518,523,524],charmm2lammp:13,charmm:[0,2,3,5],chartreus:207,cheap:335,cheaper:[236,422,460],check:[3,6,8,9,11,12,14,16,38,39,41,58,75,99,199,200,217,225,226,227,232,243,246,252,253,303,316,321,335,343,345,350,358,360,373,376,386,387,388,389,390,393,415,427,430,448,459,490,492,494,495,497,505,511,514,515,516,524],checkf:199,checkout:519,checkqeq:459,checku:199,chem:[6,13,19,20,24,39,40,43,45,46,95,96,117,123,153,184,185,195,221,230,235,238,247,248,255,257,270,271,272,289,294,295,300,304,307,309,317,322,323,335,338,339,342,343,344,345,352,361,370,372,377,378,385,388,395,400,404,405,408,409,410,412,413,414,418,421,422,424,425,431,435,436,439,443,447,448,450,451,453,466,475,483,506,509,511,518],chemic:[9,40,88,89,130,172,177,203,204,216,217,246,308,313,314,342,378,420,451,458,459,471,479],chemistri:[307,308,310,395,399,418,458,459],chen:347,cheng:408,chenoweth:[458,459],chenoweth_2008:[458,459],chi:[102,167,202,298,308,310,373,419,422,525],chiefli:457,child:8,chip:[7,9,16,17,393,510],chipot:230,chiral:370,chmod:[11,12],cho:443,chocol:[7,207],choic:[3,6,9,12,14,15,17,40,41,54,74,95,153,156,157,171,182,197,199,219,225,228,231,232,248,254,257,269,271,300,304,308,317,342,353,371,378,384,385,388,390,393,426,439,448,454,459,497,506,507,510,511,517,518,523],choos:[1,3,6,7,8,9,12,16,17,28,39,54,95,128,168,169,206,226,227,228,229,232,243,254,257,269,271,273,274,275,276,277,278,279,303,304,322,335,339,353,377,378,385,486,492,494,506,512],chose:[480,482],chosen:[2,3,6,12,16,152,178,181,190,199,206,212,217,229,232,243,246,247,255,257,269,271,276,300,303,314,335,339,342,343,348,350,351,357,378,379,385,393,414,418,423,430,433,461,480,492,506,511,512,518],chri:176,christian:[7,9,16],christoph:7,chunk:[0,2,3],chunkid:[69,79,86,98,103,114,116,125,158,173,175,219,332],chute:[4,9,10,249],ciccotti:321,cieplak:[6,184,509],cii:220,cij:220,circl:[42,75,330],circular:[3,6,156,201],circumst:17,circumv:[100,117,312],citat:0,cite:[3,7,8,12,254,466],civ:9,cl1:177,clarendon:[28,412],clarifi:[7,480,482],clariti:360,clark:453,class2:[2,3],classic:[0,3,5,6,7,8,9,15,244,300,307,312,347,372,418],classifi:[476,485],claus:495,clean:[6,12,14,16,505],cleanli:[496,515,528],clear:[2,3,6,8,11],clearli:7,clebsch:152,clermont:[9,13],clever:501,click:[2,11,21,36,44,55,178,186,198,206,251,362,371,388,406,476,519],client:[251,253],climb:[270,388,511],clinic:[7,13],clo:[167,202,525],clock:[12,492,511,516],clockwis:[184,353],clone:519,close:[3,6,11,12,13,39,41,70,75,153,181,203,227,228,229,248,255,257,271,287,294,317,321,353,356,376,378,381,384,385,388,393,395,399,409,410,429,443,448,450,451,458,462,464,478,482,501,507,518,519,521],closer:[3,10,41,127,176,202,203,225,229,233,344,388],closest:[227,298,317,350,422,460,475,486],cloud:[466,518],clovertown:17,clsuter:76,clump1:[302,317],clump2:[302,317],clump3:[302,317],clump:317,cluster:[2,3,6,7,12,15,63,65,75],clutter:3,cmap:497,cmatrix:248,cmax:443,cmd:[11,12,300,508],cmdarg:11,cmin:443,cmm:7,cmoput:145,cn1:220,cn2:220,cna:[2,3,7,65,74],cnn:220,cnr:13,cnrs:9,cnt:[426,501],co2:[40,177,318,321,387,420],coars:[7,9,10,28,35,40,54,190,242,302,317,318,335,420,424,451,461,479,506,509],coarser:[378,524],coarsest:152,code:[0,1,3,5],coeff:[3,7,8,12,20,21,32,44,50,184,185,186,191,197,361,362,368,406,426,430,448,463,465,468,497,526],coeffcient:497,coeffici:[0,2,3,4],coefficienct:413,coefficient0:416,coefficient1:416,coeffieci:[6,397,429],coeffincientn:416,coexist:[246,418],cohes:[6,419,443],coincid:[134,356,404,440,441,492],colberg:205,cold:[6,163,246,250,389,518],coldest:343,coleman8:9,coleman:[9,130,177,319],colin:9,collabor:[7,8,14],collect:[3,6,7,8,9,13,40,42,69,79,86,91,98,103,108,114,116,125,158,166,173,175,178,203,204,207,219,230,260,267,302,312,315,317,358,377,387,389,407,497,504,510,516,529],collid:[236,335,357],colliex:177,collinear:[3,302],collis:[3,257,335,353,357,415,423,489],colllis:335,colloid:[2,3,4,6,7],colombo:39,colon:[208,358,498,516],color1:207,color2:207,color:[3,9,41,203,206,207,225,247,307,312],column:[3,6,9,12,13,42,65,68,69,70,71,73,74,75,79,81,84,86,87,89,98,100,102,103,114,116,117,119,121,124,125,126,127,128,129,131,152,153,158,166,173,175,176,177,199,203,204,207,210,218,219,220,222,223,260,268,269,307,317,336,337,347,357,395,421,425,458,459,498,512,514,524],columnar:176,colvar:[0,2,9,12],colvarmodul:12,com:[2,3,6,7,9,13,14,42,65,75],comamnd:231,comand:228,comannd:393,comb3:[2,3],comb:[2,3,4,7,9,210,308],comb_1:309,comb_2:309,combiant:410,combin:[3,6,7,9,11,13,35,40,65,68,73,84,95,102,113,119,126,156,157,171,197,203,206,216,222,238,246,251,260,263,271,287,293,300,306,322,339,348,356,359,361,377,378,380,385,393,407,409,410,414,418,419,420,426,438,439,467,477,480,482,483,485,488,500,505,510,518,524,526],come:[0,2,3],comfort:[12,13],comid:332,comit:519,comm:[0,3,11,12,63,77,205,251,253,254,378,388,393,413,448,455,478,479,499],comm_modifi:[2,3,6,39],comm_modift:63,comm_styl:[2,3,41,63],comm_world:11,command:[0,1],comment:[2,4,7,11,12,37,56,184,199,203,241,242,255,317,318,347,387,388,394,416,417,419,420,430,443,450,451,452,459,466,467,477,478,479,480,481,482,485,494,495,497,518,519,524],commerci:7,commit:[9,519],commmand:[3,6,12,61,118,295,429,491,492,494,511,528],common:[0,1],commonli:[3,6,9,12,16,24,59,61,115,117,180,203,206,208,372,424,433,467,480,482,497,500,509],commun:[1,3,6,7,8,9,10,11,12,14,15,17,40,41,60,63,64,75,176,181,182,206,207,225,226,227,229,230,231,251,253,257,259,260,261,271,299,306,308,309,310,317,322,335,347,358,375,377,389,390,391,393,414,415,454,490,494,495,506,507,524,527,529],communc:377,comp:[7,205,253,254,287,293,321,378,388,418,448,455,460,474,478,479,481],compact:[65,210,406,476],compani:[5,7],compar:[1,3,4,6,8,12,15,16,39,94,121,130,161,177,186,198,207,235,308,358,360,377,378,386,388,443,466,492,511,512,518,523],comparison:0,compart:382,compass:[7,9,20,21,36,43,44,55,185,186,198,361,362,371,405,476],compat:[3,5,7,8,9,11,12,13,16,17,41,75,128,131,189,203,208,212,218,219,220,222,223,225,238,299,311,339,342,349,352,355,377,393,427,446,448,478,494,495,524],compens:[6,226,227,315,389,418],compet:346,competit:378,compil:[3,7,8,9,12,13,14,15,16,17,18,176,203,205,206,208,251,346,378,393,446,497,498,502,518,524],compl:16,complain:[11,12,16],complement:443,complementari:[7,409,431],complet:[3,6,9,11,12,14,41,61,75,207,225,230,260,300,303,306,335,346,348,359,360,376,388,393,419,463,465,484,492,497,502,505,509,511,514,518,524],complex:[4,6,8,11,12,13,24,40,42,64,100,117,152,154,166,178,179,257,287,330,356,375,388,418,446,478,479,495,497,500,524],compli:[342,346],complic:[6,7,9,12,13,129,217,246,495],complier:12,compon:[3,6,8,12,63,65,69,70,74,77,86,87,96,97,98,99,100,103,104,107,112,114,115,116,117,118,119,120,121,123,124,128,129,139,142,143,144,145,148,149,150,152,153,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,173,174,175,202,203,204,206,207,213,214,218,219,220,221,222,223,224,228,229,231,232,237,238,244,249,253,254,257,260,262,263,267,268,270,271,272,276,277,278,279,291,292,294,296,297,299,300,301,304,315,317,320,321,323,327,328,331,335,338,339,340,342,349,350,355,356,357,377,380,385,386,387,388,393,413,418,423,440,441,463,465,466,467,497,498,507,515,524,525],componenet:6,componennt:129,composit:[6,217,257,416],compound:[408,418,419,485],compres:[75,125,219],compress:[3,6],compris:[40,356,420,460,484],compton:[130,177],comptu:3,compuat:378,comput:[0,1],computation:[3,6,226,227,347,399],computational:518,compute_arrai:8,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[2,3,65],compute_peratom:8,compute_sa:[130,319],compute_scalar:8,compute_temp:8,compute_vector:8,compute_xrd:177,concaten:[2,3,528],concav:356,concentr:[75,242,318,416,420,451,479],concept:[6,158,168,219,506],conceptu:[3,6,75,166,229,231,388,409,426,443,502],concern:[6,77,95,205,247],concetr:75,concis:[11,346],conclud:12,concret:8,concurr:[15,378,524],conden:[347,480,482],condens:[6,160,347,395,411,416,431,485],condit:[2,3,5,6],conducit:6,conduct:[0,2,3,4],cone:500,confer:[15,446],confid:[3,511],config:[12,203,494],configfil:230,configur:[1,2,6,12,14,15,16,37,61,134,180,199,202,203,206,210,229,230,231,232,236,246,253,254,285,300,308,346,375,386,388,395,399,417,443,446,477,480,482,485,492,497,499,500,511,515,519],confin:[497,511],confirm:516,conflict:[3,12,40,204,448,495,519],conform:[3,6,13,61,228,229,270,316,323,346,370,388,418,509],confus:[3,485],conjuct:[9,413],conjug:[7,8,254,385,418,458,459],conjunct:[6,7,75,94,95,125,161,166,172,178,182,207,211,212,254,257,261,285,303,304,308,309,310,312,317,322,335,343,350,355,377,378,388,400,402,406,409,413,418,425,431,448,453,461,483,497,500,504,518,529],connect:[3,6,9,95,163,181,228,251,302,317,321,331,382,388,410,423,458,459,475,482,494,495,497,501,518],conner:395,connor:395,conput:3,consecut:[3,11,12,39,75,178,207,211,212,232,251,252,409,431,435,492,498,500],consequ:[1,6,217,347,430,511],conserv:[3,9,28,210,217,228,235,236,247,250,254,256,257,261,267,269,271,285,287,289,317,318,321,322,338,339,343,350,351,355,388,412,413,414,423,437,466,506,511],consid:[6,74,75,82,95,126,129,160,163,164,181,203,204,207,211,212,218,220,225,227,228,232,258,272,299,317,342,343,346,347,350,378,406,418,426,459,460,466,475,492,493,495,498,499,500,502,505,507,515,518,524],consider:[6,8,254,255,338,339,340,393,459,506],consist:[3,6,8,9,11,12,40,42,68,73,84,102,114,119,122,123,126,129,158,161,163,178,190,202,208,213,214,219,231,232,235,237,244,247,254,255,256,268,271,273,274,275,276,277,278,279,280,281,283,284,285,286,289,290,291,292,294,295,296,304,307,312,314,315,316,317,318,338,339,340,341,351,377,378,380,382,387,388,393,395,399,401,407,409,418,422,426,429,440,441,443,446,448,450,451,460,463,465,466,478,479,486,495,497,498,499,500,501,502,509,518,524],consistent_fe_initi:216,consit:317,constant:[0,3,4],constantli:238,constitu:[3,6,260,317,352,356,407,460],constitut:[463,465],constrain:[3,6,8,9,155,156,157,158,159,161,164,165,166,167,168,170,171,210,219,232,238,246,247,252,260,263,265,287,293,302,303,315,317,321,333,343,350,386,387,418,502,509,518],constraint:[3,5],construct:[6,8,12,37,54,56,63,66,70,74,76,77,81,100,117,130,152,177,229,271,299,316,318,356,389,393,412,446,448,475,477,478,479,500,501,516,524],constructor:[8,11],consult:[15,459],consum:[1,312,454,524],consumpt:375,contact:[0,2,3,4,5,8,9,12,13,40,42,65],contact_stiff:[462,464],contain:[0,1,2,3,4,6,8,9,11,12,13,16,17,18,37,40,41,56,65,95,99,127,130,152,154,158,166,176,177,178,180,184,186,198,199,203,204,206,207,208,210,211,212,216,218,219,220,222,223,225,230,232,237,241,242,248,252,253,254,257,269,285,298,299,302,303,305,306,307,310,314,317,318,319,324,335,342,346,347,356,357,360,376,378,387,388,391,392,394,395,396,399,408,409,412,416,417,418,420,426,427,443,446,450,451,452,456,457,458,459,467,477,478,479,480,481,482,483,485,492,493,494,495,497,498,499,500,502,504,506,509,511,512,514,515,518,519,524,527,529],content:[4,8,9,12,17,459,513,515],context:[3,6,8,12,15,16,127,128,207,226,227,232,302,314,351,385,488,497,504,513,523,524,525],contibut:74,contigu:494,contin:15,continu:[0,2,3,5,6,9,12,13,41,75,87,113,114,174,207,210,211,212,217,219,220,221,222,223,225,228,229,230,231,232,238,246,247,248,250,251,252,254,255,256,262,268,269,271,273,274,275,276,277,278,279,291,292,294,295,296,301,303,306,307,317,319,323,334,335,337,344,345,347,353,356,360,376,392,393,399,413,415,433,436,458,459,460,463,465,481,492,495,497,499,500,505,511,512,514,515,524,527],continuum:[6,7,9,216,347,463,465],contour_integr:216,contract:[61,229,231,271,304,317],contradictori:3,contrain:321,contraint:285,contrari:[248,255],contrast:[1,6,42,55,66,160,163,204,231,358,463,465,488,528],contrib:347,contribut:[3,4,5,6,7,8,9,12,13,16,65,67,69,71,72,74,75,78,79,81,83,85,86,92,95,96,97,98,99,101,103,112,114,116,118,119,120,121,123,125,128,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,212,217,218,219,220,222,223,229,246,254,257,260,261,266,272,294,295,302,303,311,314,317,319,321,349,377,386,388,396,413,415,416,418,426,440,441,446,448,458,459,466,509,515,518,519],contributor:12,control:[3,5,6,7,8,9,11,13,15,26,28,41,95,99,134,152,187,203,204,206,210,216,217,225,229,230,231,250,251,254,255,271,273,274,275,276,277,278,279,304,309,317,318,325,326,338,339,340,347,351,375,377,390,418,422,446,458,459,462,464,477,482,492,494,506,512,513],control_typ:216,controlfil:459,convect:99,conveni:[6,12,28,203,208,223,319,380,467,483,516,519,524],convent:[3,8,28,189,196,198,204,207,316,331,359,416,418,524],converg:[3,6,41,96,203,204,206,208,213,225,228,229,237,244,276,287,293,307,309,312,316,321,384,385,386,388,408,409,431,466,492,504,511,516],convers:[3,8,152,206,207,217,220,304,377,409,410,411,418,431,435,439,453,495,511,523],convert:[2,3,4,5,6,7,8,12,13,19,20,23,27,31,34,35,61,65,75,99,178,185,203,206,207,220,223,269,303,306,358,361,363,367,370,380,388,394,416,446,480,482,489,495,497,498,499,504,514,518,523,524,527,529],convex:[42,356],convinc:[7,12],cook:9,cooki:7,cool:[7,168,238,250,315],cooordin:[203,204],cooper:[5,7],coord123:125,coord1:[3,125,219],coord2:[3,125,219],coord3:[3,125,219],coord:[2,3,6,7,11,61,65,75,76,80],coordb:466,coordbb:466,coordiat:386,coordin:[1,3,4,6,7,8,11,13,14,16,40,41,42,61,63,64,65,69,71,75,78,79,81,86,87,95,97,98,103,113,114,116,124,125,127,129,146,152,161,167,173,175,176,178,182,202,203,204,205,206,207,208,210,213,218,219,222,225,226,227,228,229,230,231,232,235,237,238,239,244,246,249,250,251,252,253,254,255,268,270,271,273,274,275,277,278,279,294,297,298,299,302,303,304,314,315,317,320,321,323,328,331,332,333,334,335,337,345,346,347,354,355,357,358,380,386,387,388,393,394,395,398,417,466,492,497,498,499,500,502,505,507,511,518,524,525],coordn:[125,219],coords:466,copi:[0,3,4,8,9,11,12,14,16,40,131,206,347,388,406,458,495,519],copper:489,coprocessor:[1,7,9,15,16,393,510],coproprocessor:16,copy_arrai:8,copyright:[7,8,302],coral:207,core:[0,1,3,4],core_shel:160,cores:518,coreshel:[4,6,9],coreshell:[4,6],cornel:[6,184,509],corner123i:124,corner123x:124,corner123z:124,corner1i:124,corner1x:124,corner1z:124,corner2i:124,corner2x:124,corner2z:124,corner3i:124,corner3x:124,corner3z:124,corner:[3,6,40,124,206,356,357,380,484,497,519],cornflowerblu:207,cornsilk:207,corp:9,corpor:15,corr:408,correct:[3,6,9,11,12,16,61,86,95,96,112,113,118,121,127,160,165,172,184,204,206,231,238,246,248,254,271,272,294,302,304,307,346,352,356,377,388,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,497,512,515,518,519],correction_max_iter:216,correctli:[3,8,11,16,75,87,112,113,114,155,156,157,159,161,163,164,165,166,167,170,171,174,203,207,213,232,237,244,255,265,271,272,310,317,321,331,334,353,356,388,389,393,411,441,446,494,495,497,507,519,523,525],correl:[2,3,6,99,100,152,174,210,219],correpond:[241,242],correspond:[1,2,4,6,8,9,10,11,12,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,40,42,43,44,45,46,47,48,49,51,53,54,56,74,75,95,106,107,123,124,125,126,129,130,131,139,142,143,144,145,146,148,149,150,152,155,156,165,172,176,177,184,185,186,187,188,189,190,192,193,195,196,197,199,202,203,204,206,207,211,212,213,219,221,222,224,227,229,231,238,239,242,244,245,249,254,257,258,267,268,269,271,273,274,275,276,277,278,279,280,281,285,289,291,292,294,296,298,299,300,304,309,310,317,318,320,321,342,352,353,355,356,357,359,361,362,363,364,366,367,370,372,378,383,385,387,388,394,395,397,400,401,402,403,404,405,406,407,408,409,412,413,416,417,418,419,420,421,422,423,424,425,426,429,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,451,452,453,455,456,458,459,460,461,466,467,468,477,478,479,480,481,482,483,485,487,488,489,492,494,495,497,498,500,510,511,512,514,515,518,524],correspondingli:[440,441,506],corrupt:3,cosin:[2,6,7,21],cosineshift:26,cosmo:[248,253],cossq:2,cost:[1,6,10,11,12,16,39,41,75,120,130,153,177,206,207,219,225,226,227,243,271,289,309,318,347,377,378,391,409,431,435,446,448,477,494,506],costheta0:[477,480,482,485],costheta:456,costli:[11,15,96,248,389],couett:4,coul:[2,3,6,9,15,35,45,46,76,95,118,127,172,184,211,212,348,378,386],could:[2,3,6,9,11,12,16,32,41,50,61,69,75,79,86,95,98,103,114,116,120,123,125,158,168,173,175,191,203,204,206,207,211,212,219,220,225,231,244,253,306,307,308,312,315,317,320,335,336,342,346,347,348,352,356,358,360,368,374,376,384,386,389,393,395,396,421,425,426,429,458,459,493,494,495,497,499,501,504,505,512,513,518,524,525],coulomb:[3,5,6,7,8,9,10,12,14,17,76,96,118,119,127,153,179,183,308,310,348,377,378,386,393,400,402,403,404,405,408,409,410,411,412,418,423,424,426,431,435,439,442,448,453,458,459,461,466,476,482,483,485,488,502,509,515,518,523],coulommb:6,cound:3,count:[1,3,6,8,11,12,41,65,71,81,99,125,127,128,166,176,182,184,213,214,217,219,222,224,225,232,237,243,246,252,271,285,303,320,321,338,339,356,378,386,387,388,390,393,421,425,448,515,516,524],counter:[3,353,492,503,505,511],counteract:246,counterbal:[238,250],counterbalanc:28,counterclockwis:184,counterpart:[203,492],counterproduct:17,coupl:[0,3,4],couple:[4,6,11,12],courant:324,cours:[3,8,15,138,140,172,203,211,212,247,316,331,346,352,354,355,357,358,378,440,468,494,497,510,518,524,527],courtesi:380,cov:466,coval:[6,9,28,418,443,466,518],covari:248,cover:[6,12,75,199,207,216,257,418,484],coverag:75,cpc:253,cpp:[1,3,6,8,9,11,12,13,95,203,211,212,244,321],cpu:[1,3,9,10,12,14,15,16,17,65,75,207,221,235,255,348,375,378,393,406,476,492,510,511,514,515,516,524],cpuinfo:15,cpuremain:515,cpus:12,cr2:177,cr3:177,crack:[4,389],crada:[5,7],crai:[5,7,13,17,203],crash:[3,12,389,518],craympi:393,creat:[0,1,2,3,4,6,7,8,9,11,12,13,14,16,37,39,41,42,56,60,61,64,65,75,87,99,113,114,119,120,123,126,130,146,155,161,162,174,176,178,179,180,181,199,203,204,205,206,207,210,215,216,219,222,223,225,226],create_atom:[2,3,6,7,8,40,41,61,99],create_bond:[2,3],create_box:[2,3,6,21,40,41,44,59,60,61,64,75,99,176,178,179],create_elementset:216,create_faceset:216,create_group:205,create_nodeset:216,createatom:0,creation:[3,5],crimson:207,critchlei:302,criteria:[3,127,179,206,207,226,227,228,266,386,455,484,499,502,524],criterion:[12,41,133,178,181,217,225,228,246,285,309,324,353,358,386,388,408,418,423,466,502,511,512],criterioni:511,critic:[6,48,49,269,342,347,386],crmax:75,crmin:75,cross:[3,12,15,21,75,97,129,156,176,186,203,204,206,218,227,231,268,270,294,317,327,331,334,343,350,362,380,388,404,413,415,416,424,425,426,431,433,435,456,461,463,465,480,482,489,497,501,507,527],crossov:1,crossterm:497,crozier:[0,7,13],crucial:307,crystal:[3,4,6,13,15,74,77,117,298,299,345,380,389,497,501,515,518],crystallin:[6,113,299,380,481,518],crystallis:342,crystallogr:[130,177],crystallograph:[380,515],crystallographi:[130,177,380],cs1:177,cs_chunk:6,cs_im:[40,497],cs_re:[40,497],csanyi:[152,457,467],cscl:443,csequ:6,csh:[11,12,15,406],cshrc:[11,12],csic:[417,477,480,482,485],csinfo:6,csisi:[417,477,480,482,485],csld:[2,3,210],cst:416,cstherm:6,cstyle:494,csvr:[2,3,6,210],ctcm:[394,416],ctemp_core:235,cterm:323,ctr:9,ctype:11,cu1:177,cu2:177,cu3au:443,cube:[6,176,181,235,356,380,518],cubes:[41,225],cubic:[2,3,37,56,117,199,241,257,298,335,378,380,416],cuda:[1,3,7,9,12,14,16,393,510,524],cuda_arch:[9,14],cuda_get:14,cuda_home:[9,14],cuda_prec:[9,14],cuh:399,cummul:[3,6,223,226,227,228,230,243,248,254,256,335,338,339,340,341,343,350,425,515],cumul:[6,217,219,222,236,246,254,269,271,276,285,317,319,388],curli:2,current:[0,1,3,5,6,7,8,9,10,11,12,13,14,15,16,17,40,41,42,57,61,63,65,75,77,87,95,113,119,127,128,142,153,158,166,168,174,176,179,182,202,203,204,205,206,207,208,211,212,216,219,223,225,226,227,228,229,230,231,232,236,237,238,244,246,248,251,252,254,260,266,268,271,272,277,278,279,285,287,291,292,293,294,296,302,303,308,309,311,314,315,316,317,318,321,322,323,324,325,326,327,328,330,332,333,334,335,338,339,340,346,347,350,351,352,353,354,355,357,358,360,375,376,377,378,381,382,383,385,386,387,388,393,399,406,408,412,416,418,419,423,426,427,430,440,441,443,444,445,448,456,458,459,462,463,464,465,468,480,482,483,486,492,493,494,495,497,498,499,500,501,503,504,505,507,509,511,512,514,515,519,524,525,526,527,528,529],curv:[6,178,246,287,293,299],curvatur:[422,460,489],custom:[0,2,3,6],cut0:495,cut1:506,cut2:506,cut:[1,2,3,6,9,12,14,15,16,17,18,41],cuthi:[298,310],cutinn:[401,440,441],cutlo:[298,310],cutmax:456,cutoff1:[405,412,431,435,439,442,453,461],cutoff2:[400,402,403,405,411,412,431,435,439,442,453,461,483],cutoff:[3,6,8,10,15,17,39,45,46,54,55,63,74,76,77,81,95,100,117,119,126,127,152,176,179,181,182,227,228,233,241,242,298,307,308,310,312,314,317,322,335,348,352,356,358,375,377,378,386,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,409,410,411,412,413,414,415,416,417,418,419,420,421,422,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,458,459,460,461,466,467,468,469,470,471,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,495,499,502,506,518,524],cutoffa:417,cutoffc:417,cuu3:416,cval:177,cvd:342,cvel:323,cvff:[2,7,15,362],cwiggl:[3,268,352,355,357,524],cyan:[2,206,207],cycl:[3,246,269,271,272,276],cyclic:[3,184,199],cygwin:12,cylind:[3,4,75,206,219,252,293,303,353,356,382,500],cylinder_d:382,cylindr:[6,252,331,353],cypress:393,cyrot:399,cyrstal:299,d3q15:257,d3q19:257,d_double_double:14,d_e:347,d_flag2:306,d_flag:306,d_name:[124,203,306,337,507],d_single_double:14,d_single_single:14,d_sx:306,d_sy:306,d_sz:306,daan:345,dai:12,daili:12,daivi:294,damag:[2,3,9,65],dammak:312,damp:[3,6,210,215,254,255,256,261,271,272,276,293,304,307,308,312,317,338,339,351,353,354,385,386,388,400,402,404,409,412,418,423,431,439,453,461,476,483,511,518],damp_com:255,damp_drud:255,dampen:[317,518],dampflag:[353,423],dan:16,danger:[3,12,246,358,413,515],dangl:181,daniel:9,darden:[378,412],darkblu:207,darkcyan:207,darken:206,darkgoldenrod:207,darkgrai:207,darkgreen:207,darkkhaki:207,darkmagenta:207,darkolivegreen:207,darkorang:207,darkorchid:207,darkr:207,darksalmon:207,darkseagreen:207,darkslateblu:207,darkslategrai:207,darkturquois:207,darkviolet:207,dasgupta:308,dash:[423,514],dat:[6,99,199,216,493],data2xmovi:0,data:[1,2,3,4],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:0,datafil:[12,13,319],dataset:319,datatyp:3,date:[0,4,6,12,13,202,458,459,524],datom1:[84,126],datom2:[84,126],datom3:[84,126],datom4:[84,126],datum:[3,6,42,68,71,73,84,102,119,126,203,220],davenport:442,davi:352,david:[9,18,377,378,480,482],daw:[416,456],dcd:[3,6,7,203,205,206,207,208,300,498,502],dcs:9,ddim:202,deactiv:439,dealt:253,debug:[6,7,11,12,13,16,57,130,134,177,178,300,305,375,377,427,448,486,495,496,504,507,514,524],deby:[2,3,7,211,212,312],decai:[100,409,489],decid:[3,6,12,15,75,268,306,317,348,512,519],decipher:380,deck:306,declar:205,declin:335,decod:206,decompos:[95,467],decomposit:[3,5,7,17,64,216,300,322],decoupl:[6,518],decreas:[3,15,203,204,213,214,221,228,231,237,238,244,246,254,346,377],decrement:323,dedic:[15,393],deepli:374,deeppink:207,deepskyblu:207,def:[12,13,495],defaul:63,defect:[6,74,176,446],defgrad:2,defin:[2,3,5,6,7,8,11,12,16,19,20,21,22,23,24,25,26,27,28,29,30,31,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,184,185,186,187,188,189,190,192,193,195,196,197,198,199,200,201,202,203,204,205,206,207,210,211,212,213,214,215,216,217,218,219,220,222,223,224,225,226,227,228,229,231,232,235,236,237,240,242,244,245,246,249,252,253,254,255,256,257,266,268,270,271,272,273,274,275,276,277,278,279,281,282,283,286,289,290,291,292,294,295,296,298,299,300,302,303,304,306,308,310,315,317,318,319,320,321,324,328,332,333,335,337,338,339,340,341,343,344,345,347,349,350,352,353,354,355,356,357,358,360,361,362,363,364,365,366,367,370,371,372,373,375,377,378,380,383,385,386,387,388,389,390,391,392,393,395,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,417,418,420,421,422,423,424,425,426,427,429,431,432,433,434,435,436,437,438,439,440,441,442,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,463,464,465,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,500,501,502,503,506,507,508,509,511,512,514,515,518,520,521,522,523,524,525,526],definit:[2,3,6,8,12,13,82,85,127,152,207,219,220,221,222,223,231,240,252,276,319,337,349,352,355,357,359,371,375,387,396,399,407,414,418,429,456,463,465,467,484,495,497,499,506,508,523,524],defint:515,deform:[2,3,6,7,8,40,42,59,61,63,65,85,122,134,138,139,153],deg2theta:177,deg:518,degener:[3,302],degrad:[8,17,299,378,506],degre:[3,6,8,19,20,23,27,28,31,34,35,37,68,84,100,102,104,106,107,109,111,112,117,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,177,178,184,185,188,189,196,197,199,202,206,219,228,235,246,248,249,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,316,317,321,338,339,340,345,361,363,367,370,372,386,412,416,425,507,515,518,525],degrees:199,degress:[158,219],del:511,delai:[3,6,12,389,415,515],deleg:426,delet:[2,3,7,8,12,54,59,62,65,176,181,182,210,219,220,222,223,226,228,243,246,271,319,338,339,358,360,376,387,389,392,448,475,497,498,499,500,508,509,514,519,520,522,524,525],delete_atom:[2,3,7,178],delete_bond:[2,3,43,45,46,47,48,49,50,51,53,54,55,56,68,73,126,179],delete_el:216,deli:202,delimit:[318,495,524],dellago:[6,238],deloc:[272,418,466],delr:443,delt_lo:511,delta:[2,21],delta_1:399,delta_3:399,delta_7:399,delta_conf:3,delta_ij:[443,456],delta_pi:399,delta_r:456,delta_sigma:399,deltah_f:242,delx:202,delz:202,demand:312,demo:11,demon:297,demonstr:[307,443],den:303,dendrim:425,dendtrit:382,denniston:[9,257,259,260,261,299],denomin:[7,183],denot:[130,235,238,255,299,310,312,409,424,426,459,463,465],dens:[75,228,318,418],densiti:[3,6,7,9,17,40,41,61,110,127,138,152,164,176,178,211,212,216,219,225,231,244,257,260,264,265,299,303,304,306,308,347,352,380,383,387,394,395,399,416,443,444,445,450,451,456,460,466,470,472,473,474,497,506,507,515,523],density_continuity:465,density_summation:465,dent:382,depart:[0,7],departur:[269,307],deped:8,depend:[1,2,3,6,8,9,11,12,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,44,45,46,47,48,49,51,53,54,56,63,65,68,71,73,74,75,84,100,102,113,119,123,124,125,126,129,131,152,154,155,161,165,166,172,178,179,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,206,207,210,211,212,213,214,217,219,221,222,223,224,225,227,229,231,237,239,242,245,248,249,250,252,254,255,257,259,260,268,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,298,309,310,312,314,317,318,320,321,322,328,335,338,339,340,342,344,346,347,349,352,355,356,357,358,360,361,362,363,364,366,367,370,372,378,380,386,387,389,390,391,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,416,417,418,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,447,449,450,451,452,453,455,456,458,459,460,461,466,467,468,476,477,478,480,481,482,483,485,487,488,489,492,494,497,499,500,503,507,509,511,514,515,517,524,525],dependend:6,depflags:12,dephas:[492,511],depos:232,deposit:[2,3,4,112,180,210,217],deprec:[3,308,458],deprect:219,depth:[51,156,206,347,420,422,460],dequidt:9,der:[95,118,407,408,439,458,459,488],deriv:[6,7,8,9,37,56,65,95,152,172,199,220,229,231,238,246,254,268,271,273,274,275,276,277,278,279,298,304,308,312,344,345,347,352,353,356,385,387,395,399,407,412,418,419,424,433,437,438,443,446,458,459,476,478,479,488,518],derjagin:488,derlet:298,descend:207,descent:[7,385],descib:[40,206,308],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,37,39,40,41,42,56,64,65,71,74,75,77,96,121,124,127,130,142,152,153,156,157,158,162,163,166,169,171,172,176,177,178,180,181,190,195,199,203,204,205,210,211,212,219,220,221,222,223,225,228,229,230,231,232,234,235,241,242,247,248,251,252,253,254,255,256,257,259,260,261,266,270,271,272,276,284,295,298,300,305,306,307,308,309,310,317,318,323,331,335,336,337,338,339,340,341,342,343,344,345,350,352,353,355,360,377,378,380,384,385,386,387,388,392,395,396,398,400,401,402,404,405,406,407,408,409,412,416,418,419,420,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,450,451,455,456,457,458,459,460,461,466,467,468,475,476,477,478,479,480,481,482,483,485,487,488,489,490,492,494,495,497,498,499,500,501,507,510,511,514,519,524,525,527],descript:[2,3,6,8,9,11,12,13,17],descriptor:[152,203,427],deserno:378,design:[0,3,6,7,8,11,13,14,16,130,160,163,177,216,228,234,235,271,272,298,299,319,342,347,396,397,398,401,404,409,411,418,439,440,441,444,445,456,459,478],desir:[2,3,6,7,9,11,12,14,15,32,40,50,61,75,96,99,123,128,153,160,178,191,202,219,223,229,231,244,246,247,254,255,256,260,271,294,302,303,304,305,308,312,317,320,321,335,338,339,340,341,346,353,368,374,377,378,380,384,386,387,388,413,416,425,440,441,477,480,482,493,494,495,497,501,506,511,512,514,515,516,524,525,527],desk:7,desktop:[4,6,7,10,12,206],despit:518,destabil:399,destre:370,destroi:[9,11,39,226,227],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,21,36,40,41,42,55,65,69,70,71,75,79,82,86,98,99,103,114,116,118,120,121,122,123,125,128,129,131,152,153,155,156,157,158,161,171,172,173,175,178,179,182,183,186,198,202,203,204,206,207,210,211,212,216,219,220,221,222,223,225,227,228,229,230,231,232,238,244,246,247,248,249,251,252,254,256,257,261,268,269,270,271,272,273,274,275,276,277,278,279,283,285,291,292,294,295,296,299,302,303,304,306,307,309,310,311,317,321,322,335,338,339,340,341,342,343,345,346,347,348,349,350,351,358,360,362,371,377,378,381,386,387,389,390,393,394,395,396,398,399,401,403,404,405,406,407,408,409,412,413,418,419,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,442,443,447,448,450,451,455,458,459,460,466,467,468,476,484,487,488,490,495,497,498,499,500,502,503,506,507,509,512,515,516,519,524,525,529],detect:[2,3,12,42,63,65,94,100,245,303,346,388,408,425,430,492,494,497,508,511,524],determin:[1,3,6,8,9,12,14,15,39,40,42,51,59,60,61,63,64,71,75,95,112,118,119,123,126,129,130,131,139,153,166,167,176,177,178,202,203,204,206,207,208,209,213,214,215,218,219,220,221,222,223,224,225,229,231,232,235,237,242,246,249,250,252,254,255,260,266,268,269,271,277,278,279,291,292,294,296,298,300,303,304,307,314,315,316,317,318,319,320,324,326,328,335,338,339,340,342,348,349,352,353,354,355,356,357,358,371,377,378,380,387,389,390,393,395,396,403,408,412,415,416,420,421,423,426,427,435,443,446,448,451,459,460,466,475,478,479,483,488,494,497,498,500,502,504,507,511,513,514,516,523,524,525],determinist:322,detil:119,devan:[9,461],devanathan:482,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,42,251,276,302,307,308,311,395,399,418,445,446,466,485,499],devemi:9,deviat:[269,276,298,421],deviator:9,devic:[1,3,12,14,16,251,393],device_typ:393,devin:[309,408],devis:445,dfactor:206,dff:518,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_single:[3,12,378],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,311,446],dhi:[61,202,231,303],dhug:[269,307],dhugoniot:[269,307],dia:443,diag:318,diagnost:[2,5],diagon:[3,6,91,129,152,153,154,229,271,304,317,350,463,465],diagonalstyl:467,diagram:[41,84,130,177,198,225,300],diallo:425,diam:[206,207,303,387],diamet:[3,6,40,42,124,178,203,204,206,207,211,212,254,303,306,317,335,337,351,353,387,407,422,423,433,460,484,488,497,498,507],diamond:[380,418,443],diamter:[40,303],dick:6,dicsuss:268,dictat:[217,269],did:[3,12,386,413,415,416,423,448,480,482,505],didn:3,die:17,diel:2,dielectr:2,diff:[3,6,12,15,174,349,377],differ:[1,2,3,4,6,7,8,9,11,12,14,15,16,17,21,36,37,39,41,42,54,55,56,63,66,71,74,75,95,100,104,106,107,132,152,154,155,156,157,158,159,161,164,165,166,167,168,170,171,172,178,179,181,186,198,199,202,203,206,207,210,212,215,217,219,222,225,226,227,228,229,230,231,235,238,241,245,246,247,248,249,250,251,254,255,257,268,271,272,273,274,275,277,278,279,281,283,286,289,290,291,292,296,298,300,302,304,307,308,309,312,315,317,321,323,331,333,335,338,339,340,343,344,345,347,350,351,352,353,356,360,361,371,374,376,377,378,380,381,384,385,387,388,390,391,392,393,394,395,399,403,404,406,407,408,413,414,416,418,420,422,423,424,426,429,431,432,434,435,442,443,444,445,447,448,449,450,451,452,456,458,459,460,461,462,463,465,466,467,468,476,477,478,479,480,482,484,485,488,491,492,494,495,497,499,500,501,502,505,506,507,509,511,512,514,515,516,518,523,524,525,527],differenti:[1,3,6,28,199,318,377,409,456,481],difficult:[229,300,393,425,506,516],difficulti:[100,117,321,458],diffract:[7,9,130,177,319],diffus:[0,4],diffuse:[4,6],digit:[2,3,207,360,446,524],dih_table1:199,dih_table2:199,dihedr:[0,2,3,7],dihedral_coeff:[2,3,184,185],dihedral_cosine_shift_exp:26,dihedral_styl:0,dihedralcoeff:[3,200],dihedraltyp:227,dihydrid:418,dij:321,dilat:[2,3,61,63,65,82],dim1:3,dim2:3,dim:[3,61,75,155,159,160,161,164,165,166,167,168,170,178,202,231,252,353,380,443,500,523,524,525],dimdim:524,dimems:299,dimens:[1,2,3,6,7,12,41,59,60,61,63,65,75,99,125,129,153,158,165,166,167,178,180],dimensinon:75,dimension:[3,39,100,123,130,152,155,158,159,160,161,164,165,166,167,168,170,177,201,219,270,299,347,380,384,388,456,497,507],dimensionless:[115,133,134,136,139,141,143,148,152,347,378,467,488],dimensions:319,diment:3,dimentionless:147,dimer:[6,317,443],dimgrai:207,dimstr:[41,225],dinola:[304,338],dintel_offload_noaffinity:15,dipol:[0,2,3,4],dipolar:[4,28,40,203,204,337,518],dir1:508,dir2:508,dir:[1,3,4,8,10,11,12,269,298,307,334,456,458,459,495,508,524],dirac:152,direc:456,direct:[2,3,6,7,12,13,15,28,59,74,75,117,130,152,176,177,178,184,202,203,206,210,213,214,215,231,232],directli:[3,6,8,9,11,12,95,124,129,152,154,203,204,205,206,213,237,248,252,257,299,318,319,339,351,353,354,355,356,380,385,393,394,395,400,402,403,409,412,416,418,431,435,448,453,461,475,495,507,508,509,515,524],directori:[0,1,2,3],disabl:[3,12,15,347,393,430,495,510,524],disadvantag:[6,225],disallow:[203,231,271],disappear:499,discard:[2,3,41,75,221,225,348,356,494,499,500],discontinu:[199,386,437],discourag:443,discov:[13,348],discret:[6,8,40,42,206,207,254,257,293],discuss:[0,1,2,3],disk:[6,92,93,100,171,201,232,246,303,495],disloc:[74,446],disord:[39,74,446],disp:[0,2,3],dispar:460,disperion:[412,435],dispers:[3,6,7,9,176,299,377,378,403,412,435,440,448,459,478,485],displac:[2,3,6,7,12,42,61,65],displace_atom:[2,3,7,113],displace_box:61,displacemet:500,displai:[11,13,21,36,44,55,186,198,203,206,362,371,406,476],dispters:3,disregard:446,dissip:[6,9,40,88,89,240,247,254,299,322,344,345,401,413,414,423,440,441,476],dissolut:226,dist:[6,73,99,119,128,203,300,316,415,475,492,525],distanc:[2,3,6,7,8,9,12,19,20,39,43,45,46,47,48,49,51,53,54,55,56,57,58,60,61,63,65,66,69,73,75,76,77,78,79,80,81,86,87,94,97,98,100,103,113,114,115,116,117,119,125,126,127,128,129,130,132,146,152,167,173,176,178,179,180,181,185,202,203,204,206,207,215,219,226,227,228,229,231,232,233,236,238,246,252,257,268,269,270,271,276,285,298,299,303,307,308,315,316,317,321,323,327,331,332,333,334,335,342,343,345,346,347,350,352,353,354,355,356,357,361],distinct:[6,235,314,377,460],distinguish:[6,94,152,260,418,496,524],distort:[176,394],distrbut:394,distribut:[0,2,4,5,6],distro:[122,406,455,456],ditto:[8,12,14,16,17,42,126,227,317,489,495],div:[8,15],divd:128,diverg:[3,12,39,317,345,395,499,518,527],divid:[3,6,15,41,99,123,128,138,140,153,175,176,186,198,207,219,220,222,225,231,298,343,350,355,377,386,388,419,459,466,485,506,514,524],divis:[6,197,257,399,429,439,494,515,524],dl_poly:[6,7],dlambda:172,dlammps_async_imd:251,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,206],dlammps_gzip:[3,12,203,206,346,497,498,502],dlammps_jpeg:[3,12,206],dlammps_longlong_to_long:12,dlammps_memalign:[9,12,15],dlammps_png:[3,12,206],dlammps_smallbig:12,dlammps_smallsmall:12,dlammps_xdr:[12,203],dlen:507,dlm:[271,289],dlmp_intel_offload:[9,15],dlo:[61,202,231,303],dlopen:6,dlvo:[7,407,488],dm_lb:257,dmax:[335,384],dmpvtk:204,dmpvtp:204,dna:7,doc:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,16,17,21,36,40,42,55,59,61,65,69,71,79,84,86,95,98,102,103,114,115,116,118,120,121,122,123,125,128,129,131,153,156,157,158,171,173,175,178,179,180,186,198,202,203,204,205,206,207,208,210,211,212,217,218,219,220,221,222,223,232,246,254,255,266,271,272,277,278,279,283,291,292,294,295,296,303,306,317,331,335,338,339,340,349,353,356,358,360,362,371,376,386,387,388,393,394,395,398,406,408,409,416,417,419,425,426,428,429,443,444,445,448,452,455,456,457,467,476,477,480,482,484,485,495,497,498,499,500,502,505,506,507,514,515,519,524,525,527,528],docuement:460,dodd:42,dodgerblu:207,doe:[0,1,2,3,5,6,7,8,9,11,12,14,16,17,32,37,39,41,42,50,54,56,61,64,65,70,74,75,76,95,96,99,114,118,121,127,128,130,154,156,158,160,161,166,168,172,177,178,179,180,182,184,186,191,198,199,202,203,204,205,206,207,210,216,217,219,224,225,227,228,229,231,235,237,238,241,242,243,246,247,250,252,254,255,257,260,267,271,272,273,274,275,277,278,279,291,292,293,294,295,296,304,305,306,310,312,315,317,335,338,340,342,343,347,350,351,352,355,356,357,358,363,364,365,367,368,370,376,377,378,379,380,387,388,389,394,395,396,397,398,399,401,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,426,427,428,429,430,433,434,436,437,438,440,441,443,444,445,446,448,450,451,456,457,458,459,460,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,493,494,495,497,498,499,500,501,504,505,507,508,509,510,511,514,515,518,519,524,529],doegenomestolif:7,doesn:[3,7,8,12,178,203,204,217,331,387,389,393,395,408,417,428,458,459,477,480,481,482,485,497,499],dof:[3,8,123,156,157,158,171,219,317,525],dof_per_atom:[158,219],dof_per_chunk:[158,219],doff:[387,497],doi:[6,230,298],domain:[3,6,7,12,13,17,39,41,42,60,63,64,75,130,167,177,180,202,205,206,207,210,217,225,229,231,232,250,253,257,271,272,300,312,317,322,347,352,353,377,378,388,393,415,448,492,494,497,501,514],domin:[1,418,511],don:[0,8,9,12,13,15,127,181,213,237,255,356,443,466,495,497,519],donadio:339,done:[1,3,6,7,8,12,14,16,17,37,39,41,56,61,64,75,172,175,178,181,197,199,203,206,207,216,217,219,221,222,223,225,226,227,228,229,231,232,241,242,244,246,251,252,254,255,262,271,277,278,279,291,292,294,296,297,299,300,301,303,306,314,317,319,321,335,338,339,340,342,344,345,358,360,376,377,378,386,388,389,392,393,395,403,416,426,427,428,435,441,442,443,448,450,451,458,475,478,479,484,492,493,494,495,498,501,502,505,515,516,518,519,524,525],donor:425,dot:[153,174,213,237,249,270],doti:[399,456],doubl:[1,2,3,6,8,9,11,12,14,15,16,39,95,184,231,244,305,356,360,376,378,392,393,399,419,424,446,458,459,493,497,501,505,510,524,525],dover:216,down:[3,6,7,8,11,39,75,229,246,254,335,351,418,448,466,496,516],downhil:[384,385],download:[5,7,8,9,11,12,13,16,251,427,457],downsid:6,downward:314,dozen:[8,9,12,118,210,458,459],dpack_array:12,dpack_memcpy:12,dpack_pointer:12,dpd:[2,3,6,7],dpde:264,dpdtheta:[40,88,89,414],dpdtheta_i:[240,241,242],dproduct:396,dr_ewald:[130,319],drag:[2,6,99,210],dragforc:257,drai:[206,269,307],drain:[250,351,386],dramat:[9,61,202,226,227,228,229,231,271,335,338,339,378,448,466,494],drautz:399,draw:206,drawback:306,drawn:[42,203,206,207,247,492],drayleigh:[269,307],dreid:[2,3,4,6,9],dreiding:0,drfourth:115,drho:[124,394,416,450,451],drift:[6,113,115,238,247,248,250,254,255,267,315,335,506,514,518],drive:[11,12,214,229,231,249,271,298,304,317,354,388],driven:[6,190],driver:[6,12,14,210,244,251],drop:[3,207,413],droplet:426,drsquar:115,drude:[0,2],drudes:[255,518],dry:243,dsecriptor:427,dsf:[2,3],dsmc:[2,3,9],dstyle:303,dt_collis:257,dt_lb:257,dt_md:257,dt_srd:335,dtilt:[61,231],dtneb:511,dtqm:307,dtype:[84,126,227],dual:[16,335,393],dudarev:177,due:[1,3,6,9,12,15,16,18,40,54,57,59,60,63,69,74,75,78,79,86,87,94,96,97,98,103,112,113,114,115,116,121,127,130,138,152,153,155,156,157,159,161,164,165,166,167,168,170,171,173,177,178,181,182,203,204,206,210,213,214,222,224,226,227,228,229,230,231,232,237,239,243,244,247,248,251,252,254,255,256,257,260,261,262,267,268,269,270,271,276,285,298,301,303,315,316,317,320,331,332,334,335,336,338,339,340,341,342,344,345,347,351,352,354,355,356,358,377,378,384,386,388,389,390,410,413,414,416,421,422,426,440,441,448,456,458,460,461,475,478,480,482,486,488,489,492,494,497,498,499,506,511,514,515,516,518,524,525],duffi:347,duin:[9,308,313,458,459],duke:378,dullweb:[271,289],dumbbel:382,dummi:[12,28,481],dump0:204,dump10000:204,dump1:502,dump20000:204,dump2:502,dump2vtk_tri:146,dump:[0,1,2,3,4],dump_0:204,dump_1:204,dump_atom:8,dump_custom:8,dump_h5md:205,dump_modifi:[2,3,6,203,204,205,206],dump_p:204,dumpcustom:8,dumptimestep:502,dunbrack:[6,19,184,404,509],dunweg:[254,256],duplic:[2,3,14,16,41,42,179,204,225,248,298,497,523],dupont:[5,7,13],durat:[36,55,155,156,157,159,160,161,163,164,165,166,167,170,171,198,207,219,246,312,347,371,423,476],dure:[2,3,6,8,9,12,15,16,37,39,41,56,75,95,129,138,140,154,160,179,182,184,199,203,204,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,236,237,238,239,241,242,243,244,245,246,247,248,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,267,268,270,271,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,319,320,321,323,327,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,378,386,388,392,413,439,446,448,449,450,451,459,478,479,492,493,495,497,500,502,504,505,507,509,511,512,515,516,524,528,529],dvector:8,dvlo:488,dvx:6,dx_lb:257,dy3:177,dyamic:12,dyanam:6,dyanmic:511,dynam:[0,2,3,4,5,6,7,9,11,12,13,14,15,39,40,41,61,63,75,88,89,112,115,127,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,155,156,157,158,159,161,163,164,165,166,167,168,170,171,176,178,182,203,206,207,210,213,216,225,228,230,231,232,237,240,243,246,247,248,253,254,255,256,261,269,271,272,276,282,285,287,299,300,303,306,307],dynamo:[5,394,416,443],dyne:523,dyre:436,dysam:500,e28637:28,e_1:399,e_2:399,e_a:318,e_b:419,e_data:204,e_ee:418,e_hbond:425,e_i:[6,399,419],e_j:[6,399],e_k:399,e_ke:418,e_kl:6,e_lj:[395,412],e_n:399,e_ne:418,e_nn:418,e_pr:418,e_rebo:395,e_torsion:395,e_tot:446,e_vol:446,eaa:361,eaat:185,each:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,32,34,35,36,37,39,40,41,42,43,45,46,47,48,49,50,51,53,54,55,56,57,59,61,63,64,65,66,67,69,70,71,72,74,75,76,77,78,79,80,81,82,83,85,86,87,89,91,93,95,97,98,100,101,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,120,121,122,123,124,125,126,127,128,129,130,131,132,146,152,153,154,156,157,158,159,160,161,162,165,166,167,168,170,171,172,173,174,175,176,177,178,181,182,184,185,186,187,188,189,190,191,192,193,195,196,197,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,239,241,242,243,244,246,247,248,249,250,251,252,253,254,255,256,257,258,260,261,262,263,264,265,267,268,269,270,271,273,274,275,276,277,278,279,280,281,282,283,285,286,287,288,289,290,291,292,294,295,296,298,299,300,301,302,303,304,305,306,308,309,310,312,314,317,318,319,320,321,322,323,327,328,330,331,332,333,334,335,336,337,338,339,340,342,345,346,347,348,349,350,351,352,353,355,356,357,358,360,361,363,364,365,366,367,368,370,371,372,376,377,378,380,385,386,387,388,389,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,448,449,450,451,452,453,455,456,458,459,460,461,462,466,467,468,469,470,471,472,473,474,475,476,477,478,479,482,483,484,485,486,487,488,489,490,491,492,494,495,497,498,499,500,501,502,504,505,506,507,509,511,512,514,515,516,517,518,523,524,525,527,529],eacn:[41,225],eam0d:299,eam3d:299,eam:[0,2,3,5,7,8,9,10,12],eam_databas:13,eam_gener:13,eangl:515,earli:[41,219,222,223,225,311,319],earlier:[7,8,12,61,207,388,423,443,448,511],earliest:511,earth:418,easi:[6,7,8,9,10,11,13,95,153,203,211,212,213,214,224,237,249,250,252,254,255,320,328,338,339,340,352,355,357,387,497,500,505,507,525],easier:[8,9,13,15,203,204,206,299],easili:[8,11,206,207,351,388,494,504,513,524],eastwood:[377,378],eat:185,eatom:358,eaxmpl:6,eba:20,ebb13:185,ebb:20,ebond:[235,255,514,515,524],ebt:185,ec_ii:443,ec_ij:443,ec_jj:443,echo:[2,3,11,12,62,130,177],eco:[458,459],ecoa:[458,459],ecoul:[118,154,235,255,458,459,515],ecp:[418,497],edg:[3,6,41,42,61,75,130,176,177,180,181,203,205,206,215,252,320,352,355,356,357,358,380,497,500,507],edge:[2,3,352,355,357,500],edge_histo:176,edge_threshold:176,edih:515,edim:343,edip:[2,7],edit:[3,8,9,12,13,14,15,16,17,18,518,519],edition:15,editor:13,edu:[7,9,11,13,416,440,455,458,459],edward:[9,16],eebt:185,eff:[0,2,7,8],effect:[1,2,3,6,8,9,11,12,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,43,45,46,47,48,49,51,53,54,56,69,75,78,79,86,87,97,98,103,113,114,115,116,123,153,155,160,165,166,173,176,182,184,185,187,188,189,190,192,193,195,196,198,199,202,203,204,206,207,211,212,213,216,217,220,223,224,226,227,228,229,231,232,238,239,241,245,246,247,248,249,250,251,252,254,255,270,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,297,298,300,303,304,306,307,308,309,310,312,315,316,317,320,321,334,335,338,339,340,342,343,345,347,350,351,352,353,354,355,356,357,358,361,363,364,366,367,370,372,377,378,380,385,386,387,388,389,394,395,397,399,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,459,460,461,462,464,466,468,476,477,478,479,480,481,482,483,484,485,487,488,489,492,494,495,499,500,502,506,507,509,515,516,523,524,527],effectiv:[254,380],efffect:501,efficaci:39,effici:[0,1,3,6,7,8,9,10,12,14,15,16,17,39,60,63,70,123,154,197,203,204,205,206,207,220,221,229,231,235,248,271,300,302,303,312,317,321,335,377,378,384,389,393,399,407,409,426,431,435,446,450,451,460,478,504,529],efficienc:15,efficient:[9,302],effort:[5,7,498],efftemp:[106,107,164],efi:[458,459],efield:[2,3,210,217],eflux:250,eforc:204,eggebrecht:[409,466],ehanc:210,ehb:[458,459],ehex:[2,6,210],eigensolv:3,eigenvalu:[299,300,377],eigtol:3,eike:172,eim:[2,3,4,7,9],eimp:515,eindhoven:9,einstein:[6,312,345],either:[1,2,3,6,8,9,10,11,12,14,15,16,21,32,41,44,50,61,65,74,75,113,118,124,127,130,152,153,158,160,161,176,177,178,181,186,191,199,203,204,205,206,207,210,218,220,222,223,225,228,229,230,231,232,238,246,252,253,257,261,268,269,271,272,276,294,298,306,314,318,320,321,323,331,335,342,349,353,356,360,362,375,377,378,380,385,386,390,393,399,401,407,416,420,423,426,427,429,440,441,443,446,448,451,454,456,459,475,479,480,482,484,492,495,497,499,500,504,506,509,512,514,524],ejtehadi:[407,422,460],elaplong:[211,212,252,500,515,524],elaps:[3,202,211,212,213,214,224,231,237,249,250,252,254,255,268,303,320,328,338,339,340,352,353,355,357,468,492,500,502,503,507,511,515,516,524],elast:[4,6,7,9,44,45,46,55,122,210,270,299,353,385,388,423,455,481],elastic:[0,4],elastic_t:4,elba:28,electr:[6,210,216,237,255,377,378,419,458,459,489,518,523],electric:15,electrolyt:[9,488],electron:[3,6,7,9,13,40,106,107,124,130,162,164,169,204,210,216,234,235,255,256,272,284,295,310,341,347,385,387,394,396,408,412,416,418,419,443,446,456,457,466,482,485,489,497,517,518,523],electron_integr:216,electron_temperatur:216,electron_unit:418,electroneg:[6,308,309,310,408,419,466],electroneg_compon:466,electronic_dens:3,electronic_specific_heat:3,electronic_thermal_conduct:3,electrostat:[6,9,15,17,217,246,308,310,311,348,377,378,407,412,418,431,439,441,459,466,488],eleftheri:317,elem1:[419,443,467],elem2:[419,443,467],elem:466,element1:[314,394,416,466],element2:[314,394,416,466],element:[3,6,7,8,9,12,13,42,65,87,97,113,115,123,128,131,146,152,153,154,155,156,157,158,159,160,161,165,166,167,168,170,171,174,203,204,205,206,207,208,210,211,216,220,222,223,299,314,342,349,394,395,399,408,416,417,418,419,426,427,428,443,444,445,446,452,456,457,458,459,466,467,477,480,481,482,485,515,518,524,528],elementn:[394,416],elementset:216,elev:511,elif:[152,360],elig:[3,217,226,227,243,246,425],elimin:[3,6,75,176,247,254,255,317,321,344,345,492],elj:412,ellad:9,elliot:9,elliott:9,ellips:[4,6,9,75,90,156,201],ellipsoid:[3,4,6,7,9,13,40,42,75,90,124,142,156,178,201,202,203,204,254,268,273,277,281,282,287,291,317,335,382,383,386,422,441,460,476,497,507,527],ellipsoidflag:497,elong:[235,255,515],elp:[458,459],els:[3,7,8,12,75,118,127,128,131,206,218,219,220,222,223,246,271,317,335,347,348,349,358,360,377,426,496,508,524,528],elsewher:[8,268,335,443,457,458,459,509,515,524],elt:443,emac:0,email:[0,3,5,7,8,9,11,419],emb:[3,9,356],emb_lin_neg:443,embed:[3,4,5,7,9,11,12,13,28,96,154,176,347,394,416,419,439,443,444,445,456,476,486,495],embt:185,emi:[7,9],emile:9,emol:[458,459,515],emphas:423,empir:[9,216,339,418],empiric:395,emploi:[238,299,308,312,481],empti:[3,59,75,176,180,317,377,389,430,497,508,509,524],empty:3,enabl:[3,6,8,9,11,12,13,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,32,34,36,37,39,40,43,45,46,47,48,49,50,51,53,54,55,56,62,63,64,66,70,82,85,88,89,91,95,96,106,107,108,109,110,111,115,118,122,123,129,130,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,154,155,156,157,160,162,164,165,169,170,172,176,177,184,185,187,188,189,190,191,192,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71,272,294,295,304,307,308,309,310,343,344,345,350,408,409,458,459,493,507],equilibria:350,equilibribum:[226,227],equilibrium:[1,3,4,6,7,20,23,25,26,27,28,31,34,35,37,38,43,47,48,49,51,53,56,58,61,161,162,185,187,229,231,246,247,248,255,257,271,276,294,307,308,312,316,321,323,331,335,342,343,345,350,361,363,367,370,408,443,452,466,518],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:216,equival:[6,12,13,28,61,63,136,137,145,150,176,180,207,222,223,229,231,246,254,271,294,304,316,317,355,395,413,418,466,480,482,483,497,500,505,506,515,518],equlibrium:6,equliibr:[308,310],er3:177,eradiu:[40,124,204,418,497],eras:[320,344],erat:[231,441],erc:409,erfc:[409,431,448],erforc:[124,204],erg:523,erhart:[217,416,480,482],ermscal:396,ernst:9,eror:3,eros:443,erose_form:443,erot:[2,3,6,9,65],errata:[480,482],erratum:352,erron:3,error:[0,1,2],erta:423,ervel:[124,204,497],escap:[232,518],especi:[8,15,166,178,210,217,225,246,307,312,315,316,393,494,516],espresso:[9,311],essenti:[11,12,26,96,140,159,160,161,164,165,166,167,168,170,187,220,299,351,378,395,409,431,482,502,515],essential:[8,276],essex:28,establish:[95,250],estim:[1,3,6,10,12,37,41,56,74,99,153,216,225,236,269,318,335,342,377,378,384,448,459,478,479,511,515],estimat:3,esu:523,esub:443,eta:[6,257,271,307,308,310,351,417,419,422,456,481,485,523],eta_dot:271,eta_ij:456,eta_ji:419,etag:[40,497],etail:515,etap:271,etap_dot:271,etc:[1,2,3,4,6,7,8,9,10,11,12,13,14,15,39,40,42,54,63,71,97,98,99,104,120,121,124,126,129,153,155,158,159,160,161,162,164,165,166,167,168,170,172,178,180,181,182,191,203,204,206,207,210,211,216,217,218,219,222,223,226,227,231,232,244,246,247,254,271,303,314,319,347,348,356,360,376,377,386,387,388,389,391,416,417,426,439,441,446,454,458,459,477,480,482,485,492,495,497,498,499,504,506,507,511,512,513,514,515,516,518,523,524,527,529],ethernet:17,etol:[386,388,492,511],etot0:307,etot:[6,104,106,107,121,153,164,207,235,255,269,307,514,515],eu2:177,eu3:177,euler:[318,386,388],eulerian:216,euqat:469,europhi:257,ev_tal:8,evalu:[2,3,9,11,12,37,56,75,95,96,99,118,128,131,152,154,158,168,176,178,184,202,203,204,206,207,211,212,213,214,216,218,219,220,221,222,223,224,231,237,247,249,250,252,253,254,255,299,305,308,318,320,324,328,338,339,340,349,352,355,357,358,360,384,386,446,448,450,451,456,462,464,466,478,479,492,493,495,499,500,502,504,505,506,507,511,513,515,524,525],evaluat:[377,378,524],evalut:[360,495],evan:[166,294],evanseck:[6,19,184,404,509],evapor:[2,3,9,59,112,210,217],evaul:[8,386],evdwl:[118,154,458,459,515],even:[3,6,8,12,14,15,16,17,33,39,41,52,57,59,61,63,65,74,75,96,118,131,176,179,180,194,197,199,203,204,207,210,211,212,217,218,219,222,223,225,226,227,229,231,232,235,238,252,255,269,271,272,299,303,312,314,317,319,330,335,343,347,350,352,356,358,369,377,384,386,388,393,398,418,419,423,426,429,448,460,485,486,490,497,498,500,502,503,504,506,507,509,512,514,515,516,518,529],evenli:[3,41,57,153,199,225,257,429,486],event:[2,3,6,8,65],eventu:[3,6,12,14,180,511],eventual:308,ever:[9,54,56,253,335],everaer:[407,422,460,476],everi:[0,1,2,3,6,8,9,11,12,14,15,39,41,75,76,99,124,131,140,166,181,203,204,205,206,207,208,210,211,212,213,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,236,238,243,244,246,248,250,251,252,257,258,267,271,272,276,287,293,297,298,299,303,304,305,306,307,308,309,310,312,314,315,317,318,319,321,323,332,335,337,338,339,340,341,342,343,346,347,348,349,350,358,360,376,378,388,389,390,393,413,415,426,439,458,459,466,472,491,492,493,497,499,501,502,504,505,506,511,512,513,515,516,519,524,529],everyth:[8,118,519],everywher:[127,433],eviri:418,evolut:[238,248,257,300,492],evolv:[257,300,348],ewald:[2,3,5,6,7,8,9,12,96,121,130,153,348,377,378,386,400,402,403,409,412,418,431,435,453,461,476,478,483],ewald_disp:412,ewalddisp:3,exact:[21,41,44,75,134,172,181,186,225,228,247,248,254,255,256,303,312,313,335,347,362,377,406,499,504,511,524,527,529],exactli:[3,6,12,16,37,41,42,56,61,75,76,99,127,156,162,169,178,199,211,212,222,225,231,236,241,247,254,255,256,272,284,285,295,299,306,307,335,340,341,354,393,406,413,416,423,426,440,448,450,451,478,479,499,500,507,511,524],exager:518,examin:[6,8,16,228,299,318],examp:[495,524],exampl:[0,1,2,3],exce:[3,6,15,16,17,41,60,75,180,218,219,222,223,225,229,231,236,243,271,299,314,319,325,326,335,386,393,497,524],exceed:[3,41,61,225,231,271,335,459,505],excel:418,except:[1,2,5,6,8,10,11,15,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,37,40,41,43,44,45,46,47,48,49,51,53,54,55,56,61,62,65,75,97,98,119,123,128,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,178,182,184,185,186,187,188,189,190,192,193,195,196,198,199,202,203,204,207,210,213,219,220,222,224,225,229,231,239,245,246,249,252,254,256,271,272,273,274,275,276,277,278,279,280,281,284,285,289,291,292,294,295,296,300,309,310,317,320,321,331,335,341,347,355,358,359,360,361,362,363,364,366,367,370,371,372,377,378,380,383,387,388,389,391,392,393,394,395,397,400,401,402,403,404,405,406,407,408,409,411,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,444,449,452,453,455,458,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,494,495,497,499,500,502,505,506,507,508,509,511,515,518,523,524,525,528],exception:495,excess:[221,418],exchang:[2,3,6,8,63,64,210,216,217,238,246,250,254,309,317,343,347,350,377,393,418,512],exchange:377,excit:418,excite:418,exclud:[3,6,9,12,15,16,65,75,112,123,129,152,158,165,166,182,203,219,226,227,258,267,302,315,317,342,353,358,386,387,389,401,423,426,429,440,441,448,475,509],exclude:389,exclus:[1,3,12,15,95,184,408,446,448,506,516],excurs:[271,492],exectubl:12,execut:[1,2,3,4,6,8,9,11,12,16,62,179,206,251,311,360,376,379,392,493,495,505,508,511,524],exempl:466,exemplari:247,exemplifi:418,exert:[6,252,255,287,312,354,355,356,378],exhaust:[216,392,524],exhibit:[100,238,250,271,385,418,506],exist:[3,6,7,8,11,12,13,36,55,57,61,71,74,134,178,179,198,205,206,207,210,215,224,227,229,232,246,302,303,305,306,358,359,361,363,364,365,367,371,381,387,414,426,458,475,486,493,495,497,498,499,508,509,510,519,524,525,527],exit:[2,3,11,12,41,59,203,225,376,392,495,496,505,514,515,516,524],exlanatori:3,exp6:2,exp:2,expand:[2,3,44],expans:[12,152,197,203,508,524],expect:[1,3,8,12,13,14,15,16,17,18,41,42,75,112,159,170,176,199,225,237,246,248,268,298,304,306,307,312,317,358,378,389,406,443,446,448,492,495,497,499,502,506,511,524],expens:[6,75,207,298,302,317,347,358,377,378,389,393,495],experi:[6,13,14,224,232,251,260,270,304,316,317,384,388,413,448,506,511],experienc:[6,12,15,259,260],experiment:[16,246,377,393,511],expert:12,expertis:7,expir:[515,516],explain:[1,3,6,8,9,11,12,17,41,61,65,68,71,73,75,76,77,80,81,84,94,102,129,158,166,199,203,204,206,207,210,219,220,223,225,227,229,231,271,287,298,306,317,331,358,360,376,377,380,387,388,392,398,416,429,466,468,484,495,498,499,502,504,507,518,519,524,529],explan:[3,6,61,124,129,152,203,204,219,270,298,426,491,494,495,497,506],explanatori:[3,8,128,203,204,218,219,222,317,387,494,524],explantori:[3,313],explic:447,explicit:[6,9,11,21,44,81,95,124,127,172,186,211,212,231,318,325,326,362,377,383,395,396,399,404,406,416,418,430,440,483,491,494,498,501,519],explicitli:[3,6,8,12,14,15,16,17,18,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,75,123,155,165,168,176,178,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,231,239,245,247,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,306,307,309,310,317,320,321,340,341,347,355,361,363,364,366,367,370,372,387,393,394,395,397,400,401,402,403,404,405,406,407,408,409,410,412,413,415,416,417,419,420,421,422,423,424,425,426,430,431,432,433,434,435,436,437,438,439,440,444,446,448,449,450,451,452,453,455,459,460,461,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,485,487,488,489,497,499,500,506,507,509,510,516,518,519],explictli:[15,510],exploit:[14,16,300],explor:[130,177],expon:[3,308,310,318,416,420,422,425,439,447,461],exponenti:[95,318,420,456,477,485,489,511,524],expos:11,exposit:[216,413,415],express:[6,152,164,178,211,212,229,268,298,308,318,347,353,360,399,416,418,433,443,466,467,476,524],expression:360,expressiont:399,extend:[0,3,6,7],extens:[3,6,9,15,16,44,45,46,53,55,65,67,72,83,90,91,92,95,96,99,101,104,107,108,118,120,128,131,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,204,210,213,214,217,223,224,230,233,237,238,244,245,246,248,249,250,252,254,256,269,271,276,285,298,299,315,316,317,320,323,328,331,332,334,338,339,340,341,342,344,345,347,349,352,356,357,422,443,446,459,460,467,514,515,523],extensiv:[65,210,515],extent:[1,3,41,42,45,59,75,176,180,203,215,225,252,354,357,377,380,395,462,464,478,479,494,497,500],exterior:[3,6,176,356],extern:[2,3,9,94,95,176,206,210,224,229,237],extra:[3,6,8,11,12,15,16,40,41,46,63,75,112,120,121,123,130,153,155,156,157,159,161,164,165,166,167,168,170,171,177,178,179,180,207,222,225,227,271,305,306,307,317,335,386,387,390,391,393,412,423,426,429,443,448,494,495,497,500,509,518,524],extract:[3,6,11,13,35,65,67,72,83,95,101,118,126,128,131,211,212,310,388,409,419,443,467,495,502,514],extract_atom:11,extract_comput:[11,495],extract_fix:11,extract_glob:11,extract_vari:11,extramake:[12,14],extrapol:1,extrem:[1,3,6,16,60,206,221,229,231,271,345,418,481,518],extrema:439,extreme:418,extrins:216,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[174,349],f_a:[480,481,482],f_ave:128,f_c:481,f_f:482,f_fix_id:307,f_foo:524,f_harm:345,f_i:[28,456],f_id:[6,75,128,131,203,204,210,218,219,220,221,222,223,266,337,349,515,524],f_ij:456,f_indent:223,f_int:344,f_j:28,f_jj:99,f_k:456,f_langevin:347,f_max:[307,312],f_msst:269,f_r:[255,480,481,482],f_sigma:399,f_solid:345,f_ss:6,face:[3,6,59,61,75,166,176,180,215,352,354,355,356,357,380,422,443,460,497,500],face_threshold:176,facet:176,facil:[0,12],facilit:[6,13,42],fact:[6,8,15,248,303,335,345,423,458,466,509],factor:[1,3,6,12,17,23,27,31,34,35,39,41,46,47,59,60,61,76,95,99,112,119,126,127,130,152,172,177,180,184,195,202,203,206,207,211,212,220,225,229,231,232,238,246,251,254,256,257,269,271,272,276,300,304,308,316,318,321,324,326,335,339,343,350,351,352,356,367,378,380,387,393,395,396,399,400,402,404,409,410,411,413,414,418,423,426,430,431,443,446,448,450,451,452,453,459,461,468,477,483,494,497,500,501,506,509,511,512,515,518,523,524],factori:[3,495],factoriz:377,fail:[3,9,11,12,61,182,229,232,377,386,388,411,459,495],failur:[133,463,496,524],fairli:[11,448,506,511,519],faken:77,falcon:251,fall:[3,6,207,222,303,495,524],fals:[94,358,466,524],fame:8,famili:[485,494],familiar:[0,11,519],fan:456,far:[3,6,12,16,59,61,63,94,203,204,207,208,225,226,227,229,232,271,298,316,317,335,352,363,367,384,388,389,484,495,497,502,515],farago:254,farrel:[480,482],farther:203,fashion:[6,8,41,75,178,207,210,211,212,217,225,227,232,246,248,252,268,269,271,273,274,275,276,277,278,279,288,291,292,294,295,296,306,307,309,317,323,327,334,337,345,347,351,352,353,355,357,388,426,440,500,509,524,528],fasolino:428,fast:[6,7,9,12,13,15,16,39,203,204,282,307,318,348,377,378,401,440,441,446,476,478,479,499,504,506,515,525,529],faster:[1,6,9,11,12,14,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,63,65,115,123,155,165,184,185,187,188,189,190,192,193,195,196,199,203,204,207,213,224,225,231,239,245,249,253,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,304,308,309,310,317,320,321,335,342,344,347,351,355,361,363,364,366,367,370,372,377,378,390,391,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,476,477,478,480,481,482,483,485,487,488,489,492,500,506,510,518],fastest:[1,6,16,166,347,348,393,494],fatal:[3,514],fault:[74,459],faulti:12,fava:422,favor:228,favorit:7,fbmc:342,fcc:[2,3,6,7,66,74,77,99,117,210],fcm:[288,524],fcold:238,fdirect:235,fdotr:427,fdt:[2,9,240,241,242,318,322],fdti:95,fe2:177,fe3:177,fe_md_boundari:216,featu:8,featur:[0,3,5,6],fecr:416,feedback:[7,251],feel:[7,251,252,260,298,356,358,388,448],fehlberg:318,felling:445,felt:356,femtosecond:523,fene:[2,3,6,7,10,15,44],fennel:[409,431],fep:[0,2],ferguson:[6,184,509],fermi:[1,9,10,12,14,164,393,482],fermion:418,fernando:442,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,17,39,65,208,218,219,220,222,223,238,255,271,303,306,308,321,349,377,386,387,388,395,466,494,497,502,506,508,516,527],fewer:[1,3,11,14,15,63,260,506],fewest:3,fextern:244,feynman:300,fff:495,ffield:[408,419,458,459,466],fflag1:206,fflag2:206,ffmpeg:[3,12,206],ffplai:206,fft:[1,3,7,9,11,12,14,96,120,121,153,299,377,378,506],fft_inc:[12,378],fft_lib:12,fft_path:12,fftbench:[377,516],fftw2:12,fftw3:12,fftw:[9,12],fhg:[7,9],fhot:238,ficiti:475,fictiti:[6,213,214,237,244,248,300,316,409,431,435,475],field1:[498,502],field2:498,field:[0,2,3,5],fifth:[6,331,420,452],figshar:298,figur:[1,3,8,12,15,307,494,495,519],fij:412,file0:298,file1:[11,13,242,298,346,360,387,502,504,508],file2:[11,13,242,346,360,387,502,504,508],file:[0,1,2,3,4],file_from:205,filen:387,filenam:[3,12,13,15,37,41,56,199,203,204,206,207,208,216,219,220,221,222,223,225,230,241,242,298,302,305,308,309,310,313,314,317,318,319,346,347,374,375,376,387,388,394,395,399,409,416,417,419,420,428,443,444,445,450,451,452,456,457,458,459,466,467,477,478,479,480,481,482,485,493,494,495,498,499,504,508,515,524,527,528,529],filennam:504,filep:[3,203,204,207,499,504,529],filepo:314,fill:[7,9,178,206,303,347,380,389,399,446,459,500,519],filter:[207,216],final_integr:8,final_integrate_respa:8,finchham:[6,160,411],find:[0,3,4,6,7,8,9,11,12,13,15,37,39,56,63,75,77,95,128,181,199,208,217,228,229,241,242,243,246,270,298,303,304,312,316,384,386,388,389,409,426,431,435,443,450,451,466,476,478,479,518,519,524],find_custom:8,fine:[15,16,182,213,237,345,389,393,519,524],finer:[152,178,524],finest:377,finger:[178,202,268,500],finish:[6,11,41,225,360,374,376,377,390,392,393,484,502,524,525],finit:[0,3,4],finni:[7,416,476],finverse:235,fiorin:[9,230],fire:[2,3,210],firebrick:207,first:[0,1,2,3,5,6,8,9,10,11,12,14,15,16,20,37,39,41,42,45,46,54,56,59,61,63,64,74,75,87,96,99,113,114,115,117,123,127,128,139,142,145,146,150,153,163,166,172,174,176,177,179,180,181,185,199,203,204,205,206,207,208,210,211,219,220,222,223,225,228,231,241,242,246,247,252,257,268,269,270,271,298,300,305,306,307,309,314,317,321,323,331,332,333,335,336,337,344,345,346,347,349,358,360,361,368,380,386,387,388,389,392,393,394,395,398,399,400,402,404,406,408,409,416,418,419,420,423,424,426,427,428,429,430,431,435,440,441,443,445,446,448,450,451,452,456,458,459,466,467,475,477,478,479,480,481,482,485,489,492,493,494,495,497,498,499,502,504,506,509,510,511,514,515,518,519,524,525,526,527,529],fischer:[6,9,18,19,184,404,509],fit:[3,6,9,12,37,56,199,241,316,335,395,399,428,443,448,450,451,471,478,479,481,505,519,524],five:[77,164,307,387,399,444,497,511],fix:[0,1],fix_deposit:3,fix_flux:216,fix_heat:238,fix_id:[3,229,269,271,273,274,275,276,277,278,279,304,307],fix_manifoldforc:519,fix_modifi:[2,3,6,8,120,121,160,163,210],fix_nh:8,fix_nv:519,fix_poem:3,fix_pour:3,fix_qeq:3,fix_rattl:321,fix_reax_bond:458,fix_saed_vtk:319,fix_setforc:8,fix_shak:321,fix_srd:3,fixedpoint:[229,271],fixextern:244,fixid:[206,216],fji:412,flag1:[234,391],flag2:[234,391],flag:[3,8,9,11,12,14,15,16,38,40,58,69,78,79,86,87,94,97,98,103,113,114,116,129,130,173,177,181,200,203,204,206,207,208,223,228,230,234,251,254,258,260,267,268,299,306,317,331,334,335,342,346,355,358,373,375,378,387,391,392,393,395,425,430,443,446,475,490,492,494,495,497,498,499,501,502,503,507,519,524],flag_buck:403,flag_coul:[403,412,435],flag_lj:[412,435],flagfld:[401,440,441],flaghi:[3,401,440,441],flaglog:[401,440,441],flagn:234,flagvf:[401,440,441],flat:[6,15,347,352,353,357],flavor:[2,7,12],fld:[352,440,441],flen:396,flex_press:396,flexibl:[3,6,8,179,206,219,230,248,272,343,350,418,481,515],flip:[3,6,231,271,354,355],floor:524,flop:12,floralwhit:207,flow:[4,5],fluctuat:[6,66,95,229,246,247,254,257,271,276,298,299,304,322,345,347,370,414],fluid:[2,6,7,9,10,40,69,79,86,96,103,116,127,128,158,173,175,229,231,249],fluid_veloc:261,flush:[3,207,514],flux:[2,3,6,65],flv:206,fly:[7,9,12,41,206,210,216,221,232,235,317,321,348,399,446,515,518],fmackai:9,fmag:233,fmass:300,fmax:[386,515],fmomentum:235,fmsec:[2,207,254,255,268,271,304,317,338,339,506,517,523,525],fname:376,fno:[9,15],fnorm:[386,515],fnpt:235,fnve:238,fnvt:235,foce:426,fock:396,focu:321,fogarti:[9,310,459],foil:[152,298,467],fold:[15,333,506],folk:7,follow:[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17,18,19,22,23,24,25,26,27,28,29,30,31,34,35,37,40,41,42,43,45,46,47,48,49,51,53,54,56,61,65,66,74,75,77,88,99,100,106,107,117,124,127,128,131,152,153,156,157,158,164,166,171,174,176,178,179,184,187,188,189,190,192,193,195,196,197,199,203,205,206,207,210,216,217,218,219,220,221,222,223,225,230,231,232,235,236,240,241,242,244,246,247,248,251,253,254,255,257,260,269,271,276,277,278,279,291,292,294,296,299,300,302,305,306,307,308,310,312,314,316,317,318,319,321,337,338,339,340,343,344,345,346,347,349,350,358,359,363,364,365,366,367,370,372,375,380,383,386,387,388,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,447,448,449,450,451,452,453,455,456,457,458,459,460,461,463,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,483,484,485,487,488,489,490,492,494,495,497,498,500,502,504,505,506,509,511,512,513,518,519,524,525,528],foo:[4,8,11,12,203,206,244,318,495,508,524],foo_species:318,foot:6,footprint:[12,393],fopenmp:[9,17],forc:[0,1,2,3,5],force_uvm:16,forceatom:260,forcefield:[316,425],forcegroup:257,forcezero:384,ford:412,forestgreen:207,forev:75,forget:[255,518],forgiv:271,fork:[12,203],form:[2,3,6,8,12,18,21,44,54,57,65,69,78,79,81,86,87,95,97,98,100,103,113,114,116,127,152,153,172,173,182,186,207,210,211,212,227,247,248,254,256,260,268,294,299,310,312,316,317,318,347,352,356,361,362,365,370,383,385,387,388,395,396,399,406,414,416,418,421,425,426,430,442,443,445,446,450,451,452,453,456,458,459,460,466,467,468,476,478,480,481,482,488,491,494,495,497,502,507,514,518,524],formal:[6,82,85,99,247,248,254,271,300,335,343,466],format:[2,3,6,7,8,9,12,13,21,37,41,44,56,57,71,81,186,199,203,204,205,206,207,208,219,222,223,225,227,241,242,299,302,306,308,310,313,317,318,319,330,346,347,358,359,362,383,387,388,394,395,399,406,416,419,420,430,443,445,450,451,457,458,459,461,467,478,479,485,486,494,495,497,498,499,502,513,514,515,524,526,527],formation:242,former:[6,12,39,41,207,225,347,351,399,401,503,509,524],formerli:[7,13],formul:[1,6,9,40,66,153,213,237,254,271,294,308,310,316,321,346,377,395,399,416,418,422,443,455],formula:[2,3,6,7,13,20,21,36,44,54,55,74,77,95,97,98,99,104,106,107,116,123,130,131,153,155,156,157,158,159,160,161,162,164,165,166,167,168,169,170,171,177,178,183,185,186,198,202,203,211,212,213,214,219,220,221,222,223,224,231,237,249,250,252,254,255,268,298,299,305,314,320,328,333,335,338,339,340,349,352,353,355,357,358,360,361,362,364,371,380,387,395,396,398,399,404,405,406,407,412,413,416,417,422,423,424,425,427,430,431,433,434,435,437,438,440,441,443,447,448,449,460,461,468,476,477,478,480,481,482,485,487,488,493,497,500,507,514,515,523,524,525],forth:[1,6,11,12,13,14,392,495,500,504],fortran:[3,6,9,11,12,13,244,416,426,443,458,459],fortun:8,forward:[3,8,95,376,388,393],foster:[399,455,456],foul:181,found:[3,6,9,12,77,172,203,228,230,238,246,251,257,263,299,342,348,360,376,389,406,409,412,492,498,499,514],four:[6,11,54,87,113,114,152,174,269,347,370,387,388,446,492],fourier:[2,6,12],fourth:[6,15,115,316,331,342,404,420,452,466],fox:[6,130,184,474,509],fphi:[37,56,478,479],fpic:12,fplo:[37,56,478,479],fprime:[478,479],fqdn:253,fqq:412,fraction:[1,3,6,8,12,15,39,41,85,120,153,181,202,206,207,217,226,227,228,229,269,303,307,314,315,318,335,340,341,380,388,393,399,401,420,423,440,441,502,507],fragment:[42,251,314],fraig:42,frame:[91,152,207,216,269,307,354,422],framer:[206,207],framework:[5,248,394,467],franc:9,frattl:238,fraunhof:9,free:[5,6,7,9,13,28,62,65,74,95,172,211,212,298,335,344,345,346,347,385,388,396,418,439,446,449,456,488,494],freedom:[3,6,8,104,106,107,109,111,112,123,155,156,157,158,159,160,161,162,163,164,165,166,167,168,170,171,219,228,235,246,248,254,255,260,271,272,276,277,278,279,291,292,294,296,300,302,317,321,338,339,340,345,386,412,515,518,525],freeli:[0,6,7,12,156,157,171,176,206],freez:[2,3,6,210,215],frenkel:[6,238,246,345],freq:215,frequenc:[3,6,15,39,113,207,221,285,299,300,307,312,318,375,413,418,459,466,492,506,511,524,528],frequent:[3,66,70,74,76,77,81,96,100,117,152,207,226,227,238,243,343,350,448,483,504,516],fri:[269,307],friction:[4,5,6,9,10,42,210,248,254,307,312,317,347,351,353,423,507],friedrich:324,from:[0,1,2,3,5],front:[269,307,354],frontend:[206,311],frozen:[6,123,182,245,247,255,389,421],fs2:[6,99],fscale:251,fstr:524,fstring:495,fstyle:353,ftol:[386,388,492,511],fuchsia:207,fuction:409,fudg:321,fugac:246,fugacity_coeff:246,fulfil:6,full:[1,2,3,6,9,12,15,16,37,39,40,99,206,220,221,230,238,257,298,318,377,378,393,399,416,418,419,422,459,483,497,499,504,505,509,511,516,518,528],full_energi:[3,246],fuller:386,fulli:[3,6,82,248,253,298,386,388,409,456,457,497,519,526,527],fulton:416,fumi:400,func:[495,524],funcfl:416,functionaliri:230,fund:[0,7],fundament:[335,523],funnel_flow:330,funrol:446,further:[3,4,6,8,12,13,63,65,67,72,75,83,94,101,115,118,127,206,207,210,219,222,223,226,232,236,257,261,300,308,319,322,324,335,347,349,358,378,384,386,387,388,389,394,398,408,446,466,492,511,512,524],furthermor:[26,187,238,318,414,418],furthest:63,futher:3,futur:0,g_ewald:3,g_ewald_6:3,g_ewald_disp:3,g_jik:456,g_p:347,ga3:177,gaa:399,gahler:385,gai:[3,422,476],gain:[15,342],gainsboro:207,galindo:447,game:251,gamma0:28,gamma:[3,6,28,254,257,261,299,307,308,310,312,351,413,414,417,422,443,447,470,473,474,477,480,482,485,515],gamma_:[3,347,353],gamma_ijk:480,gamma_n:[353,423],gamma_p:[3,347],gamma_t:[353,423],gammaa:447,gammafactor:257,gammar:447,gan:[456,477,480,482,485],gan_sw:456,gan_tersoff:456,ganzenmuel:[7,9],ganzenmul:9,gao:[6,19,184,404,509],gap:[199,440,441,457,467],gap_2014_5_8_60_17_10_38_466:457,gap_exampl:457,gaseou:7,gass:246,gather:[11,505],gather_atom:11,gather_scatter_loop_unrol:9,gathert_atom:11,gauch:190,gaug:12,gauss:[2,3,118,172,211,212,410],gaussian:[6,40,65,99,113,115,232,247,248,254,300,316,335,339,357,377,413,415,418,421,457,476,492,524,525],gave:[3,448],gavhan:15,gaybern:[2,3,6,7,9,15,156,386],gcc:16,gcmc:[2,3,7,9,210,217],gcores:235,gd3:177,gdot:441,gdrudes:235,ge4:177,gec:[480,482],gen:[271,272],gener:0,genom:7,gentler:[352,355,357],gentli:417,geom:[6,377,415,492,525],geometr:[3,6,7,8,42,59,61,75,86,129,168,169,178,180,203,207,213,224,225,232,237,250,271,277,278,279,291,292,294,296,317,320,328,338,339,340,356,358,377,380,388,398,401,405,407,409,412,418,420,422,424,431,432,433,434,435,436,437,438,439,440,441,442,447,448,451,460,468,479,483,484,487,488,490,497,500,507,515,524],geometri:[3,6,7,9,13,24,38,41,58,75,86,166,178,200,225,226,227,229,232,252,322,373,380,448,497,500],georg:[7,9],georgia:13,gerar:524,gerber:439,germani:9,germann:[276,433,492,511],germano:422,gerolf:13,get:[0,1,3,6,8,9,11],get_natom:[11,495],get_rank:11,get_siz:11,getenv:524,gettimeofdai:12,gewald:[6,377],gezelt:[409,431],gflop:12,gflp:12,gfortran:9,ghost:[3,6,7,12,15,60,63,64,77,176,181,182,229,231,255,271,306,317,319,375,377,389,393,413,414,415,418,423,430,490,502,507,518],ghostwhit:207,giacomo:9,gif:[4,206],gifsicl:206,gigabit:17,giko:2,gikot:2,gillan:467,gingold:[470,471,473],gio:2,git:[7,12,519],github:[8,13,16,230,248,253,457],give:[0,1,2,3,4,5,6,7,8,9,10,11,12,14,15,16,17,54,75,100,117,124,158,161,165,178,203,204,207,213,215,219,220,222,223,229,231,248,271,289,294,298,299,304,312,314,317,349,377,378,386,389,390,393,395,399,415,418,425,426,443,446,448,460,480,481,482,492,494,495,497,507,511,518,525],given:[3,4,5,6,7,9,11,12,15,16,21,26,36,44,55,63,65,66,70,75,117,124,135,136,137,139,140,143,144,145,146,147,148,149,150,151,152,153,172,176,180,186,187,198,199,203,204,205,207,210,217,219,221,226,227,229,231,232,236,238,246,247,248,249,251,257,263,265,268,270,271,276,297,298,299,300,307,308,314,316,318,321,330,331,333,335,337,342,347,348,351,352,353,356,362,371,377,378,393,394,395,399,400,402,403,405,406,407,408,409,410,413,414,415,416,418,419,420,422,423,425,431,432,433,435,443,444,445,446,447,448,449,450,451,452,453,456,460,461,463,465,466,467,476,489,492,495,497,499,500,506,507,511,523,528,529],gjf:254,gjwagn:7,gkio:2,gko:2,gkot:2,gld:[2,3,210],gle4md:[248,253],gle:2,glitch:3,glob:508,global:3,glosli:[378,446],glotzer:[317,413],glue:11,gmail:[7,9,13],gmake:[12,16],gmask:[3,524],gnu:[0,7,9,12,16],gnuplot:[11,13],goal:[5,12,39],goddard:[6,9,24,308,309,310,372,418,425,458,459,509],goe:[12,54,152,178,202,238,268,327,386,389,412,417,424,433,436,468,489,50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12,317,319,323,334,345,347,380,423,446,492,495,514,525],indetermin:[203,204,207],index:[0,3,6,8,11,12,37,39,40,56,57,68,71,73,84,102,119,128,129,131,176,199,203,207,218,220,241,242,251,253,300,319,347,358,359,360,383,392,448,450,451,458,459,478,479,486,497,512,524],indianr:207,indic:[2,3,6,8,11,12,15,20,40,42,54,67,70,72,78,83,87,88,89,96,97,99,101,113,115,123,126,128,153,155,156,157,158,159,160,161,162,163,165,166,167,168,169,170,171,174,185,199,203,206,211,212,229,271,299,317,347,358,361,370,377,387,389,408,415,419,426,443,446,448,452,458,459,466,480,482,494,496,497,499,515,519,524],indigo:207,indirectli:[6,306,524],indistinguish:254,indium:467,individu:[0,1],induc:[0,3],industri:7,ineffici:[3,6,40,66,70,74,76,77,81,100,117,152,166,206,231,271,299,377,390],inelig:217,inerti:441,inertia:[2,3,6,40,42,65,90,91,92,93],inertiai:129,inertiax:129,inertiaz:129,inexpens:[248,506],inf:[2,3,12,350,500],infer:[3,104,106,107,172,213,214,225,226,227,237,251,302,335,343,350,380,406,419,497,509,515],infil:[3,13,317,494],infin:[3,386,502,515],infininti:206,infinit:[3,232,245,252,254,257,299,335,347,353,354,378,380,418,497,501,523],infinitesim:6,inflect:[410,433,476],influenc:[3,9,41,85,160,268,303,377,378,448,480,481,482],inform:[0,1,2,3,6,7,8,9,11,12,13,14,15,16,39,41,42,61,63,64,65,71,96,126,128,129,130,177,178,184,203,204,205,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,235,236,237,238,239,243,244,245,246,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,267,270,280,281,282,283,284,285,286,287,288,289,290,293,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,316,317,319,320,321,324,331,332,333,335,336,338,339,340,341,342,343,344,346,349,350,351,352,354,355,356,357,359,375,377,378,381,385,386,387,388,389,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,412,413,415,416,417,418,419,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,487,488,489,490,494,495,497,498,499,501,502,504,509,511,512,514,516,524,526,527,528,529],informat:[8,12,498],infrequ:[6,271,413,492,511,516],infti:[410,440,441],ingtegr:399,inher:[377,386,448],inherit:[6,483],inhomogen:[17,347,448],inidividu:386,init:[3,8,315,466],init_fil:347,init_list:8,init_on:8,init_styl:8,initi:[2,3,4,6,7,8,11,12,13,37,39,40,41,56,59,61,64,75,85,87,94,95,113,114,142,174,179,180,199,202,203,204,206,207,208,211,212,215,216,220,225,227,228,229,231,239,241,242,246,247,251,252,253,254,255,257,262,267,268,269,270,271,276,285,287,299,300,301,306,307,312,315,316,317,318,320,322,332,334,335,337,342,344,345,346,347,348,349,352,353,354,355,357,358,360,377,381,385,386,388,395,396,412,413,415,446,450,451,457,458,459,466,478,479,492,494,495,497,499,500,502,504,505,507,511,512,515,518,524,525,527,529],initial:[2,3,6,87,113,180,524],initial_integr:8,initial_integrate_respa:8,initialis:457,initialt:347,inlclud:11,inlin:495,inner2:[404,424],inner:[3,8,15,57,203,252,360,376,384,385,386,388,392,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,486,487,488,489,490,506,511,524],inner_distance_cutoff:425,innergroup:260,innermost:[37,56,75,391,478,479,506],innernod:260,innner:437,inordin:348,inorgan:[6,485],inp:[230,360,467,485],input1:[71,124,125,128,129,131,337],input2:[71,124,125,128,129,131,337],input:[0,1],input_doubl:3,inquir:324,insensit:12,insert:[3,5,7,8,9,12,61,178,210,232,246,252,303,377,467,475,495,501,518],insertion:[3,232,246,303],insid:[2,3,6,8,11,75,129,141,147,178,203,204,207,218,232,233,238,243,246,252,257,260,303,317,335,352,354,355,356,357,358,375,380,495,496,497,499,500,507,524],inside:[257,433,495,511],insight:[6,13],instabl:[257,412,465],instal:[1,3,6,8,9,11,12,14,15,16,176,203,205,206,208,378,388,403,404,427,431,435,439,446,492,498,499,504,512,519,529],install:[0,8],instanc:[6,9,11,211,230,248,354,421,426,448,456,495,518],instantan:[6,65,228,229,247,248,271,276,299,304,307,312,314,317,342,503,515],instanti:[6,11,12,216,426,494],instead:[1,3,6,8,11,12,13,15,16,17,40,41,61,63,65,74,75,98,113,128,156,160,182,184,199,203,204,212,219,222,223,225,229,230,246,254,257,260,261,299,305,306,315,317,337,355,375,377,378,381,389,393,402,403,416,430,432,439,443,446,449,459,476,483,492,500,504,511,513,518,524],institut:[9,251,302],instruct:[3,4,6,8,9,10,11,12,13,15,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,43,45,46,47,48,49,51,53,54,56,123,155,165,176,184,185,187,188,189,190,192,193,195,196,199,201,206,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,500,506,518],instruction:11,insuffici:[3,6,12],insult:271,insur:[3,6,11,12,16,39,40,63,77,112,114,178,179,199,203,204,206,207,213,226,227,232,237,239,243,244,246,249,254,267,305,306,315,317,335,347,352,356,357,358,360,376,387,389,393,407,422,426,454,460,478,490,494,495,497,498,502,505,506,514,515,524,525],insure:16,int_max:3,inteatom:10,integ:[3,6,8,11,12,39,40,42,66,71,74,75,117,124,126,128,131,152,176,178,181,182,184,188,189,193,197,199,202,203,206,207,217,219,226,227,228,232,234,244,246,247,248,251,254,255,256,257,299,302,303,306,307,312,317,318,335,337,339,342,346,347,366,377,380,401,413,414,415,429,443,458,459,463,465,467,492,494,495,496,497,505,506,507,511,514,524,525],integer:[3,497],integr:[2,3,5],integral:[300,450,451],integrate_ulsph:325,intel:[1,2,3,7],intel_coprocessor:15,intel_cpu:12,intel_cpu_intelmpi:15,intel_cpu_mpich:15,intel_cpu_openpmi:15,intel_phi:12,intend:[3,6,8,12,13,35,221,247,457,497],intens:[1,3,6,9,65,69,78,79,86,94,97,98,99,103,113,114,115,116,123,125,127,128,130,131,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,173,174,175,177,210,219,220,222,223,225,226,227,228,236,243,250,260,269,271,276,314,317,319,335,343,347,349,350,514,515,523],intensiv:[65,210,515],intepol:524,inter:[17,42,63,64,158,181,182,203,228,254,256,270,309,317,377,388,399,507,518,524,527,529],interact:[1,3,6,7,8,9,10,11,12,14,16,21,28,32,33,36,39,40,42,44,50,52,54,55,57,59,63,65,68,73,76,81,84,95,96,100,102,117,118,119,121,123,126,127,134,135,136,137,139,140,141,142,143,144,145,147,148,149,150,152,153,154,156,157,171,172,176,179,180,181,182,183,184,186,190,191,194,197,198,203,204,210,211,212,226,227,228,245,246,251,252,254,256,260,285,298,300,302,303,308,310,316,317,318,325,326,335,336,342,347,351,352,353,356,357,362,363,364,365,367,369,371,377,378,386,387,388,389,390,391,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,453,454,455,456,459,460,461,463,465,466,467,468,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,492,495,497,499,501,502,506,507,509,514,515,518,527],interatom:[3,4,7,9,10,178,203,270,344,345,394,399,416,418,427,443,446,466,481,524],intercept:130,interchang:6,interconnect:17,interconvert:418,intereract:39,interesect:356,interest:[1,5,7,8,9,11,13,75,177,300,342,345,378,417,441,458,459,495,524],interf:[393,519],interfac:[0,3],interfer:[12,271,395],interg:[6,518],intergr:506,interi:441,interior:[3,6,41,356,500],interlac:443,interleav:[6,178,505],intermedi:[6,12,61,206,270,298,370,388,495,496,505,509],intermix:492,intermolecular:[154,395],intern:[0,2,3,5,6,9,11,15,19,20,23,27,31,34,35,39,40,42,65,88,89,95,109,111,129],internal:[3,206,212,303,524],internal_element_set:216,internal_quadratur:216,internat:[15,130,177,216],internet:253,interpenetr:443,interpentr:[470,471,473],interpol:[6,14,37,56,110,199,206,207,216,241,242,257,298,377,378,388,399,448,450,451,459,472,478,479,480],interpret:[2,6,11,197,206,222,423,468,492,495,511,524],interrupt:307,intersect:[3,6,130,207,356,358,500],intersert:356,interspers:386,interstiti:[176,446],intertia:[3,103],interv:[3,6,99,205,220,254,271,307,312,313,326,466,472,492,511,524],intestieti:130,intial:[6,393,395],intiial:[41,502],intiti:[3,334],intra:317,intra_energi:246,intramolecular:[28,154,246],introduc:[6,9,100,117,206,238,271,307,312,317,370,377,394,409,418,431,435,439,477,511,524],introduct:0,intuit:380,inv:[130,177,319],invalid:[3,12,75,97,181,285,388,440,441,499],invari:[117,145,150,152],invent:321,invers:[3,6,51,130,177,207],inverse:518,invert:[1,6,182,299],invis:356,invoc:[176,228,393,463,465,495],invok:[1,3,6,7,8,9,11,12,13,15,16,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,43,45,46,47,48,49,51,53,54,56,57,61,65,69,75,78,79,86,87,95,96,97,98,103,113,114,116,121,122,123,128,131,155,165,172,173,176,178,179,181,182,184,185,187,188,189,190,192,193,195,196,199,203,204,206,207,208,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,231,232,233,234,236,237,238,239,243,244,245,246,247,249,250,251,252,254,255,256,257,258,259,260,261,262,263,264,265,267,268,270,271,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,301,302,303,304,305,306,308,309,310,311,312,313,314,315,317,319,320,321,323,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,361,363,364,366,367,370,372,376,377,378,379,380,386,388,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,426,427,431,432,433,434,435,436,437,438,439,440,441,444,448,449,452,453,455,459,460,461,463,465,467,468,477,478,480,481,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296,299,338,339,340,341,344,345,386,388,395,401,498,518],proceed:[12,446],procesor:[41,494],process:[1,3,4],processor:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,39,40,41,42,60,61,63,64,65,68,71,73,75,84,102,119,124,126,127,129,166,176,178,180,181,182,202,203,204,206,207,210,216,219,225,226,227,228,229,231,244,247,248,254,255,257,271,300,306,309,312,317,321,322,335,347,358,374,375,376,377,381,388,390,391,392,393,413,415,454,466,491,492],processsor:[41,225,494],procp1:[203,204],procsessor:516,procssor:506,produc:[1,3,4,6,7,12,13,14,15,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,40,41,42,43,45,46,47,48,49,51,53,54,56,65,68,71,73,75,84,102,119,121,123,124,125,126,128,129,131,153,155,165,176,184,185,187,188,189,190,192,193,195,196,199,203,204,206,207,210,213,218,219,220,222,223,224,225,228,231,239,244,245,247,248,249,254,255,256,266,268,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,303,307,308,309,310,312,317,318,319,320,321,336,337,347,348,349,352,355,360,361,363,364,366,367,370,372,378,386,388,391,393,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,444,449,452,453,455,456,459,460,461,468,477,478,479,480,481,482,483,485,487,488,489,492,494,499,500,502,503,506,511,512,515,524,525],product:[6,15,16,17,152,176,231,294,308,318,348,393,396,418,420,451,459,479,494,524],proessor:393,prof:302,profi:167,profil:[2,3,6,65,156,157,158,161],program:[3,4,6,7,9,11,12,13,15,16,154,203,206,207,208,210,230,244,251,257,311,416,495,496,508,524],programm:[13,16],progress:[1,41,225,251,269,307,385,386,388,515,518],prohibit:507,project:[6,7,13,385,476,519],promis:7,promot:399,prompt:[8,11,12,251,508],proni:[3,247,248],pronounc:250,proofread:8,prop:[6,306],propag:[4,9,215,271,307,324,418,426],propens:6,proper:[228,298,443,495,519],properati:306,properli:[213,237,317,322,330,387,388,414,495,525],properti:[0,2,3],propoerti:335,proport:[6,39,41,95,113,114,174,225,254,255,256,307,318,343,350,351,423],proportion:254,propos:[6,152,217,229,246,271,294,312,431,445,481,483],prospect:7,protect:335,protein:[7,10,15,178,315,317,333,497,505],protocol:251,proton:[482,489,523],prototyp:[42,455],prouduc:[223,349],prove:[88,89,240,257,322],proven:294,provid:[1,3,4,6,7,8,9,10,11,12,13,14,15,16,17,28,40,42,63,70,74,130,151,154,172,176,177,178,205,206,208,211,218,219,223,228,229,230,231,244,246,251,253,257,261,269,271,299,306,307,308,311,312,317,322,323,342,344,345,348,349,360,375,377,378,384,388,393,395,399,401,406,408,409,413,417,418,423,425,428,430,439,440,443,445,446,456,457,458,459,466,467,475,476,477,480,481,482,485,494,499,505,507,510,511,515,516,519,524],proxim:202,psa:355,pscreen:[3,12,506],pscrozi:[0,7,13],psec:[207,231,250,254,255,271,304,317,338,339,517,523],psend:494,pseudo:[418,492,497,502],pseudodynam:342,pseudopotenti:[9,446],psf:6,psi:[419,488],psi_ij:419,pstart:[3,271,272,276,304,317],pstop:[3,271,272,276,304,317],pstyle:[95,118,211,212],psu:[458,459],psuedo:502,psxevar:15,pt2:177,pt4:177,ptarget:229,pthread:[12,15,16],ptr:[6,11,244,495],ptype1:126,ptype2:126,pu3:177,pu4:177,pu6:177,publicli:5,publish:[7,257,261,287,293,308,382,409,443,446,480,482],pull:[323,331,519],puls:347,pump:[440,441],punctuat:[2,492,511],purchas:206,purdu:[9,13],pure:[11,335,426,444,445,480,482,506],purg:[3,498],purpl:[2,207],purport:11,purpos:[3,6,7,9,12,42,63,75,130,140,146,161,162,177,178,180,182,199,203,223,228,229,254,298,300,303,305,316,335,377,403,429,435,446,448,484,490,497,500,504,507,509,510,524,529],push:[3,8,213,224,231,252,270,298,315,323,386,423,468,519],pushd:252,put:[3,6,8,11,12,13,39,61,166,178,203,232,236,354,355,358,380,458,495,497,501],putenv:[508,524],px1:506,px2:506,pxx:[229,271,304,317,377,378,514,515],pxy:[3,6,515],pxz:[3,6,515],py1:506,py2:506,pydir:11,pyi:[229,271,304,317,377,378,515],pymol:[7,11,13],pymol_aspher:0,pympi:11,pypar:11,python:[0,2,3,4,6,7],pythonpath:11,pyz:[3,6,515],pz1:506,pz2:506,pzz:[229,269,271,304,307,317,377,378,515],q_1:466,q_2:466,q_3:466,q_d:518,q_i:[419,439],q_j:439,qbmsst:[2,9],qcore:308,qdamp:308,qdist:[409,431,435,439],qeq1:308,qeq2:308,qeq:[2,3,4,6,7],qeqall:466,qeqallparallel:466,qfile:[308,409],qin:250,qinitmod:466,qmin:385,qmmm:2,qmol:311,qoffload:15,qopenmp:15,qout:250,qoverrid:15,qstep:308,qtb:2,quad:[12,17,393,494],quadrant:15,quadrat:[2,3],quadratur:[95,216],quadrupl:394,quadruplet:[194,198,200,361,363,364,365,367,369,370,371,373],qualifi:[3,253],qualiti:[7,206,207,395],quantic:466,quantit:[78,87,113,114,115,174,423],quantiti:[1,3,4],quantum:[6,9,152,244,248,300,307,311,312,395,399,418,446,466,476],quantum_temperatur:307,quartic:[2,3,7],quartic_spher:216,quartz:[307,312],quasi:300,quat:[3,507],quaternion:[3,6,40,90,124,129,142,156,157,178,273,274,277,278,281,282,283,291,292,422,497,507],quati:[124,129,497],quatj:[124,129,497],quatk:[124,129,497],quatw:[124,129,497],queen:13,quench:[358,492,511],queri:[3,11,54,288,495,524],quest:[6,244],question:[8,9,12,13,287,298,358,455,519,524],queteschin:9,quick:[0,4,12,14,15,16,17,18],quickli:[3,4,8,12,13,39,100,225,231,246,251,335,385,386,388,395],quickmin:[263,287,293,384,385,386,388,511],quicktim:[4,206],quip:2,quit:[2,257,342,360,467],quot:[2,3,12,205,305,360,443,492,493,495,505,524],quotat:466,r0m:332,r10:399,r12:422,r_1:152,r_2:152,r_c:[410,412,421,482],r_cut:[399,442],r_d:518,r_e:419,r_ewald:319,r_fu:[440,441],r_i:[28,152],r_ii:152,r_ij:[28,399,418,456,489],r_ik:456,r_j:28,r_jik:456,r_m:442,r_me:410,r_mh:421,r_min:411,r_ub:19,r_x86_64_32:12,ra2:177,rad2theta:177,rad:358,radhi:500,radial:[65,75,106,107,124,127,152,162,164,169,219,256,272,284,295,331,341,386,418,425,448,450,451,497,500],radian:[19,20,23,27,31,34,35,37,129,177,185,196,199,316,361,363,367,370,497,500,507],radians:199,radiat:[130,177,347],radic:[180,497],radii:[75,80,119,126,152,228,232,407,416,422,423,440,441,446,462,464,488,500],radit:418,radiu:[2,3,6,40,42,65,75,80,92,93,97,98,119,124,126,130],radlo:500,rafferti:350,rahman:[6,7,229,269,271,272,307,455],rai:[9,16,177],ram:482,raman:15,ramirez:221,ramp:[2,3,6,9,65,161,162,166],ran:[3,6,11],random:[3,6,39,178,181,202,206,215,217,226,227,228,230,232,243,246,247,248,254,255,256,257,267,271,300,303,307,312,315,317,322,335,339,342,347,351,354,401,413,414,415,492,507,512,518,524,525],random_se:492,randomli:[178,181,217,232,246,254,303,335,357,511,512],rang:[1,3,6,7,8,9,10,12,14,15,17,37,39,56,63,75,76,81,96,117,119,120,121,123,127,128,133,152,153,164,172,177,179,182,183,190,199,203,204,206,207,216,217,227,231,232,246,248,266,303,319,335,336,342,343,348,350,377,378,386,389,390,393,395,397,399,400,401,402,403,404,405,407,409,410,411,412,413,415,416,418,420,422,424,425,426,428,431,432,433,434,435,436,437,438,439,440,441,442,443,446,447,448,449,453,456,459,460,461,466,475,476,478,479,482,483,487,488,489,491,495,506,507,515,528],rank:[6,11,12,251,348,375,494],rankin:276,raphson:3,rapid:[4,6,11],rapidli:[3,8,12,75,228,254,269,271,317,338,339,351,409,413],rapp:[308,309,310],rappe_and_goddard:309,rare:6,rasmol:[6,7],rasmussen:422,raster3d:[6,7],rate:[2,6,12,15,136],rather:[2,6,9,12,40,41,64,123,161,206,225,231,247,248,317,339,347,351,353,354,355,358,418,450,451,458,478,479,498,502,507,509,514,524],ratio:[6,61,95,111,152,217,225,231,254,256,335,343,350,351,377,391,422,423,460,470,484,494,497,507,511],rational:[348,509],rattl:[2,3,9,210,238,263],rattle:[3,9,210,238,248,287,293,321],rattle_debug:321,ravelo:[276,433],raw:15,rayleigh:[269,307],rb1:177,rbb:466,rbg:207,rcb:[3,41,225],rcm:[97,98],rcmx:[97,98],rcmy:[97,98],rcold:238,rcut:63,rcutfac:[152,467],rd1:388,rdc:16,rdf:[2,3,65],rdn:388,rdt:388,rdx:4,reach:[6,12,41,131,221,225,227,229,255,276,318,327,335,342,360,376,392,410,516,518,524],reacquaint:519,react:6,reactant:[318,418],reaction:[9,242,318,323,333,346,357,388,418,420,451,479],reactiv:[9,314,395],read:[2,3,6,7,8,9,11,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,37,38,40,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,58,61,126,176,178,179,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,202,203,204,206,207,208,209,210,216,217,228,229,231,232,241,242,246,248,251,268,269,271,273,274,275,276,277,278,279,291,292,294,295,296,299,300,302,303,305,306,310,317,318,321,323,327,330,334,337,345,346,347,353,359,361,362,363,364,365,366,367,369,370,371,372,373,374,376,383,387,388,392,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,412,413,414,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,449,450,451,453,455,456,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,484,485,486,487,488,489,490,492,494,497,498,499,501,502,503,504,505,507,508,509,511,524,525,526,527,529],read_data:[2,3,6,7,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,36,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,58,59,60,61,64,69,75,78,79,86,87,90,97,98,103,113,114,116,126,173,176,178,179,180,181,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,200,201,203,206,227,228,231,268,300,306,316,318,346,361,362,363,364,365,366,367,369,370,371,372,373,383,387,388,391,392,393,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,418,421,422,424,425,426,429,431,432,433,434,435,436,437,438,439,440,441,442,447,449,453,455,456,458,459,460,461,466,468,475,476,484,487,488,490,494],read_dump:[2,3,203,388,497],read_restart:[2,3,6,8,9,12,13,19,20,21,22,23,24,25,26,27,28,29,30,31,34,36,39,40,41,43,44,45,46,47,48,49,51,53,54,55,59,60,61,64,178,184,185,186,187,188,189,190,192,193,195,196,198,210,216,217,229,230,231,232,246,257,268,269,271,273,274,275,276,277,278,279,291,292,294,295,296,300,306,317,323,334,337,347,353,361,362,363,364,365,366,367,370,371,372,383,388,396,397,398,400,401,402,403,404,405,406,407,409,410,412,413,414,415,418,421,422,423,424,426,429,431,432,433,434,435,436,437,438,439,440,441,442,447,449,453,455,460,461,468,475,476,484,487,488,490,494,497,498],read_restart_set:8,readabl:[204,206,387,504,529],reader:[3,13,498],readi:[11,12,179,181,182,251,507,518,527,528,529],readme:[1,4,6,8,9,10,11,12,13,15,176,203,204,208,311,427,446,458,459,495],real:[3,6,7,11,26,29,30,61,75,99,100,117,152,167,178,187,202,207,215,231,232,235,251,252,255,268,300,307,312,315,351,352,354,355,357,366,377,378,380,384,390,409,446,448,458,459,482,497,500,506,514,517,523,525],realist:[3,232,501],realiz:[75,210,495],realli:[1,3,8,12,123,134,153,207,252,389,426,509,519],realloc:3,realtim:251,reamin:[352,356],rearrang:[204,388],reason:[3,6,7,11,12,18,39,159,170,178,197,219,254,304,317,344,345,348,358,387,388,393,406,410,418,419,421,441,448,484,486,501,506,525],reax:[0,2,3,4],reax_def:3,reaxc:7,reaxff:[3,4,5,7,9,13,210,308,310,313,314,426,458,459,476,509],rebal:[41,225],rebalanc:[41,225],rebo:[2,7,9,314],rebuild:[11,12,14,15,246,389,413,515],rebuilt:[3,12,203,204,205,206,208,389,393],recalcul:[75,95,335],receiv:[3,224,251,253,298,494],recent:[2,3,11,12,15,210,219,222,223,225,226,227,250,267],reciproc:[6,12,130,176,177,299,377,400,402,403,409,412,418,431,435,453,461,511],recog:12,recoginz:3,recogn:[3,12,77,180,226,227,271,318,387,416,443,458,495,497,504,505,518],recomend:6,recommed:318,recommend:[7,12,15,206,207,238,307,345,377,418,426,440,441,446,459,460,463,465,466,506,516,519],recompil:[1,3,9,12,208,321],recomput:[112,140,182,236,323,415,509],reconstruct:[3,230,466],record:[208,230,323],recov:[229,238,271],recreat:359,rectangl:[41,225,380],rectangular:[7,41,64,180,225,246,380,497,499,501],rectilinear:[130,177,204],rector:53,recurs:[41,225,399,484],recust:41,recv:494,red:[2,206,207,228,300],redefin:[3,499,505,524],redirect:12,redo:12,reduc:[1,2,3,6,12,16,17,18,26,41,65,75,96,120,121,123,124,125,126],reduct:[17,18,128,130,177,269,307,377],redund:419,ree:471,reed:[269,307],rees:[7,9,13],ref:[344,345,385],refactor:6,refer:[2,3,6,7,8,9,11,12,14,15,28,65,71,75,85,91,94,95,112,113,114,124,126,128,131,156,157,158,171,178,202,203,204,205,210,216,218,219,220,222,223,228,229,231,232,238,245,269,271,272,276,298,300,302,303,305,306,307,317,321,323,342,349,354,360,361,372,377,378,385,389,394,401,415,422,429,443,445,446,460,473,474,480,482,492,493,495,499,502,505,506,507,510,511,515],referenc:[3,6,12,65,71,75,125,131,203,204,210,220,246,306,349,378,409,425,452,460,495,515,524],reflect:[2,3,6,75,130,152,177,198,206,210,226,227,232,260,269,297,299,317,352,354],refman:9,reformat:7,refresh:216,reg:500,regard:[6,61,268,321,322,327,455,459],regardless:[14,75,178,181,202,222,231,254,271,273,274,275,277,278,279,304,317,328,335,393,494,500,507],regim:[6,343,350,410,506],region:[0,2,3,6,7],region_spher:8,region_styl:356,regist:[8,127,154,330],regoin:6,regress:524,regspher:178,regstrip:358,regul:6,regular:[1,3,41,64,96,176,180,203,206,217,225,246,306,347,378,410,429,494,497,499,501],reigon:524,reinder:15,reinhardt:[344,345],reject:[178,228,458,512],rel:[1,6,26,35,41,61,75,100,113,134,142,152,156,160,161,163,178,187,207,210,217,225,231,232,235,238,246,252,255,267,268,294,298,303,312,314,315,318,323,331,335,337,342,343,347,354,358,377,378,386,418,422,423,440,441,443,460,488,498,506,511,515,518,525],relat:[1,6,8,9,10,12],relationship:[6,241,308,360,377,466,488,518,524],relax:[2,3,4,6,7,210],releas:[0,5,7,8,13,226],relect:[3,448],reles:42,relev:[2,6,12,41,82,85,122,140,178,182,207,211,212,215,216,217,218,219,220,221,222,223,225,226,227,231,232,236,238,239,243,245,246,247,250,251,257,258,259,261,262,263,264,265,267,268,270,280,281,282,283,284,285,286,287,288,289,290,293,297,301,302,303,305,306,311,313,314,315,319,321,328,333,335,336,337,342,343,346,347,348,349,350,351,352,353,354,355,357,358,377,382,386,396,397,401,407,409,410,412,413,415,418,421,422,423,424,425,430,432,433,434,436,437,438,440,441,448,449,450,451,455,460,468,475,478,479,487,488,489,494,510,525],reli:[3,12,309,418,459,489,497,507],reloc:12,reltol:318,remain:[7,12,32,36,41,50,55,61,75,95,114,158,159,160,161,165,166,167,168,170,181,191,197,198,199,203,211,212,217,219,220,229,231,254,255,262,271,272,277,278,279,291,292,294,296,301,302,326,335,338,339,340,346,347,358,360,368,371,387,399,418,426,439,446,448,476,492,497,498,502,507,509,511,515,516,518,519,524,525],remaina:399,remaind:[9,178,203,232,303,335,348,482,497],remap:[3,6,12,61,63,75,161,178,202,231,252,268,294,377,497,498,499],remedi:[6,518],rememb:[2,519],remot:519,remov:[2,3,6,8,13,54,75,76,81,100,117,125,127,152,156,157,158,159,160,161,165,166,167,168,170,171,178,181,182,204,210,219,226,243,254,255,260,263,267,269,271,277,278,279,291,292,294,296,302,308,317,318,319,321,335,338,339,340,342,358,377,388,412,441,446,497,500,508,509,519,524,525],remove_bia:8,remove_bias_al:8,remove_molecul:216,remove_sourc:216,remove_speci:216,ren:177,renam:[12,359,508,519],render:[12,13,203,206,207],rendon:[271,272],reneighbor:[3,8,12,39,59,75,225,246,335,348,358,413,514,515],renssela:302,renumb:75,reorder:[3,12,39,494],rep:512,repeat:[2,6,206,207,228,229,246,318,327,380,399,480,482,484,492,511],repeatedli:2,repel:252,repes:203,replac:[2,3,6,11,12,41,65,97,98,128,155,156,157,158,159,160,161,164,165,166,167,168,170,171,203,204,206,207,208,219,220,222,223,225,228,232,254,276,305,306,312,314,353,393,395,409,423,433,450,451,478,498,499,504,505,515,524,525,527,529],replic:[2,3,7,380,494,497],replica:[0,2,3,4],replica_fil:12,report:[0,1],repositori:[7,9,12,427,457,458,459],reprens:347,repres:[1,3,6,8,9,12,14,40,41,42,61,70,74,75,98,124,127,129,190,199,203,204,206,219,220,221,222,223,229,235,242,247,249,254,257,271,300,302,304,312,317,318,319,323,331,332,347,349,356,378,388,394,399,422,429,439,440,441,443,444,445,453,456,458,459,483,484,492,494,497,507,509,512,518,524,527],represent:[3,6,8,9,59,61,146,180,203,247,248,300,347,399,418,422,446,460,497,500,518],reprocess:502,reproduc:[3,15,271,353,409,416,423],repul:443,repuls:[6,7,35,40,45,46,119,252,308,352,353,356,395,399,407,409,413,418,420,423,425,439,443,447,466,475,482,485,488,489,507],reqir:[308,310],request:[3,6,8,12,41,113,181,199,203,251,257,315,322,335,337,375,377,448,458,459,492,502,507,511,516,519,524,525,527],requir:[1,2,3,4,6,7,8,9,11],rerun:[2,3,7,76,81,100,117,127,152,203,206,448,498],rescal:[2,3,6,155,159,160,161,165,166,167,168,170,210,217,220,222,223,238,246,248,250,254,255,267,271,276,294,302,304,312,317,335,338,339],research:[5,7,88,89,240,257,261,322,446,492,511],resembl:[312,519],resepct:6,reserv:[12,251,518],reservoir:[99,238,246,250,254,347],reset:[2,3,6,8,11,12,63,69,75,78,79,86,87,97,98,103,113,114,116,173,182,210,211,212,229,231],reset_atomic_reference_posit:216,reset_dt:8,reset_target:8,reset_tim:216,reset_timestep:[2,6,99,498,502],resid:13,residu:251,residue1:389,resist:[6,251],resolut:[221,466,478,479],resolv:[229,300,335,441,519],resort:3,resourc:[7,394,416],respa:[3,15,213,214,224,233,236,237,249,251,252,266,271,298,309,316,320,323,331,332,333,334,351,352,356,391,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,505,506,516,517,524],respecifi:446,respect:[1,6,9,13,14,16,19,20,22,23,24,25,26,27,28,29,30,31,34,37,42,43,45,46,47,48,49,51,53,54,56,61,74,75,95,97,106,107,123,130,134,154,155,160,163,165,172,176,177,184,185,187,188,189,190,192,193,195,196,199,204,206,207,213,222,224,227,228,229,231,238,239,245,249,252,254,255,257,271,273,274,275,276,277,278,279,280,281,287,289,291,292,294,296,308,309,310,317,319,321,323,331,334,347,352,355,361,363,364,366,367,370,372,375,377,378,383,386,387,392,393,394,395,397,399,400,401,402,403,404,405,407,408,409,412,413,416,417,419,420,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,443,444,446,448,449,452,453,455,459,460,461,465,466,467,468,477,478,480,481,482,483,485,487,488,489,494,498,507,510,516,518,524,526,527,529],respon:9,respond:[6,7,161,231,418,455],respons:[6,7,269,343,350],resquar:[2,3,6,7,9,422],rest:[6,8,12,38,58,200,306,310,316,373,399,441,443,490,514,515,518],restart1:300,restart2:300,restart2data:[0,12],restart:[0,1,2,3],restartfil:[12,13],restor:[3,8,62,63,113,178,211,212,266,306,323,331,332,337,359,514,515],restore_bia:8,restore_bias_al:8,restrain:[2,3,28,210,217,246,269],restraint:[9,230,269,316,334,430],restratin:316,restrict:[1,2,3,6,8,9,12],result:[1,2,3,6,7,9,10,11,12,13,14,15,17,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,41,43,45,46,47,48,49,51,53,54,56,65,66,69,70,75,79,86,95,98,99,103,113,114,116,121,123,125,126,127,128,130,131,153,155,158,161,165,172,173,175,177,178,181,184,185,187,188,189,190,192,193,195,196,199,202,203,204,206,207,210,213,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,235,238,239,241,245,246,247,249,254,255,257,261,269,271,273,274,275,276,277,278,279,280,281,289,291,292,294,295,296,299,300,308,309,310,314,315,317,318,320,321,335,343,344,345,347,348,349,352,353,355,357,360,361,363,364,366,367,370,372,377,378,388,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,418,419,421,422,423,424,425,426,431,432,433,434,435,436,437,438,439,440,441,443,444,446,448,449,450,451,452,453,455,459,460,461,468,477,478,479,480,481,482,483,485,487,488,489,492,494,497,499,500,502,506,507,508,509,511,523,524,525],resum:524,retain:[2,226,227,395,399,446,494],retart:[32,50,191,368],retir:[3,458],retreiv:8,retriev:[6,8,244,444,445,524],reus:[3,509],rev:[6,13,66,74,100,117,121,152,153,166,217,248,254,256,269,271,272,276,294,299,309,312,317,323,335,339,342,344,345,350,385,399,407,408,409,412,416,417,418,422,423,428,433,440,441,442,443,445,450,451,456,460,467,477,480,481,482,485,492],revers:[2,6,8,95,189,228,252,271,289,297,298,308,327,343,344,350,388,439,506,518],review:[152,308,323,342,446,457,467,492,511,518,519],rewind:376,rewrap:203,rewrit:[5,12],rewritten:18,rezwanur:455,rfac0:[152,467],rfactor:335,rfile:317,rg0:333,rgb:207,rh3:177,rh4:177,rhaphson:3,rheolog:6,rhi:[450,451,478,479],rho0:[443,463,465,473,474],rho0_meam:443,rho:[2,3,40],rho_0:[473,474],rho_alpha_beta:416,rho_bkgd:443,rho_colloid:352,rho_e:347,rho_fin:346,rho_i:[444,445],rho_initi:346,rho_ref_meam:443,rho_wal:352,rhodo:[9,10],rhodopsin:[1,10,15],rhohi:303,rholo:303,rhosum:[2,110,469,470,471],rhot:238,rhs:318,ribier:385,richard:9,richardson:317,richi:[9,18],rick:[308,309,408,466],rick_and_stuart:309,ridg:[9,18],right:[3,6,11,12,41,74,154,178,196,198,202,204,225,228,252,257,268,297,298,318,360,380,409,497,500,507,519,524],rightmost:[41,225],rigid:[2,3,4],rigidid:129,rigidifi:317,rii:[97,98],rij:[100,117,226,227,298,413,414,450,451,475],rin:[425,436,437],ring:[2,3,6,127,184,300,302],rino:[77,485],rinv:377,rirj:[353,423],risi:[152,467],risk:[8,316,506],rix:[97,98],rjk:[226,227],rjone:[7,9,13],rk4:318,rkf45:318,rlo:[450,451,478,479],rmask:[3,524],rmass:[3,306],rmax:[75,179,226],rmdir:508,rmin0:[152,467],rmin:[75,179,227,433],rms:[318,377,378],rmsd:346,rnemd:6,robert:9,robin:207,robust:[384,385,386,459],rock:443,rockett:456,rod:317,rodata:12,rodnei:312,roi:7,role:[6,342],roll:12,ronchetti:117,room:[59,61],root:[11,95,97,98,205,342,346,416,504],rosati:39,rose:443,ross:443,rosski:300,rosybrown:207,rot:[6,99,300,316,342,525],rotat:[2,3,4,6,7,9,40,65,90,91,92,93,104,142,152,156,157,158],rotate:327,rotation:117,rotaton:500,rough:[6,178,206,357],roughli:[7,10,12,41,161,206,221,246,254,255,263,270,271,285,304,317,335,338,339,342,378,388,393,462,464,499,506],round:[1,3,12,19,20,22,23,24,25,26,27,28,29,30,31,34,37,39,40,42,43,45,46,47,48,49,51,53,54,56,75,123,155,165,184,185,187,188,189,190,192,193,195,196,199,207,213,224,231,239,245,249,254,271,273,274,275,276,277,278,279,280,281,289,291,292,294,296,309,310,317,320,321,355,361,363,364,366,367,370,372,378,391,394,395,397,400,401,402,403,404,405,407,408,409,412,413,416,417,419,421,422,423,424,425,429,431,432,433,434,435,436,437,438,439,440,444,449,450,451,452,453,455,459,460,461,468,477,478,480,481,482,483,485,487,488,489,499,500,506,523,524],rous:247,rout:[95,425,439],routin:[5,6,8,11,14,15,37,39,56,96,182,257,446,457,478,479,510],roux:[6,235,255,483,518],row:[6,68,69,71,73,79,84,86,98,102,103,114,116,119,125,126,127,129,131,158,166,173,175,176,177,219,220,222,223,260,317,347,349,357,418],royalblu:207,rozero:443,rperp:[268,327],rpi:302,rpm:12,rrespa:[1,3,5,7,8,15,211,212,268,271,389,394,395,396,397,398,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,447,449,450,451,453,455,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,506],rspace:3,rsq:[450,451,478,479,486],rsurfac:347,ru3:177,ru4:177,rub:19,rubia:[444,445],rudd:[448,478,479],rudra:[7,9],rudranarayan:[7,302],ruiz:217,rule:0,run1:[6,392,524],run2:[6,374,376,392,524],run3:[6,392,524],run4:[6,392,524],run5:[6,392,524],run6:[6,392,524],run7:[6,392,497,498,502,524],run8:[6,392,524],run:[0,1,2,3,4],run_styl:[2,3,7,8,9,12,15,17,271,272,355,386,389,391,393,394,395,396,397,398,399,400,401,402,403,404,405,407,408,409,410,412,413,415,416,417,418,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,440,441,442,443,444,445,446,447,449,450,451,453,455,457,458,459,460,461,466,467,468,469,470,471,472,473,474,475,477,478,479,480,481,482,484,485,487,488,489,490,491,492,494,505],rung:318,runloop:376,runtim:[12,16,206,393],russia:9,rutherford:347,rutuparna:[480,482],rxn:[318,479],ryan:9,ryckaert:[321,370],rycroft:176,rydberg:446,s00:455,s0st:6,s2050:1,s2629:416,s319:216,s_fact:324,s_i:[6,418],s_ij:6,sack:7,saddl:[270,388],saddlebrown:207,sadigh:[217,416,444,445],saed:319,saed_vtk:130,safe:[12,206,235,255,393,519],safe_zone:3,safest:[3,335],safeti:324,safezon:459,safran:488,sagui:[378,412],sai:[1,3,12,13,207,458,459,495,519],said:386,sakai:481,sall:[9,466],salmon:207,salt:[410,421,443,497],salter:466,same:[1,2,3,4,6,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,30,31,32,34,37,39,40,41,43,44,45,46,47,48,49,50,51,53,54,56,59,61,64,65,68,73,75,76,81,84,87,90,92,93,95,96,97,98,99,100,102,104,107,113,114,115,117,119,121,123,124,126,127,128,152,153,154,155,156,157,158,159,160,161,164,165,166,167,168,170,171,172,174,176,178,179,180,181,182,184,185,186,187,188,189,190,191,192,193,195,196,199,201,202,203,204,205,206,207,210,211,212,213,216,217,219,222,223,224,225,226,227,228,229,231,232,236,237,238,239,245,246,247,248,249,250,251,252,253,254,255,256,257,260,268,271,273,274,275,276,277,278,279,280,281,289,291,292,294,295,296,298,299,300,302,303,304,306,307,308,309,310,312,313,314,315,316,317,320,321,323,328,331,334,335,336,337,338,339,340,341,342,343,344,345,346,347,349,350,351,353,354,355,356,358,359,360,361,362,363,364,366,367,370,372,377,378,380,381,382,383,387,388,389,390,391,392,393,394,395,397,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,415,416,417,418,419,421,422,423,424,425,426,427,430,431,432,433,434,435,436,437,438,439,440,441,443,444,447,448,449,452,453,455,456,459,460,4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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","angle_style zero command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","bond_write command","bond_style zero command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral command","compute dihedral/local command","compute dilatation/atom command","compute dipole/chunk command","compute displace/atom command","compute dpd command","compute dpd/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso/e/atom command","compute meso/rho/atom command","compute meso/t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute rigid/local command","compute saed command","compute slice command","compute smd/contact/radius command","compute smd/damage command","compute smd/hourglass/error command","compute smd/internal/energy command","compute smd/plastic/strain command","compute smd/plastic/strain/rate command","compute smd/rho command","compute smd/tlsph/defgrad command","compute smd/tlsph/dt command","compute smd/tlsph/num/neighs command","compute smd/tlsph/shape command","compute smd/tlsph/strain command","compute smd/tlsph/strain/rate command","compute smd/tlsph/stress command","compute smd/triangle/mesh/vertices","compute smd/ulsph/num/neighs command","compute smd/ulsph/strain command","compute smd/ulsph/strain/rate command","compute smd/ulsph/stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dihedral_style table command","dihedral_style zero command","dimension command","displace_atoms command","dump command","dump custom/vtk command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix ehex command","fix enforce2d command","fix eos/cv command","fix eos/table command","fix eos/table/rx command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix manifoldforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/manifold/rattle command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/manifold/rattle command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix rx command","fix saed/vtk command","fix setforce command","fix shake command","fix shardlow command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/chunk command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","improper_style zero command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","Description","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style table/rx command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","pair_style zero command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","Tutorial for Thermalized Drude oscillators in LAMMPS","LAMMPS GitHub tutorial","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_coeff command","write_data command","write_dump command","write_restart command"],titleterms:{"break":226,"default":[36,39,40,55,59,60,61,63,64,74,75,95,96,100,112,113,115,117,118,119,126,130,134,135,152,158,166,167,171,177,178,181,183,198,201,202,203,204,206,207,208,209,211,212,213,215,216,217,219,223,226,227,229,230,231,232,236,243,246,247,252,254,255,256,257,258,260,266,269,271,272,276,294,295,299,300,303,304,305,306,307,309,312,314,315,317,319,335,337,342,343,344,345,348,350,352,354,358,371,375,377,378,380,381,384,385,387,389,390,391,393,396,399,401,418,440,441,446,448,458,459,475,476,492,493,494,497,498,500,502,504,505,506,509,511,513,514,515,516,517,523,525,527,528],"function":524,"long":[221,400,402,403,404,405,409,411,412,431,435,439,453,461,483],"new":8,"static":12,acceler:1,account:519,ackland:66,acknowledg:7,adapt:[211,212],addforc:213,adding:519,addition:[12,13,519],addtorqu:214,adiabat:6,adjust_dt:324,adp:394,after:519,airebo:395,alloi:416,amber2lmp:13,amber:6,angl:[8,67,68],angle_coeff:21,angle_styl:[2,19,20,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:69,append:215,arrai:6,aspher:[6,90,156,273,277,281,282,291],asphere:9,atc:[9,216],atom:[6,7,8,66,70,74,75,76,77,80,81,82,85,87,89,93,100,105,106,109,110,111,117,121,122,124,152,153,176,215,217,218,306,524],atom_modifi:39,atom_styl:40,attract:5,aveforc:224,awpmd:[9,396],axel:519,balanc:[41,225],barostat:6,basal:70,bcc:298,beck:397,berendsen:[304,338],between:6,binary2txt:13,bodi:[6,8,42,71,157,274,278,283,292,398],body:9,bond:[8,13,72,73,226,227,228,313],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56,58],bond_writ:57,bop:399,born:[400,411],boundari:[7,59],box:[6,60,229],branch:519,brownian:401,buck:[402,403,411,442],bug:3,build:[11,12],calcul:6,call:12,categori:2,centro:74,ch2lmp:13,chain:13,chang:519,change_box:61,charmm:[6,19,184,404,439],chunk:[6,69,75,79,86,98,103,114,116,125,158,173,175,219,332],citat:7,class2:[9,20,43,185,361,405],clear:62,cluster:76,cmm:9,cna:77,code:6,coeffici:6,colloid:[9,352,407,488],colvar:[13,230],colvars:9,com:[78,79,159],comb3:408,comb:[309,408],come:5,comm_modifi:63,comm_styl:64,command:[2,6,8,12,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,524],compute_modifi:112,condit:7,conduct:[6,343],constant:[6,524],constraint:7,contact:[80,132],coord:81,core:6,coreshell:9,correl:[220,221],cosin:[22,23,24,25,26,27,187],cossq:363,coul:[400,402,403,404,405,409,410,411,424,431,435,439,453,461],coupl:6,creat:227,create_atom:178,create_bond:179,create_box:180,createatom:13,creation:7,csld:339,csvr:339,cubic:433,custom:[8,203,204],cut:[49,396,402,405,409,412,418,421,431,432,439,447,453,483],cvff:364,damag:[82,133],data2xmovi:13,data:6,databas:13,deby:[409,431],defgrad:139,deform:[161,162,231],delete_atom:181,delete_bond:182,delta:23,deposit:232,descript:[19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,509,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],diagnost:7,diel:410,dielectr:183,diffraction:9,diffus:6,dihedr:[8,83,84],dihedral_coeff:186,dihedral_styl:[2,184,185,187,188,189,190,191,192,193,194,195,196,197,198,199,200],dilat:85,dimens:201,dipol:[6,28,86,412],dipole:9,direct:235,directori:4,discuss:6,disp:6,displac:[87,94],displace_atom:202,distanc:365,distribut:[7,12],document:0,dpd:[9,88,89,413,414],drag:233,dreid:425,dreiding:6,drude:[6,9,163,234,235,255,518],dsf:[409,431],dsmc:415,dump:[6,8,203,204,205,206,208],dump_modifi:207,dynam:308,eam:[13,416],echo:209,edip:417,eff:[9,13,106,107,162,164,169,256,272,284,295,341,418],efield:237,ehex:238,eim:419,elastic:6,emac:13,energi:[135,414],enforce2d:239,ensembl:7,erot:[90,91,92,93],error:[3,134],evapor:243,event:94,exampl:[4,6,11,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,330,331,332,333,334,335,336,337,338,339,340,341,342,343,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,490,491,492,493,494,495,496,497,498,499,500,501,502,503,504,505,506,507,508,510,511,512,513,514,515,516,517,520,521,522,523,524,525,526,527,528,529],exp6:420,exp:[26,187],expand:[46,434],extend:[8,11],extern:244,fcc:298,fdt:414,featur:[7,8,519,524],fene:[45,46],fep:[9,13,95,212],field:[6,7],file:6,finit:6,fire:308,fix:[2,6,8,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,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\ No newline at end of file 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7,40,63,96,163],comand:61,combiant:106,combin:[2,3,18,32,56,58,59,63,68,71,81,82,103,105,106,110,113,114,115,129,130,149,155,156,158,159,161],come:[0,2,13,62,68,77,78,139,155,156,158,159,163],comit:163,comm:[0,3,30,92,109,139],comm_modifi:[2,97,103,109,113,118],comm_styl:[19,60],comm_world:3,command:[0,1],comment:[3,46,65,74,79,92,93,111,112,114,115,121,134,141,142,143,148,149,155,156,157,158,159,163],commit:163,commmand:2,common:[0,1,2,3,4,30,62,71,81,82,118,120,155,156,158],commonli:[2,9,37,38,58,89,119,124,149,156,158],commun:[1,2,3,4,19,58,60,62,67,68,79,110],comp:[75,92,113,139,146,153,157],compar:[1,2,4,41,44,57,91,92,134,148],comparison:0,compart:90,compass:[6,20,47,57,82,102],compat:[3,19,50,60,63,80,137,139],compens:[2,113],compil:[4,58,137],complain:3,complement:134,complementari:[105,122],complet:[2,3,19,60,71,92,114],complex:[2,3,9,36,38,42,45,67,81,92,113,137],complic:[2,40],compon:[2,29,30,33,34,35,36,37,38,39,40,42,43,58,61,62,63,67,68,69,71,75,81,91,92,109,113,118,131,132,148,149],componenet:2,componennt:40,composit:[2,67,111],compound:[104,113,114,159],compress:[2,58,69,72],compris:[81,115,146],compton:[41,44],comput:[0,1],computation:[2,79,97],compute_modifi:[61,62,68,69],compute_sa:41,compute_xrd:44,concav:81,concentr:[65,74,111,115,142],concept:2,conceptu:[2,62,92,105,134],concern:[2,30,32,66],concis:3,concurr:4,conden:[79,156,158],condens:[2,79,94,107,111,122,159],condit:[2,39,41,43,44,58,59,67,69,70,72,75,76,79,110,113,119],conducit:2,conduct:0,confer:[4,137],configur:[1,2,4,58,62,71,91,92,94,97,112,134,137,155,156,158,159,163],conflict:[139,163],conform:[2,61,62,73,88,92,113],confus:159,conjuct:109,conjug:113,conjunct:[2,32,45,67,92,98,99,105,109,113,120,122,139,144,147],connect:[2,32,61,75,90,92,106,118,154,158],conner:94,connor:94,consecut:[3,45,105,122,126],consequ:[1,2,79,121],conserv:[13,61,66,67,68,74,75,92,108,109,110,118,128,148],consid:[2,29,32,40,60,61,79,113,146,148,154],consider:2,consist:[2,3,39,40,45,51,66,68,69,72,73,74,90,92,94,97,103,105,113,117,131,132,134,137,139,141,142,146,148],consistent_fe_initi:59,constant:0,constantli:63,constitu:[2,80,81,103,146],constrain:[2,63,66,75,76,91,113],constraint:[19,39,43,60,63,75,76,80,91,132],construct:[2,28,29,30,36,38,41,42,44,62,68,73,74,81,108,137,139,154,155],constructor:3,consult:4,consum:1,contact:[0,106,112,114,117,118,146],contain:[0,1,2,3,19,32,35,41,42,44,45,46,57,58,59,60,65,67,70,72,74,79,81,92,93,94,97,104,105,108,111,112,113,115,134,137,141,142,143,145,149,155,156,157,158,159,163],context:[2,4,161],contibut:29,contin:4,continu:[0,2,19,60,61,62,63,66,68,69,72,77,78,79,81,97,109,124,127,146,157],continuum:[2,59,79],contour_integr:59,contract:[62,68],contrain:75,contrast:[1,2,161],contrib:79,contribut:[2,29,32,33,34,35,39,42,43,62,67,75,91,92,109,111,113,131,132,137,139,148,163],control:[2,3,4,11,13,19,32,35,42,48,58,59,60,62,68,69,74,79,113,117,137,155,158],control_typ:59,convect:35,conveni:[2,13,149,163],convent:[13,50,55,57,73,111,113],converg:[2,19,58,60,61,62,69,72,73,75,91,92,104,105,122,148],convers:[42,58,105,106,107,113,122,126,130,144],convert:[2,5,6,8,12,16,17,18,35,45,47,58,82,83,87,88,92,93,111,137,156,158,162],convex:81,cool:63,coord:[2,3,36,38,40,70,80,92],coordb:148,coordbb:148,coordiat:91,coordin:[1,2,3,19,32,33,34,40,42,45,58,60,61,62,63,68,70,75,76,78,79,91,92,93,94,96,112,148],coords:148,copi:[0,3,58,79,92,163],copper:162,coprocessor:[1,4],core:[0,1],coreshel:2,coreshell:[2,99,105,107],cornel:[2,46],corner:[2,58,81,163],corpor:4,corr:104,correct:[2,3,32,46,58,63,68,72,80,81,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,111,112,113,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],correction_max_iter:59,correctli:[3,68,75,81,92,107,132,137,163],correl:[2,35,36,42,66,71],correpond:65,correspond:[1,2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,29,32,39,40,41,42,44,46,47,48,49,50,51,52,53,54,55,56,58,62,63,65,67,68,69,70,71,74,75,80,81,82,83,84,86,87,88,89,92,93,94,95,98,99,100,101,102,103,104,105,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,139,140,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],correspondingli:[131,132],cosin:2,cosineshift:11,cost:[1,2,3,19,41,43,44,58,60,68,74,79,105,122,126,137,139,155],costheta0:[155,156,158,159],costheta:145,costli:[3,4],coul:[2,4,18,21,22,32,46,91],could:[2,3,19,32,34,39,58,60,72,79,80,81,91,94,116,120],coulomb:[2,43,91,98,99,100,101,102,104,105,106,107,108,113,118,119,122,126,130,133,139,144,147,148,158,159,161],coulommb:2,count:[1,2,3,19,35,46,60,68,75,81,91,92,116,120,139],counterbal:63,counterbalanc:13,counterclockwis:46,coupl:0,couple:[2,3],cours:[4,66,73,80,131,150],cov:148,coval:[2,13,113,134,148],cover:[2,59,67,113],cpp:[1,2,3,32,75],cpu:[1,4],cpuinfo:4,cr2:44,cr3:44,creat:[0,1,2,3,19,35,39,41,45,58,59,60,61,62,65,68,69,70,71,73,79,92,94,97,104,111,112,130,139,140,141,142,145,148,155,156,157,158,159,163],create_atom:[2,19,35],create_box:[2,19,35,45,62,68,154],create_elementset:59,create_faceset:59,create_nodeset:59,createatom:0,creation:45,criteria:[58,61,91],criterion:[19,45,60,61,91,92,104,113,118,148],critic:[2,24,25,79,91],cross:[4,33,40,58,92,101,109,111,119,120,122,124,126,145,147,156,158,162],crossov:1,crozier:0,crucial:72,crystal:[2,4,29,30,38,70,78],crystallin:[2,157],crystallogr:[41,44],crystallographi:[41,44],cs1:44,cs_chunk:2,csanyi:[42,149],cscl:134,csequ:2,csh:[3,4],cshrc:3,csic:[112,155,156,158,159],csinfo:2,csisi:[112,155,156,158,159],cst:111,cstherm:2,csvr:2,ctcm:[93,111],ctype:3,cu1:44,cu2:44,cu3au:134,cube:[2,81],cubes:[19,60],cubic:[38,67,70,111],cuda:1,cuh:97,cummul:[2,61,120],cumul:[2,68,69,92],current:[0,1,2,3,4,19,30,32,43,58,59,60,61,62,63,68,73,74,75,76,79,80,90,91,92,97,104,108,111,113,114,118,121,131,132,134,135,136,139,145,150,156,158,163],curv:[2,45],curvatur:[117,146,162],custom:[0,2,3,33,34,35,43,58,61,62,68,69,72,91,94,116,120],cut:[1,2,4,19],cuthi:70,cutinn:[131,132],cutlo:70,cutmax:145,cutoff1:[102,108,122,126,130,133,144,147],cutoff2:[98,99,100,102,107,108,122,126,130,133,144,147],cutoff:[2,4,21,22,28,29,30,32,36,38,42,61,65,70,72,80,81,91,93,94,95,96,97,98,99,100,101,102,103,105,106,107,108,109,110,111,112,113,114,115,116,117,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],cutoffa:112,cutoffc:112,cuu3:111,cval:44,cvff:4,cwiggl:80,cyan:58,cycl:[68,69],cyclic:46,cylind:[58,81,90],cylinder_d:90,cylindr:2,cyrot:97,d3q15:67,d3q19:67,d_e:79,daan:78,damp:[2,68,69,72,91,92,98,99,101,105,108,113,118,122,130,144,147],dampflag:118,danger:109,darden:108,darken:58,dash:118,dat:[2,35,59],data2xmovi:0,data:1,databas:0,date:[0,2],datum:2,davenport:133,davi:80,david:[156,158],daw:[111,145],dcd:[2,58,71],deactiv:130,debug:[2,3,41,44,45,71,139],decai:[36,105,162],decid:[2,4,163],decod:58,decompos:[32,149],decomposit:[59,71],decoupl:2,decreas:[4,61,63],dedic:4,defect:[2,29,137],defin:[2,3,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,64,65,67,68,69,70,71,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,94,95,96,98,99,100,101,102,103,105,106,108,109,110,112,113,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,137,138,139,140,141,142,143,144,145,146,147,149,150,151,152,153,154,155,156,157,158,159,160,161,162],definit:[2,42,64,69,80,97,103,110,113,145,149],deform:[2,43,62,68,131,132],deg2theta:44,degre:[2,5,6,8,12,13,16,17,18,36,38,39,44,45,46,47,49,50,55,56,58,61,68,69,71,73,75,78,82,83,87,88,89,91,108,111,120],delai:2,delet:[28,61,68,139,154,163],delete_atom:45,delete_bond:[20,21,22,23,24,25,26,27,28],delete_el:59,delimit:74,dellago:[2,63],deloc:[113,148],delr:134,delta_1:97,delta_3:97,delta_7:97,delta_ij:[134,145],delta_pi:97,delta_r:145,delta_sigma:97,deltah_f:65,demo:3,demonstr:[72,134],dendrim:120,dendtrit:90,denniston:67,denot:[41,63,105,119],dens:[61,74,113],densiti:[2,19,42,45,59,60,67,79,80,93,94,97,111,134,135,136,141,142,145,146,148,151,152,153],dent:90,depart:0,departur:72,depend:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,29,36,39,40,42,45,46,47,48,49,50,51,52,53,54,55,57,58,60,62,65,67,68,69,70,74,75,77,79,80,81,82,83,84,86,87,88,89,91,93,94,95,96,97,98,99,100,101,102,103,104,105,106,108,109,111,112,113,114,115,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,137,138,140,141,142,143,144,145,146,147,148,149,150,155,156,157,158,159,160,161,162],dependend:2,deposit:[68,75],depth:[26,58,79,115,117,146],der:[32,103,104,130,161],deriv:[2,32,42,62,63,68,69,70,77,78,79,80,81,94,97,103,108,113,114,119,124,128,129,134,137,161],derjagin:161,derlet:70,descib:58,describ:[0,1,2,3,4,19,29,30,41,42,43,44,45,51,54,60,61,62,65,66,67,68,69,70,71,72,74,77,78,80,91,92,94,96,98,99,101,102,103,104,105,108,111,113,114,115,117,118,119,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,141,142,145,146,147,148,149,150,154,155,156,157,158,159,160,161,162,163],descript:[2,3],descriptor:42,design:[0,2,3,41,44,59,61,68,70,79,95,96,101,105,107,113,130,131,132,135,136,145],desir:[2,3,4,35,39,43,45,62,66,68,75,91,92,109,111,120,131,132,155,156,158],desktop:[2,58],destabil:97,destre:88,destroi:3,detail:[1,2,3,4,19,34,35,39,40,42,43,45,57,58,59,60,61,62,63,66,67,68,69,72,75,78,79,90,91,93,94,96,97,100,101,102,103,104,105,108,109,113,114,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,133,134,138,139,141,142,146,148,149,150,160,161,163],detect:[36,92,104,120,121],determin:[1,2,4,26,32,39,40,41,43,44,45,58,60,62,65,68,70,71,72,73,74,80,81,94,100,104,108,111,115,116,118,126,134,137,139,142,146,148,154,161],devan:147,devanathan:158,develop:[0,2,3,4,69,72,94,97,113,136,137,148,159],deviat:[69,70,116],devic:1,devin:104,devis:136,dfactor:58,dft:137,dhug:72,dhugoniot:72,dia:134,diag:74,diagnost:[4,61,74],diagon:[2,40,42,43,62,68],diagonalstyl:149,diagram:[19,41,44,57,60,71],diallo:120,diam:58,diamet:[2,45,58,103,117,118,124,146,161],diamond:[113,134],dick:2,did:[91,109,111,118,139,156,158],dielectr:[101,105,106,107,122,126,130,144],diff:[2,4],differ:[1,2,3,4,19,28,29,32,36,42,45,57,58,60,61,62,63,66,67,68,70,71,72,75,76,77,78,79,80,81,82,92,93,94,97,100,101,103,104,109,110,111,113,115,117,118,119,122,123,125,126,133,134,135,136,138,139,140,141,142,143,145,146,147,148,149,150,155,156,158,159,161],differenti:[1,2,13,74,105,145,157],difficult:[62,71,120],difficulti:[36,38,75],diffract:[41,44],diffraction:[41,44],diffus:0,diffuse:2,digit:137,dihedr:[0,4,28,36,38,39,42,43,45,46,47,48,49,50,51,52,53,54,55,56,57,61,73,83,84,85,87,91,94,97,101],dihedral_coeff:[46,47,48,49,50,51,52,53,54,55,56,57],dihedral_cosine_shift_exp:11,dihedral_styl:[0,2,43],dihydrid:113,dij:75,dilat:[62,68,69],dim:[45,134],dimens:[1,2,19,35,40,43,45,58,60,62,67,68,69,72,80,92,139],dimension:[36,39,41,42,44,79,92,145],dimensionless:[37,42,79,149,161],dimer:[2,134],dimstr:[19,60],dintel_offload_noaffinity:4,dipol:0,dipolar:13,dipole:108,dir:[1,3,70,72,145],dirac:42,direc:145,direct:[2,4,13,29,38,41,42,44,45,46,58,67,69,70,72,77,78,79,80,81,91,92,109,110,118,132],directli:[2,3,32,40,42,58,67,74,81,93,94,98,99,100,105,108,111,113,122,126,139,144,147,154],directori:[0,1,2,3,4,77,78,92,93,94,97,104,105,111,112,114,130,134,135,136,137,143,145,148,149,155,156,157,158,159],disabl:[4,79,121],disadvantag:[2,60],disallow:68,discard:[19,60,81],discontinu:[91,128],discourag:134,discret:[2,58,67],discuss:[0,1],disk:[2,36],disloc:[29,137],disord:[29,137],disp:0,dispar:146,disperion:[108,126],dispers:[2,100,108,126,131,139,159],displac:[2,37,62,68,70,118],displai:[3,57,58],disregard:137,dissip:[2,31,64,66,77,78,109,110,118,131,132],dist:[2,35,71,73,154],distanc:[2,5,6,20,21,22,23,24,25,26,27,28,30,33,34,36,37,38,40,41,42,45,47,58,61,62,63,67,68,69,70,72,73,75,76,78,79,80,81,82],distinct:[2,146],distinguish:[2,42,113],distort:93,distrbut:93,distribut:[0,2,3,19,32,42,57,60,66,67,68,93,97,105,111,112,114,134,135,136,139,143,145,146,155,156,157,158,159],distro:145,ditto:162,div:4,diverg:[78,94],divid:[2,4,19,35,39,43,57,60,70,91,92,114,148,159],divis:[2,56,67,97,130],dl_poly:2,dlammps_ffmpeg:58,dlammps_gzip:58,dlammps_jpeg:58,dlammps_memalign:4,dlammps_png:58,dlm:68,dlmp_intel_offload:4,dlopen:2,dlvo:[103,161],dm_lb:67,doc:[0,1,2,3,32,34,37,39,40,43,45,57,58,68,81,90,91,92,93,94,96,104,105,111,112,114,120,134,135,136,139,143,145,149,155,156,158,159,163],docuement:146,doe:[0,1,2,3,19,28,29,32,35,41,44,45,46,57,58,59,60,61,62,63,65,66,67,68,79,80,81,83,84,85,87,88,92,93,94,95,96,97,100,101,102,103,104,105,106,108,109,111,112,113,115,116,117,118,119,121,124,125,127,128,129,131,132,134,135,136,137,139,141,142,145,146,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],doesn:[45,94,104,112,155,156,157,158,159],dof:39,doi:[2,70],domain:[2,19,41,44,58,60,62,67,68,71,79,80,92,139],domin:[1,113],don:[0,4,81,134,148,163],done:[1,2,19,45,56,58,59,60,61,62,65,68,71,75,77,78,91,92,94,100,111,126,132,133,134,139,141,142,154,163],donor:120,dot:43,doti:[97,145],doubl:[1,2,3,4,32,46,81,97,114,119,137],dover:59,down:[2,3,62,113,139,148],download:3,downsid:2,dpd:2,dpdtheta:[31,110],dpdtheta_i:[64,65],dr_ewald:41,drag:[2,35,68,69,76],dragforc:67,drai:[58,72],drain:91,dramat:[61,62,68,139,148],drautz:97,draw:58,drawn:[58,66],drayleigh:72,dreid:2,dreiding:0,drfourth:37,drho:[93,111,141,142],drift:[2,37,63,66],drive:[3,62,68,70,92],driven:[2,51],driver:2,drop:109,drsquar:37,drude:0,dt_collis:67,dt_lb:67,dt_md:67,dtqm:72,dudarev:44,due:[1,2,4,28,29,33,34,37,41,42,43,44,45,58,61,62,66,67,68,69,70,73,77,78,79,80,81,91,92,106,109,110,111,116,117,131,132,139,145,146,147,154,156,158,161,162],duffi:79,dullweb:68,dumbbel:90,dummi:[13,157],dump:[0,1],dump_modifi:[2,58],dunbrack:[2,5,46,101],duplic:[19,60,70],durat:[57,79,118],dure:[2,4,19,32,40,46,59,60,61,62,63,65,66,67,68,69,70,71,72,73,75,76,77,78,79,80,81,91,92,109,130,137,139,140,141,142],dvlo:161,dvx:2,dx_lb:67,dy3:44,dyanam:2,dynam:[0,2,3,4,19,31,37,45,58,59,60,61,64,66,68,69,71,72,73,77,78,79,91,92,109,110,113,131,132,139,153],dynamo:[93,111,134],dyre:127,e28637:13,e_1:97,e_2:97,e_a:74,e_b:114,e_ee:113,e_hbond:120,e_i:[2,97,114],e_j:[2,97],e_k:97,e_ke:113,e_kl:2,e_lj:[94,108],e_n:97,e_ne:113,e_nn:113,e_pr:113,e_rebo:94,e_torsion:94,e_tot:137,e_vol:137,eaa:82,eaat:47,each:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,32,33,34,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,65,66,67,68,69,70,71,74,75,76,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,158,159,160,161,162],eacn:[19,60],eam:[0,93,105],earli:[19,60],earlier:[92,118,134,139],earth:113,easi:[2,3,32,43,80],easier:[4,58],easili:[3,58,92],eat:47,eaxmpl:2,eba:6,ebb13:47,ebb:6,ebt:47,ec_ii:134,ec_ij:134,ec_jj:134,echo:[3,41,44],ecp:113,edg:[2,19,41,44,58,80,81],edge:80,edit:[4,163],edition:4,edu:[3,111,131],eebt:47,eff:0,effect:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,33,34,37,39,43,46,47,48,49,50,51,52,53,54,55,57,58,59,61,62,63,66,68,69,70,71,72,73,75,78,79,80,81,82,83,84,86,87,88,89,91,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,144,146,147,148,150,155,156,157,158,159,160,161,162],effici:[0,1,2,4,39,56,58,62,68,71,75,97,103,105,122,126,137,141,142,146],efficienc:4,efield:[75,91],eggebrecht:[105,148],ehex:2,eigenvalu:71,einstein:[2,78],either:[1,2,3,4,19,29,41,42,43,44,45,58,60,61,62,63,67,68,69,70,74,75,81,91,97,103,111,115,118,131,132,134,137,139,142,145,154,156,158],ejtehadi:[103,117,146],elaps:[80,150],elast:[2,21,22,92,118,157],elastic:0,elba:13,electr:[2,59,114,162],electric:4,electrolyt:161,electron:[2,41,59,79,93,104,108,111,113,114,134,137,145,148,158,159,162],electron_integr:59,electron_temperatur:59,electron_unit:113,electroneg:[2,104,114,148],electroneg_compon:148,electrostat:[2,4,103,108,113,122,130,132,148,161],elem1:[114,134,149],elem2:[114,134,149],elem:148,element1:[93,111,148],element2:[93,111,148],element:[2,33,37,39,42,43,58,59,93,94,97,104,111,112,113,114,134,135,136,137,143,145,148,149,155,156,157,158,159],elementn:[93,111],elementset:59,elif:42,elig:120,elimin:[2,66,75,77,78],elj:108,ellips:2,ellipsoid:[2,45,90,91,117,132,146],els:[58,68,79],elsewher:134,elt:134,emac:0,email:[0,3,114],emb:81,emb_lin_neg:134,embed:[3,13,79,93,111,114,130,134,135,136,145],embt:47,emphas:118,empir:[59,113],empiric:94,emploi:[63,157],empti:121,enabl:[2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,31,32,37,39,40,41,42,44,46,47,48,49,50,51,52,53,54,55,57,61,63,64,65,66,67,68,69,70,71,72,73,74,75,77,78,79,80,81,82,83,84,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,134,135,136,137,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162],enclos:[2,134,148],encod:58,encompass:2,encount:38,encourag:[74,76],end:[1,2,3,4,19,47,58,61,63,66,68,73,74,79,92,109,111,117,133,137,146,149,150],endbondtors:47,energet:[61,94],energi:[0,1,2,5,6,7,8,9,10,11,12,13,14,15,16,17,18,20,21,22,23,24,25,26,27,28,31,32,35,39,43,45,46,47,48,49,50,51,52,53,54,55,56,57,59,60,61,62,63,64,65,66,67,68,69,70,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109],energy_compon:148,enforc:[2,58,61,68,75,122],enforce2d:[2,91],eng:[3,104,136],engineer:[59,77,111],enginer:135,enhanc:[59,63],enlarg:58,enough:[45,60,72,80,81,105],enpub:111,ensembl:[2,32,35,68,71,72,109,148],ensight:2,ensur:[2,42,62,66,68,97,130,155,159],enter:[114,137,159],enthalpi:[74,111],entir:[0,2,3,19,31,39,40,41,43,44,45,60,61,63,66,68,69,70,71,74,76,79,108,126,139],entiti:2,entri:[40,41,65,72,97,112,134,141,142,143,149,155,156,157,158,159],entry1:[141,142],enumuer:2,environ:[1,2,3,4,58,70,93,97,104,112,113,145,156],eos:65,epair:[94,116,120],epp:108,epq:108,eps0:161,eps14:130,epsilon0:158,epsilon:[2,18,21,22,27,28,32,46,80,81,91,96,101,102,103,105,106,107,108,115,117,119,120,121,122,123,124,125,126,127,128,129,130,133,138,144,146,147,155,160,161],epsilon_0:162,epsilon_14:101,epsilon_:146,epsilon_d:106,epsilon_i:[117,139,146],epsilon_i_:146,epsilon_i_a:[117,146],epsilon_i_b:[117,146],epsilon_i_c:[117,146],epsilon_ij:139,epsilon_j:[117,139,146],epsilon_j_:146,epsilon_j_a:[117,146],epsilon_j_b:[117,146],epsilon_j_c:[117,146],epsilon_lj:146,eqp:108,eqq:108,equal:[2,3,19,28,32,35,43,45,58,60,62,66,67,69,70,71,72,73,74,77,78,79,80,91,92,94,104,109,110,116,117,120,131,137,138,145,146,148,149,150,159,162],equat:[2,35,38,39,41,44,57,62,63,64,65,67,68,69,70,71,72,74,75,79,80,90,103,108,109,110,113,114,115,118,131,132,134,139,142,146,151,152,153,162],equation:[70,88],equilibr:[2,35,45,61,62,68,72,77,78,104,105],equilibrium:[1,2,6,8,10,11,12,13,16,17,18,20,23,24,25,26,27,47,48,62,66,67,68,69,72,73,75,78,82,83,87,88,104,134,143,148],equilibrium_start:59,equival:[2,13,62,68,73,94,109,113,148,156,158],equlibrium:2,er3:44,eradiu:113,eras:77,erat:132,erc:105,erfc:[105,122,139],erhart:[111,156,158],eros:134,erose_form:134,erot:2,errata:[156,158],erratum:80,error:[0,1,2,3,11,48,58,62,63,65,68,74,79,80,81,91,105,122,139,146,154,156,158],erta:118,especi:[4,45,60,72,73],essenti:[3,11,48,94,105,122,158],essential:69,essex:13,establish:32,estim:[1,2,19,29,35,43,59,60,74,139],esub:134,eta:[2,67,68,72,112,114,117,145,157,159],eta_dot:68,eta_ij:145,eta_ji:114,etap:68,etap_dot:68,etc:[1,2,3,4,28,33,34,35,40,43,45,58,59,66,68,79,81,91,92,111,112,130,132,137,155,156,158,159],etol:[91,92],etot0:72,etot:[2,43,72],eu2:44,eu3:44,euler:[74,91,92],eulerian:59,europhi:67,evalu:[3,32,35,42,45,46,58,59,66,74,80,91,137,139,141,142,145,148],evanseck:[2,5,46,101],evaul:91,even:[2,4,19,29,56,60,62,63,68,79,80,81,91,92,96,113,114,118,139,146,159],evenli:[19,43,60,67],event:[2,68,79],eventu:2,ever:28,everaer:[103,117,146],everi:[0,1,2,3,4,19,35,58,59,60,61,62,63,67,68,69,70,72,74,75,79,92,109,130,148,163],everyth:163,everywher:124,eviri:113,evolut:[63,67,71],evolv:[67,71],ewald:[2,41,43,91,98,99,100,105,108,113,122,126,144,147],ewald_disp:108,exact:[19,60,61,66,79],exactli:[2,19,35,45,60,66,72,109,111,118,131,139,141,142],examin:[2,61,74],exampl:[0,1],exce:[2,4,19,60,62,68,91],exceed:[19,60,68],excel:113,except:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,33,34,39,43,45,46,47,48,49,50,51,52,53,54,55,57,60,62,68,69,71,75,79,82,83,84,86,87,88,89,92,93,94,95,98,99,100,101,102,103,104,105,107,108,109,111,112,113,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,132,135,140,143,144,146,147,150,155,156,157,158,159,160,161,162],excess:113,exchang:[2,59,63,79,113],excit:113,excite:113,exclud:[2,4,39,40,42,91,118,131,132,139,154],exclus:[1,4,32,46,104,137,139],excurs:68,execut:[1,2,3,58],exempl:148,exemplari:66,exemplifi:113,exert:[2,81],exhaust:59,exhibit:[36,63,68,113],exist:[2,3,29,45,57,58,62,82,83,84,85,87,110,154,163],exit:[3,19,60],expans:[42,56],expect:[1,4,19,60,70,72,134,137,139],expens:[2,70,79],experi:[2,73,92,109,139],experienc:[2,4],explain:[1,2,3,19,30,40,58,60,62,68,70,92,96,111,148,150,163],explan:[2,40,42,70],explic:138,explicit:[2,3,32,74,94,97,101,111,113,121,131,163],explicitli:[2,4,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,45,46,47,48,49,50,51,52,53,54,55,66,68,69,72,75,79,82,83,84,86,87,88,89,93,94,95,98,99,100,101,102,103,104,105,106,108,109,111,112,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,135,137,139,140,141,142,143,144,146,147,150,151,152,153,155,156,157,158,159,160,161,162,163],explictli:4,exploit:71,explor:[41,44],expon:[74,111,115,117,120,130,138,147],exponenti:[32,74,115,145,155,159,162],expos:3,exposit:[59,109],express:[2,42,45,62,70,74,79,97,111,113,124,134,148,149],expressiont:97,extend:[0,2],extens:[2,4,21,22,27,32,35,63,68,69,70,73,77,78,79,80,81,117,134,137,146,149],extent:[1,19,21,60,94],exterior:[2,81],extern:[32,58,62,66,67,68,69,79,91,135,136],extra:[2,3,4,19,22,39,41,43,44,45,60,68,72,91,108,118,134,139],extract:[2,3,18,32,92,105,114,134,149],extract_atom:3,extract_comput:3,extract_fix:3,extract_glob:3,extract_vari:3,extrapol:1,extrem:[1,2,58,62,68,78,113,157],extrema:130,extreme:113,extrins:59,f_1:2,f_a:[156,157,158],f_c:157,f_f:158,f_fix_id:72,f_harm:78,f_i:[13,145],f_id:2,f_ij:145,f_int:77,f_j:13,f_jj:35,f_k:145,f_langevin:79,f_max:72,f_r:[156,157,158],f_sigma:97,f_solid:78,f_ss:2,face:[2,80,81,117,134,146],facil:0,facilit:2,fact:[2,4,78,118,148],factor:[1,2,8,12,16,17,18,19,22,23,32,35,41,42,44,46,54,58,60,62,63,67,68,69,71,73,74,75,80,81,87,94,97,98,99,101,105,106,107,109,110,113,118,121,122,134,137,139,141,142,143,144,147,150,155],fail:[3,62,91,92,107],fairli:[3,139,163],faken:30,fall:2,fals:148,famili:159,familiar:[0,3,163],fan:145,far:[2,60,62,68,70,73,80,83,87,92],farrel:[156,158],fashion:[2,19,45,60,68,69,72,78,79,80,92,131],fast:[2,4,72,74,131,132,137],faster:[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,21,22,23,24,25,26,27,28,37,39,46,47,48,49,50,51,52,53,54,55,60,68,69,75,77,79,82,83,84,86,87,88,89,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,135,140,143,144,146,147,150,155,156,157,158,159,160,161,162],fastest:[1,2,79],fault:29,fava:117,favor:61,fcc:[2,29,30,35,38],fcold:63,fdt:[64,65,74],fdti:32,fe2:44,fe3:44,fe_md_boundari:59,featur:[0,2,3,42,58,61,66,71,81,91,163],fecr:111,feel:[70,81,92,139],fehlberg:74,felling:136,felt:81,fene:[2,4],fennel:[105,122],fep:0,ferguson:[2,46],fermi:[1,158],fermion:113,fernando:133,few:[1,2,3,63,68,75,91,92,94,148],fewer:[1,3,4],feynman:71,ffield:[104,114,148],fflag1:58,fflag2:58,ffmpeg:58,ffplai:58,fft:[1,3,43],fhot:63,ficiti:154,fictiti:[2,71,73,105,122,126,154],field:0,fifth:[2,115,143],figshar:70,figur:[1,4,72,163],fij:108,file0:70,file1:[3,65,70],file2:[3,65],file:[0,1],filenam:[4,19,58,59,60,65,70,74,79,92,93,94,97,105,111,112,114,115,134,135,136,141,142,143,145,148,149,155,156,157,158,159],fill:[45,58,79,97,137,163],filter:59,finchham:[2,107],find:[0,2,3,4,30,32,61,62,65,70,73,91,92,105,122,126,134,141,142,148,163],fine:[4,78,163],finer:[42,45],finger:45,finish:[2,3,19,60],finit:0,finni:111,fire:[91,92],first:[0,1,2,3,4,6,19,21,22,28,29,35,37,38,39,43,44,47,58,60,61,65,66,67,68,70,71,72,75,76,77,78,79,82,91,92,93,94,96,97,98,99,101,104,105,111,113,114,115,118,119,121,122,126,131,132,134,136,137,139,141,142,143,145,148,149,154,155,156,157,158,159,162,163],fischer:[2,5,46,101],fit:[2,73,94,97,134,139,141,142,157,163],five:[30,72,97,135],fix:[0,1],fix_flux:59,fix_heat:63,fix_id:[62,68,69,72],fix_manifoldforc:163,fix_modifi:2,fix_nv:163,fix_rattl:75,fix_shak:75,fixedpoint:[62,68],fixid:[58,59],fji:108,flag:[3,4,33,34,40,41,44,58,61,94,120,121,134,137,154,163],flag_buck:100,flag_coul:[100,108,126],flag_lj:[108,126],flagfld:[131,132],flaghi:[131,132],flaglog:[131,132],flagvf:[131,132],flat:[2,4,79,80],fld:[80,131,132],flexibl:[2,58,113,157],flip:[2,68],fluctuat:[2,32,62,66,67,68,69,70,78,79,88,110],fluid:[2,62],flux:2,flv:58,fly:[19,58,59,75,97,137],fmass:71,fmax:91,fmsec:68,fno:4,fnorm:91,fnve:63,focu:75,foil:[42,70,149],fold:[4,76],follow:[0,1,2,3,4,5,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,35,36,38,42,43,45,46,48,49,50,51,52,53,54,55,56,58,59,60,64,65,66,67,68,69,71,72,73,74,75,77,78,79,83,84,85,86,87,88,89,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163],foo:[3,58,74],foo_species:74,foot:2,forc:[0,1],forcefield:[73,120],forcegroup:67,ford:108,forgiv:68,fork:163,form:[2,28,32,33,34,36,42,43,66,73,74,79,80,81,82,85,88,92,94,97,110,111,113,116,120,121,133,134,136,137,141,142,143,144,145,146,148,149,150,156,157,158,161],formal:[2,35,66,68,71,148],format:[2,19,58,60,65,74,79,92,93,94,97,111,114,115,121,134,136,141,142,147,149,159],formation:65,former:[2,19,60,79,97],formul:[1,2,43,68,73,75,94,97,111,113,117,134],formula:[2,6,28,29,30,32,33,34,35,39,41,43,44,45,47,57,70,76,80,82,84,94,96,97,101,102,103,108,109,111,112,117,118,119,120,121,122,124,125,126,128,129,131,132,134,138,139,140,146,147,150,155,156,157,158,159,160,161],forth:[1,2,3],fortran:[2,3,111,134],forward:[32,92],foster:[97,145],found:[2,30,61,63,67,105,108],four:[2,3,28,42,79,88,92,137],fourier:2,fourth:[2,4,37,73,101,115,143,148],fox:[2,41,46,153],fqq:108,fraction:[1,2,4,19,43,58,61,62,72,74,92,97,115,118,131,132],frame:[42,59,72,117],framer:58,framework:[93,149],frattl:63,free:[2,13,29,32,70,77,78,79,92,113,130,137,140,145,161],freedom:[2,39,61,68,69,71,75,78,91,108],freeli:[0,2,58],freez:2,frenkel:[2,63,78],frequenc:[2,4,71,72,74,109,113,148],frequent:[29,30,36,38,42,63,139],fri:72,friction:[2,72,79,118],from:[0,1],front:72,frontend:58,frozen:[2,39,66,116],fs2:[2,35],ftol:[91,92],fuction:105,fudg:75,fulfil:2,full:[1,2,4,35,58,63,67,70,74,97,111,113,114,117],fuller:91,fulli:[2,70,91,92,105,145,163],fulton:111,fumi:98,funcfl:111,fund:0,funrol:137,further:[2,37,58,67,71,79,91,92,93,96,104,137,148],furthermor:[11,48,63,74,110,113],futur:[0,2,60,66,92,135,136],g_jik:145,g_p:79,ga3:44,gaa:97,gai:117,gain:4,galindo:138,gamma0:13,gamma:[2,13,67,72,109,110,112,117,134,138,151,152,153,155,156,158,159],gamma_:79,gamma_ijk:156,gamma_n:118,gamma_p:79,gamma_t:118,gammaa:138,gammafactor:67,gammar:138,gan:[145,155,156,158,159],gan_sw:145,gan_tersoff:145,gao:[2,5,46,101],gap:[131,132,149],gather:3,gather_atom:3,gathert_atom:3,gauch:51,gauss:106,gaussian:[2,35,37,66,71,73,109,113,116],gave:139,gavhan:4,gaybern:[2,4,91],gcmc:139,gd3:44,gdot:132,ge4:44,gec:[156,158],gen:68,gener:0,gentler:80,gentli:112,geom:2,geometr:[2,40,45,60,68,81,92,96,102,103,105,108,113,115,117,119,122,123,124,125,126,127,128,129,130,131,132,133,138,139,142,146,150,160,161],geometri:[2,9,19,45,60,62,139],gerber:130,germann:[69,124],germano:117,get:[0,1,2,3,4,19,35,40,42,45,58,60,62,81,92,105,159,163],get_natom:3,get_rank:3,get_siz:3,gewald:2,gezelt:[105,122],ghost:[2,4,30,62,68,109,110,113,118,121],gif:58,gifsicl:58,gillan:149,gingold:[151,152],git:163,give:[0,1,2,3,4,28,36,38,45,62,68,70,91,94,97,113,120,134,137,139,146,156,157,158],given:[2,3,4,11,38,42,43,48,57,62,63,66,67,68,69,70,71,72,73,74,75,76,79,80,81,93,94,97,98,99,100,102,103,104,105,106,109,110,111,113,114,115,117,118,120,122,123,124,126,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,162],glosli:137,glotzer:109,glue:3,gnu:0,gnuplot:3,goddard:[2,9,89,113,120],goe:[28,42,45,63,91,108,112,119,124,127,150,162],gold:29,goldman:72,good:[1,2,4,19,30,41,44,60,68,75,92,93,103,111,137,139,159,163],gordan:42,gordon:2,got:163,gould:[2,46],gov:[0,93,111,114],govern:67,gpa:94,gpl:0,gpt:137,gpu:[1,5,6,7,8,9,10,11,12,13,14,15,16,17,20,21,22,23,24,25,26,27,28,39,46,47,48,49,50,51,52,53,54,55,68,69,75,82,83,84,86,87,88,89,93,94],grab:2,grad:2,gradient:[2,62,63,79,92,132,141,142],graft:61,grain:[2,13,18,28,45,51,65,70,74,115,119,137,142,147],gram:111,gran:[2,80,81],grana:90,granular:0,graph:3,graphic:3,graviti:2,grdient:59,great:[72,163],greater:[1,62,66,68,70,96,98,99,100,139],greatli:[41,63],green:[2,35,58,71,97,163],green_kubo:2,grest:[21,22,61,100,118,126],grid:[19,41,44,60,67,79],grigera:2,gromac:91,gromacs:[2,91,119],groot:109,ground:[2,31,64,113],group:[2,3,4,19,29,30,31,32,33,34,35,36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89,92,93,94,95,97,98,99,100,101,102,103,104,105,108,109,111,112,114,116,117,118,119,120,122,123,124,125,126,127,128,129,130,131,134,135,136,137,139,140,143,144,145,146,147,150,154,155,156,157,158,159,160,161,162,163],yourself:[2,62,163],ypo:45,yukawa:103,z_i:[113,158,162],z_j:[158,162],z_meam:134,zannoni:117,zbl:[134,149],zblcut:158,zblcutinn:149,zblcutout:149,zblexpscal:158,zblz:149,zero:[2,3,10,11,19,24,25,29,32,34,36,37,38,39,41,42,43,44,45,46,48,55,57,58,60,62,63,66,67,68,69,71,72,74,75,78,79,80,86,91,92,97,98,99,100,101,103,105,108,109,110,113,117,119,120,122,124,126,127,130,132,133,134,137,139,140,146,147,148,154,159,162],zeta:[67,114],zfactor:58,zhang:118,zhi:[2,80],zhi_bound:2,zhou:[97,114,145,156,158],zhu:153,ziegler:[134,158,162],zimmerman2004:59,zimmerman2010:59,zimmerman:[29,59,97],zlim:148,zlo:[2,80],zlo_bound:2,zmax:67,zmin:67,zn2:44,zone:41,zoom:58,zr4:44,zwall:80,zwall_veloc:67},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","6. How-to discussions","11. Python interface to LAMMPS","5.USER-INTEL package","angle_style charmm command","angle_style class2 command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style quartic command","angle_style sdk command","balance command","bond_style class2 command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style morse command","bond_style nonlinear command","bond_style quartic command","compute centro/atom command","compute cna/atom command","compute dpd command","compute fep command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute msd/nongauss command","compute orientorder/atom command","compute pressure command","compute rigid/local command","compute saed command","compute sna/atom command","compute stress/atom command","compute xrd command","create_atoms command","dihedral_style charmm command","dihedral_style class2 command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style spherical command","dihedral_style command","dump image command","fix atc command","fix balance command","fix bond/swap command","fix box/relax command","fix ehex command","fix eos/cv command","fix eos/table/rx command","fix gld command","fix lb/fluid command","fix nvt command","fix nphug command","fix orient/fcc command","fix pimd command","fix qbmsst command","fix restrain command","fix rx command","fix shake command","fix spring/rg command","fix ti/rs command","fix ti/spring command","fix ttm command","fix wall/lj93 command","fix wall/region command","improper_style class2 command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style ring command","improper_style umbrella command","Manifolds (surfacse)","minimize command","neb command","pair_style adp command","pair_style airebo command","pair_style beck command","pair_style body command","pair_style bop command","pair_style born command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dpd/fdt command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style exp6/rx command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style multi/lucy command","pair_style multi/lucy/rx command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style polymorphic command","pair_style resquared command","pair_style lj/sdk command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/idealgas command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style sw command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style vashishta command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","LAMMPS GitHub 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\ No newline at end of file diff --git a/doc/html/tutorial_github.html b/doc/html/tutorial_github.html index 5f6c9e69b..e6170b896 100644 --- a/doc/html/tutorial_github.html +++ b/doc/html/tutorial_github.html @@ -1,365 +1,349 @@ LAMMPS GitHub tutorial — LAMMPS documentation

LAMMPS GitHub tutorial

-
-

written by Stefan Paquay

+

written by Stefan Paquay

-

This document briefly describes how to use GitHub to merge changes -into LAMMPS using GitHub. It assumes that you are familiar with +

This document briefly describes how to use GitHub to merge changes you +make into LAMMPS, using GitHub. It assumes that you are familiar with git. You may want to have a look at the Git book to reacquaint yourself.

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-
-
-

Making an account

+

Making an account

First of all, you need a GitHub account. This is fairly simple, just go to GitHub and create an account by clicking the ``Sign up for GitHub’’ button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password.

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-
-

Forking the repository

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Forking the repository

To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to LAMMPS on GitHub and make sure branch is set to ``lammps-icms’‘, see the figure below.

_images/tutorial_branch.png

Now, click on fork in the top right corner:

_images/tutorial_fork.png

This will create your own fork of the LAMMPS repository. You can make changes in this fork and later file pull requests to allow the upstream repository to merge changes from your own fork into the one we just forked from. At the same time, you can set things up, so you can include changes from upstream into your repository.

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-

Adding changes to your own fork

+

Adding changes to your own fork

Before adding changes, it is better to first create a new branch that will contain these changes, a so-called feature branch.

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Feature branches

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Feature branches

Since LAMMPS is such a big project and most user contributions come in small portions, the most ideal workflow for LAMMPS is the so-called ``Feature branch’’ workflow. It is explained in great detail here: feature branch workflow.

The idea is that every new feature for LAMMPS gets its own branch. This way, it is fairly painless to incorporate new features into the upstream repository. I will explain briefly here how to do it. In this feature branch, I will add a USER-package.

I assume that git is installed on the local machine and you know how to use a command line.

First of all, you need to clone your own fork of LAMMPS:

$ git clone https://github.com/<your user name>/lammps.git

You can find the proper url to the right of the “HTTPS” block, see figure.

_images/tutorial_https_block.png

The above command copies (``clones’‘) the git repository to your local machine. You can use this local clone to make changes and test them without interfering with the repository on github. First, however, it is recommended to make a new branch for a particular feature you would like added to LAMMPS. In this example, I will try adding a new USER-package called USER-MANIFOLD.

To create a new branch, run the following git command in your repository:

$ git checkout -b add-user-manifold

The name of this new branch is “add-user-manifold” in my case. Just name it after something that resembles the feature you want added to LAMMPS.

Now that you’ve changed branches, you can edit the files as you see fit, add new files, and commit as much as you would like. Just remember that if halfway you decide to add another, unrelated feature, you should switch branches!

After everything is done, add the files to the branch and commit them:

 $ git add src/USER-MANIFOLD examples/USER/manifold/
 $ git add doc/fix_nvt,e_manifold_rattle.txt
 $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt

After the files are added, the change should be comitted:

$ git commit -m 'Added user-manifold package'

The “-m” switch is used to add a message to the commit. Use this to indicate what type of change was commited.

-
-

Wisdom by Axel:

+

Wisdom by Axel

“Do not use “git commit -a”. the -a flag will automatically include *all modified or new files. mercurial does that and it find it hugely annoying and often leading to accidental commits of files you don’t want. use git add, git rm, git mv for adding, removing, renaming and then git commit to finalize the commit. personally, i find it very convenient to use the bundled gui for commits, i.e. git gui. typically, i will do git add and other operations, but then verify and review them with git gui. git gui also allows to do line-by-line unstaging and other convenient operations.”*

After the commit, the changes can be pushed to the same branch on GitHub:

$ git push

Git will ask you for your user name and password on GitHub if you have not configured anything. If you correctly type your user name and password, the change should be added to your fork on GitHub.

If you want to make really sure you push to the right repository (which is good practice), you can provide it explicitly:

$ git push origin

or using an explicit URL:

$ git push git@github.com:Pakketeretet2/lammps.git

After that, you can file a new pull request based on this branch. GitHub will now look like this:

_images/tutorial_pull_request_feature_branch1.png

Make sure that the current branch is set to the correct one, which, in this case, is “add-user-manifold”. Now click “New pull request”. If done correctly, the only changes you will see are those that were made on this branch, so in my case, I will see nothing related to $mathrm*pair_dzugatov*.$

This will open up a new window that lists changes made to the repository. If you are just adding new files, there is not much to do, but I suppose merge conflicts are to be resolved here if there are changes in existing files. If all changes can automatically be merged, green text at the top will say so and you can click the “Create pull request” button, see image.

_images/tutorial_pull_request2.png

After this you have to specify a short title and a comment with details about your pull request. I guess here you write what your modifications do and why they should be incorporated upstream. After that, click the “Create pull request” button, see image below.

_images/tutorial_pull_request3.png

Now just write some nice comments, click “Comment”, and that is it. It is now up to the maintainer(s) of the upstream repository to incorporate the changes into the repository and to close the pull request.

_images/tutorial_pull_request4.png -
-
-
-
-

Additional changes

+

Additional changes

Before the pull request is accepted, any additional changes you push into your repository will automatically become part of the pull request.

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-

After a merge

+

After a merge

When everything is fine the feature branch is merged into the LAMMPS repositories:

_images/tutorial_merged.png

Now one question remains: What to do with the feature branch that got merged into upstream?

It is in principle safe to delete them from your own fork. This helps keep it a bit more tidy. Note that you first have to switch to another branch!

$ git checkout lammps-icms
 $ git pull lammps-icms
 $ git branch -d add-user-manifold

If you do not pull first, it is not really a problem but git will warn you at the next statement that you are deleting a local branch that was not yet fully merged into HEAD. This is because git does not yet know your branch just got merged into lammps-icms upstream. If you first delete and then pull, everything should still be fine.

Finally, if you delete the branch locally, you might want to push this to your remote(s) as well:

$ git push origin :add-user-manifold
\ No newline at end of file diff --git a/doc/lammps.book b/doc/lammps.book index e72adeb70..f768cdc7d 100644 --- a/doc/lammps.book +++ b/doc/lammps.book @@ -1,603 +1,622 @@ #HTMLDOC 1.8.27 -t pdf14 -f "../Manual.pdf" --book --toclevels 4 --no-numbered --toctitle "Table of Contents" --title --textcolor #000000 --linkcolor #0000ff --linkstyle plain --bodycolor #ffffff --size Universal --left 1.00in --right 0.50in --top 0.50in --bottom 0.50in --header .t. --header1 ... --footer ..1 --nup 1 --tocheader .t. --tocfooter ..i --portrait --color --no-pscommands --no-xrxcomments --compression=1 --jpeg=0 --fontsize 11.0 --fontspacing 1.2 --headingfont helvetica --bodyfont times --headfootsize 11.0 --headfootfont helvetica --charset iso-8859-1 --links --embedfonts --pagemode document --pagelayout single --firstpage c1 --pageeffect none --pageduration 10 --effectduration 1.0 --no-encryption --permissions all --owner-password "" --user-password "" --browserwidth 680 --no-strict --no-overflow Manual.html Section_intro.html Section_start.html Section_commands.html Section_packages.html Section_accelerate.html accelerate_gpu.html accelerate_intel.html accelerate_kokkos.html accelerate_omp.html accelerate_opt.html Section_howto.html Section_example.html -tutorial_drude.html Section_perf.html Section_tools.html Section_modify.html Section_python.html Section_errors.html Section_history.html + +tutorial_drude.html +tutorial_github.html + +body.html +manifolds.html + +angle_coeff.html +angle_style.html +atom_modify.html +atom_style.html balance.html -box.html +bond_coeff.html +bond_style.html +bond_write.html boundary.html +box.html change_box.html clear.html -comm_style.html comm_modify.html +comm_style.html +compute.html +compute_modify.html create_atoms.html create_bonds.html create_box.html delete_atoms.html delete_bonds.html dielectric.html +dihedral_coeff.html +dihedral_style.html dimension.html displace_atoms.html +dump.html +dump_custom_vtk.html +dump_h5md.html +dump_image.html +dump_modify.html +dump_molfile.html echo.html +fix.html +fix_modify.html group.html group2ndx.html if.html +improper_coeff.html +improper_style.html include.html info.html jump.html +kspace_modify.html +kspace_style.html label.html lattice.html log.html mass.html -minimize.html -min_style.html min_modify.html +min_style.html +minimize.html molecule.html neb.html -neighbor.html neigh_modify.html +neighbor.html newton.html next.html package.html +pair_coeff.html +pair_modify.html +pair_style.html +pair_write.html partition.html prd.html print.html processors.html python.html quit.html +read_data.html +read_dump.html +read_restart.html region.html replicate.html +rerun.html reset_timestep.html +restart.html run.html run_style.html set.html shell.html special_bonds.html suffix.html tad.html temper.html thermo.html -thermo_style.html thermo_modify.html -timestep.html +thermo_style.html timer.html +timestep.html +uncompute.html +undump.html +unfix.html units.html 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-USER/atc/man_hardy_computes.html -USER/atc/man_remove_molecule.html -USER/atc/man_mesh_create_faceset_box.html -USER/atc/man_decomposition.html -tutorial_github.html - +USER/atc/man_write_atom_weights.html +USER/atc/man_write_restart.html diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index bc9aea78b..ae09f79b4 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,318 +1,318 @@ LAMMPS-ICMS Users Manual - + "LAMMPS WWW Site"_lws - "LAMMPS-ICMS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line

LAMMPS-ICMS Documentation :c,h3 -28 Jul 2016 version :c,h4 +30 Jul 2016 version :c,h4 Version info: :h4 The LAMMPS "version" is the date when it was released, such as 1 May 2010. LAMMPS is updated continuously. Whenever we fix a bug or add a feature, we release it immediately, and post a notice on "this page of the WWW site"_bug. Each dated copy of LAMMPS contains all the features and bug-fixes up to and including that version date. The version date is printed to the screen and logfile every time you run LAMMPS. It is also in the file src/version.h and in the LAMMPS directory name created when you unpack a tarball, and at the top of the first page of the manual (this page). LAMMPS-ICMS is an experimental variant of LAMMPS with additional features made available for testing before they will be submitted for inclusion into the official LAMMPS tree. The source code is based on the official LAMMPS svn repository mirror at the Institute for Computational Molecular Science at Temple University and generally kept up-to-date as much as possible. Sometimes, e.g. when additional development work is needed to adapt the upstream changes into LAMMPS-ICMS it can take longer until synchronization; and occasionally, e.g. in case of the rewrite of the multi-threading support, the development will be halted except for important bugfixes until all features of LAMMPS-ICMS fully compatible with the upstream version or replaced by alternate implementations. If you browse the HTML doc pages on the LAMMPS WWW site, they always describe the most current version of upstream LAMMPS, but may be missing some new features in LAMMPS-ICMS. :ulb,l If you browse the HTML doc pages included in your tarball, they describe the version you have, however, not all new features in LAMMPS-ICMS are documented immediately. :l The "PDF file"_Manual.pdf on the WWW site or in the tarball is updated about once per month. This is because it is large, and we don't want it to be part of every patch. :l There is also a "Developer.pdf"_Developer.pdf file in the doc directory, which describes the internal structure and algorithms of LAMMPS. :ule,l LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS is a classical molecular dynamics simulation code designed to run efficiently on parallel computers. It was developed at Sandia National Laboratories, a US Department of Energy facility, with funding from the DOE. It is an open-source code, distributed freely under the terms of the GNU Public License (GPL). The primary developers of LAMMPS are "Steve Plimpton"_sjp, Aidan Thompson, and Paul Crozier who can be contacted at sjplimp,athomps,pscrozi at sandia.gov. The "LAMMPS WWW Site"_lws at http://lammps.sandia.gov has more information about the code and its uses. :link(bug,http://lammps.sandia.gov/bug.html) :link(sjp,http://www.sandia.gov/~sjplimp) :line The LAMMPS documentation is organized into the following sections. If you find errors or omissions in this manual or have suggestions for useful information to add, please send an email to the developers so we can improve the LAMMPS documentation. Once you are familiar with LAMMPS, you may want to bookmark "this page"_Section_commands.html#comm at Section_commands.html#comm since it gives quick access to documentation for all LAMMPS commands. "PDF file"_Manual.pdf of the entire manual, generated by "htmldoc"_http://freecode.com/projects/htmldoc "Introduction"_Section_intro.html :olb,l 1.1 "What is LAMMPS"_intro_1 :ulb,b 1.2 "LAMMPS features"_intro_2 :b 1.3 "LAMMPS non-features"_intro_3 :b 1.4 "Open source distribution"_intro_4 :b 1.5 "Acknowledgments and citations"_intro_5 :ule,b "Getting started"_Section_start.html :l 2.1 "What's in the LAMMPS distribution"_start_1 :ulb,b 2.2 "Making LAMMPS"_start_2 :b 2.3 "Making LAMMPS with optional packages"_start_3 :b 2.4 "Building LAMMPS via the Make.py script"_start_4 :b 2.5 "Building LAMMPS as a library"_start_5 :b 2.6 "Running LAMMPS"_start_6 :b 2.7 "Command-line options"_start_7 :b 2.8 "Screen output"_start_8 :b 2.9 "Tips for users of previous versions"_start_9 :ule,b "Commands"_Section_commands.html :l 3.1 "LAMMPS input script"_cmd_1 :ulb,b 3.2 "Parsing rules"_cmd_2 :b 3.3 "Input script structure"_cmd_3 :b 3.4 "Commands listed by category"_cmd_4 :b 3.5 "Commands listed alphabetically"_cmd_5 :ule,b "Packages"_Section_packages.html :l 4.1 "Standard packages"_pkg_1 :ulb,b 4.2 "User packages"_pkg_2 :ule,b "Accelerating LAMMPS performance"_Section_accelerate.html :l 5.1 "Measuring performance"_acc_1 :ulb,b 5.2 "Algorithms and code options to boost performace"_acc_2 :b 5.3 "Accelerator packages with optimized styles"_acc_3 :b 5.3.1 "GPU package"_accelerate_gpu.html :ulb,b 5.3.2 "USER-INTEL package"_accelerate_intel.html :b 5.3.3 "KOKKOS package"_accelerate_kokkos.html :b 5.3.4 "USER-OMP package"_accelerate_omp.html :b 5.3.5 "OPT package"_accelerate_opt.html :ule,b 5.4 "Comparison of various accelerator packages"_acc_4 :ule,b "How-to discussions"_Section_howto.html :l 6.1 "Restarting a simulation"_howto_1 :ulb,b 6.2 "2d simulations"_howto_2 :b 6.3 "CHARMM and AMBER force fields"_howto_3 :b 6.4 "Running multiple simulations from one input script"_howto_4 :b 6.5 "Multi-replica simulations"_howto_5 :b 6.6 "Granular models"_howto_6 :b 6.7 "TIP3P water model"_howto_7 :b 6.8 "TIP4P water model"_howto_8 :b 6.9 "SPC water model"_howto_9 :b 6.10 "Coupling LAMMPS to other codes"_howto_10 :b 6.11 "Visualizing LAMMPS snapshots"_howto_11 :b 6.12 "Triclinic (non-orthogonal) simulation boxes"_howto_12 :b 6.13 "NEMD simulations"_howto_13 :b 6.14 "Finite-size spherical and aspherical particles"_howto_14 :b 6.15 "Output from LAMMPS (thermo, dumps, computes, fixes, variables)"_howto_15 :b 6.16 "Thermostatting, barostatting, and compute temperature"_howto_16 :b 6.17 "Walls"_howto_17 :b 6.18 "Elastic constants"_howto_18 :b 6.19 "Library interface to LAMMPS"_howto_19 :b 6.20 "Calculating thermal conductivity"_howto_20 :b 6.21 "Calculating viscosity"_howto_21 :b 6.22 "Calculating a diffusion coefficient"_howto_22 :b 6.23 "Using chunks to calculate system properties"_howto_23 :b 6.24 "Setting parameters for pppm/disp"_howto_24 :b 6.25 "Polarizable models"_howto_25 :b 6.26 "Adiabatic core/shell model"_howto_26 :b 6.27 "Drude induced dipoles"_howto_27 :ule,b "Example problems"_Section_example.html :l "Performance & scalability"_Section_perf.html :l "Additional tools"_Section_tools.html :l "Modifying & extending LAMMPS"_Section_modify.html :l 10.1 "Atom styles"_mod_1 :ulb,b 10.2 "Bond, angle, dihedral, improper potentials"_mod_2 :b 10.3 "Compute styles"_mod_3 :b 10.4 "Dump styles"_mod_4 :b 10.5 "Dump custom output options"_mod_5 :b 10.6 "Fix styles"_mod_6 :b 10.7 "Input script commands"_mod_7 :b 10.8 "Kspace computations"_mod_8 :b 10.9 "Minimization styles"_mod_9 :b 10.10 "Pairwise potentials"_mod_10 :b 10.11 "Region styles"_mod_11 :b 10.12 "Body styles"_mod_12 :b 10.13 "Thermodynamic output options"_mod_13 :b 10.14 "Variable options"_mod_14 :b 10.15 "Submitting new features for inclusion in LAMMPS"_mod_15 :ule,b "Python interface"_Section_python.html :l 11.1 "Overview of running LAMMPS from Python"_py_1 :ulb,b 11.2 "Overview of using Python from a LAMMPS script"_py_2 :b 11.3 "Building LAMMPS as a shared library"_py_3 :b 11.4 "Installing the Python wrapper into Python"_py_4 :b 11.5 "Extending Python with MPI to run in parallel"_py_5 :b 11.6 "Testing the Python-LAMMPS interface"_py_6 :b 11.7 "Using LAMMPS from Python"_py_7 :b 11.8 "Example Python scripts that use LAMMPS"_py_8 :ule,b "Errors"_Section_errors.html :l 12.1 "Common problems"_err_1 :ulb,b 12.2 "Reporting bugs"_err_2 :b 12.3 "Error & warning messages"_err_3 :ule,b "Future and history"_Section_history.html :l 13.1 "Coming attractions"_hist_1 :ulb,b 13.2 "Past versions"_hist_2 :ule,b :ole :link(intro_1,Section_intro.html#intro_1) :link(intro_2,Section_intro.html#intro_2) :link(intro_3,Section_intro.html#intro_3) :link(intro_4,Section_intro.html#intro_4) :link(intro_5,Section_intro.html#intro_5) :link(start_1,Section_start.html#start_1) :link(start_2,Section_start.html#start_2) :link(start_3,Section_start.html#start_3) :link(start_4,Section_start.html#start_4) :link(start_5,Section_start.html#start_5) :link(start_6,Section_start.html#start_6) :link(start_7,Section_start.html#start_7) :link(start_8,Section_start.html#start_8) :link(start_9,Section_start.html#start_9) :link(cmd_1,Section_commands.html#cmd_1) :link(cmd_2,Section_commands.html#cmd_2) :link(cmd_3,Section_commands.html#cmd_3) :link(cmd_4,Section_commands.html#cmd_4) :link(cmd_5,Section_commands.html#cmd_5) :link(pkg_1,Section_packages.html#pkg_1) :link(pkg_2,Section_packages.html#pkg_2) :link(acc_1,Section_accelerate.html#acc_1) :link(acc_2,Section_accelerate.html#acc_2) :link(acc_3,Section_accelerate.html#acc_3) :link(acc_4,Section_accelerate.html#acc_4) :link(howto_1,Section_howto.html#howto_1) :link(howto_2,Section_howto.html#howto_2) :link(howto_3,Section_howto.html#howto_3) :link(howto_4,Section_howto.html#howto_4) :link(howto_5,Section_howto.html#howto_5) :link(howto_6,Section_howto.html#howto_6) :link(howto_7,Section_howto.html#howto_7) :link(howto_8,Section_howto.html#howto_8) :link(howto_9,Section_howto.html#howto_9) :link(howto_10,Section_howto.html#howto_10) :link(howto_11,Section_howto.html#howto_11) :link(howto_12,Section_howto.html#howto_12) :link(howto_13,Section_howto.html#howto_13) :link(howto_14,Section_howto.html#howto_14) :link(howto_15,Section_howto.html#howto_15) :link(howto_16,Section_howto.html#howto_16) :link(howto_17,Section_howto.html#howto_17) :link(howto_18,Section_howto.html#howto_18) :link(howto_19,Section_howto.html#howto_19) :link(howto_20,Section_howto.html#howto_20) :link(howto_21,Section_howto.html#howto_21) :link(howto_22,Section_howto.html#howto_22) :link(howto_23,Section_howto.html#howto_23) :link(howto_24,Section_howto.html#howto_24) :link(howto_25,Section_howto.html#howto_25) :link(howto_26,Section_howto.html#howto_26) :link(howto_27,Section_howto.html#howto_27) :link(mod_1,Section_modify.html#mod_1) :link(mod_2,Section_modify.html#mod_2) :link(mod_3,Section_modify.html#mod_3) :link(mod_4,Section_modify.html#mod_4) :link(mod_5,Section_modify.html#mod_5) :link(mod_6,Section_modify.html#mod_6) :link(mod_7,Section_modify.html#mod_7) :link(mod_8,Section_modify.html#mod_8) :link(mod_9,Section_modify.html#mod_9) :link(mod_10,Section_modify.html#mod_10) :link(mod_11,Section_modify.html#mod_11) :link(mod_12,Section_modify.html#mod_12) :link(mod_13,Section_modify.html#mod_13) :link(mod_14,Section_modify.html#mod_14) :link(mod_15,Section_modify.html#mod_15) :link(py_1,Section_python.html#py_1) :link(py_2,Section_python.html#py_2) :link(py_3,Section_python.html#py_3) :link(py_4,Section_python.html#py_4) :link(py_5,Section_python.html#py_5) :link(py_6,Section_python.html#py_6) :link(err_1,Section_errors.html#err_1) :link(err_2,Section_errors.html#err_2) :link(err_3,Section_errors.html#err_3) :link(hist_1,Section_history.html#hist_1) :link(hist_2,Section_history.html#hist_2) diff --git a/doc/src/compute_rigid_local.txt b/doc/src/compute_rigid_local.txt index 21cf3aa19..5cdd58fbc 100644 --- a/doc/src/compute_rigid_local.txt +++ b/doc/src/compute_rigid_local.txt @@ -1,185 +1,185 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line compute rigid/local command :h3 [Syntax:] compute ID group-ID rigid/local rigidID input1 input2 ... :pre ID, group-ID are documented in "compute"_compute.html command :ulb,l rigid/local = style name of this compute command :l rigidID = ID of fix rigid/small command or one of its variants :l input = one or more rigid body attributes :l possible attributes = id, mol, mass, x, y, z, xu, yu, zu, ix, iy, iz vx, vy, vz, fx, fy, fz, omegax, omegay, omegaz, angmomx, angmomy, angmomz, quatw, quati, quatj, quatk, tqx, tqy, tqz, inertiax, inertiay, inertiaz id = atom ID of atom within body which owns body properties mol = molecule ID used to define body in "fix rigid/small"_fix_rigid.html command mass = total mass of body x,y,z = center of mass coords of body xu,yu,zu = unwrapped center of mass coords of body ix,iy,iz = box image that the center of mass is in vx,vy,vz = center of mass velocities fx,fy,fz = force of center of mass omegax,omegay,omegaz = angular velocity of body angmomx,angmomy,angmomz = angular momentum of body quatw,quati,quatj,quatk = quaternion components for body tqx,tqy,tqz = torque on body - inertiax,inertiay,inertiaz = diagonalized moments of inertia of body :per + inertiax,inertiay,inertiaz = diagonalized moments of inertia of body :pre :ule [Examples:] compute 1 all rigid/local myRigid mol x y z :pre [Description:] Define a computation that simply stores rigid body attributes for rigid bodies defined by the "fix rigid/small"_fix_rigid.html command or one of its NVE, NVT, NPT, NPH variants. The data is stored as local data so it can be accessed by other "output commands"_Section_howto.html#howto_15 that process local data, such as the "compute reduce"_compute_reduce.html or "dump local"_dump.html commands. Note that this command only works with the "fix rigid/small"_fix_rigid.html command or its variants, not the fix rigid command and its variants. The ID of the "fix rigid/small"_fix_rigid.html command used to define rigid bodies must be specified as {rigidID}. The "fix rigid"_fix_rigid.html command is typically used to define a handful of (potentially very large) rigid bodies. It outputs similar per-body information as this command directly from the fix as global data; see the "fix rigid"_fix_rigid.html doc page for details The local data stored by this command is generated by looping over all the atoms owned on a processor. If the atom is not in the specified {group-ID} or is not part of a rigid body it is skipped. If it is not the atom within a body that is assigned to store the body information it is skipped (only one atom per body is so assigned). If it is the assigned atom, then the info for that body is output. This means that information for N bodies is generated. N may be less than the # of bodies defined by the fix rigid command, if the atoms in some bodies are not in the {group-ID}. NOTE: Which atom in a body owns the body info is determined internal to LAMMPS; it's the one nearest the geometric center of the body. Typically you should avoid this complication, by defining the group associated with this fix to include/exclude entire bodies. Note that as atoms and bodies migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array from one timestep to the next. Here is an example of how to use this compute to dump rigid body info to a file: compute 1 all rigid/local myRigid mol x y z fx fy fz dump 1 all local 1000 tmp.dump index c_1\[1\] c_1\[2\] c_1\[3\] c_1\[4\] c_1\[5\] c_1\[6\] c_1\[7\] :pre :line This section explains the rigid body attributes that can be specified. The {id} attribute is the atomID of the atom which owns the rigid body, which is assigned by the "fix rigid/small"_fix_rigid.html command. The {mol} attribute is the molecule ID of the rigid body. It should be the molecule ID which all of the atoms in the body belong to, since that is how the "fix rigid/small"_fix_rigid.html command defines its rigid bodies. The {mass} attribute is the total mass of the rigid body. There are two options for outputting the coordinates of the center of mass (COM) of the body. The {x}, {y}, {z} attributes write the COM "unscaled", in the appropriate distance "units"_units.html (Angstroms, sigma, etc). Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by the image flags for each atobody. Unwrapped means that if the body COM has passed thru a periodic boundary one or more times, the value is generated what the COM coordinate would be if it had not been wrapped back into the periodic box. The image flags for the body can be generated directly using the {ix}, {iy}, {iz} attributes. For periodic dimensions, they specify which image of the simulation box the COM is considered to be in. An image of 0 means it is inside the box as defined. A value of 2 means add 2 box lengths to get the true value. A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as the rigid body COMs cross periodic boundaries during the simulation. The {vx}, {vy}, {vz}, {fx}, {fy}, {fz} attributes are components of the COM velocity and force on the COM of the body. The {omegax}, {omegay}, and {omegaz} attributes are the angular velocity componennts of the body around its COM. The {angmomx}, {angmomy}, and {angmomz} attributes are the angular momentum components of the body around its COM. The {quatw}, {quati}, {quatj}, and {quatk} attributes are the components of the 4-vector quaternion representing the orientation of the rigid body. See the "set"_set.html command for an explanation of the quaternion vector. The {angmomx}, {angmomy}, and {angmomz} attributes are the angular momentum components of the body around its COM. The {tqx}, {tqy}, {tqz} attributes are components of the torque acting on the body around its COM. The {inertiax}, {inertiay}, {inertiaz} attributes are components of diagonalized inertia tensor for the body, i.e the 3 moments of inertia for the body around its principal axes, as computed internally by LAMMPS. :line [Output info:] This compute calculates a local vector or local array depending on the number of keywords. The length of the vector or number of rows in the array is the number of rigid bodies. If a single keyword is specified, a local vector is produced. If two or more keywords are specified, a local array is produced where the number of columns = the number of keywords. The vector or array can be accessed by any command that uses local values from a compute as input. See "this section"_Section_howto.html#howto_15 for an overview of LAMMPS output options. The vector or array values will be in whatever "units"_units.html the corresponding attribute is in: id,mol = unitless mass = mass units x,y,z and xy,yu,zu = distance units vx,vy,vz = velocity units fx,fy,fz = force units omegax,omegay,omegaz = radians/time units angmomx,angmomy,angmomz = mass*distance^2/time units quatw,quati,quatj,quatk = unitless tqx,tqy,tqz = torque units inertiax,inertiay,inertiaz = mass*distance^2 units :ul [Restrictions:] This compute is part of the RIGID package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] "dump local"_dump.html, "compute reduce"_compute_reduce.html [Default:] none diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index 07e11aa98..dc2b0e3fa 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -1,31 +1,40 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line -[Description:] +Manifolds (surfacse) :h3 -Below is a list of currently supported manifolds, their parameters and a short description of them. -The parameters listed here are in the same order as they should be passed to the relevant fixes. +[Overview:] +This doc page is not about a LAMMPS input script command, but about +manifolds, which are generalized surfaces, as defined and used by the +USER-MANIFOLD package, to track particle motion on the manifolds. See +the src/USER-MANIFOLD/README file for more details about the package +and its commands. + +Below is a list of currently supported manifolds by the USER-MANIFOLD +package, their parameters and a short description of them. The +parameters listed here are in the same order as they should be passed +to the relevant fixes. {manifold} || {parameters} || {equation} || {description} cylinder || R || x^2 + y^2 - R^2 = 0 || Cylinder along z-axis, axis going through (0,0,0) cylinder_dent || R l a || x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise || A cylinder with a dent around z = 0 dumbbell || a A B c || -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 || A dumbbell || ellipsoid || a b c || (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 || An ellipsoid plane || a b c x0 y0 z0 || a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 || A plane with normal (a,b,c) going through point (x0,y0,z0) plane_wiggle || a w || z - a*sin(w*x) = 0 || A plane with a sinusoidal modulation on z along x. sphere || R || x^2 + y^2 + z^2 - R^2 = 0 || A sphere of radius R supersphere || R q || |x|^q + |y|^q + |z|^q - R^q = 0 || A supersphere of hyperradius R spine || a, A, B, B2, c || -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise || An approximation to a dendtritic spine spine_two || a, A, B, B2, c || -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise || Another approximation to a dendtritic spine thylakoid || wB LB lB || Various, see "(Paquay)"_#Paquay || A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB torus || R r || (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 || A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=||) :link(Paquay) [(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published, preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/. diff --git a/doc/src/pair_modify.txt b/doc/src/pair_modify.txt index fba45f7f0..eb60c6b00 100644 --- a/doc/src/pair_modify.txt +++ b/doc/src/pair_modify.txt @@ -1,261 +1,259 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line pair_modify command :h3 [Syntax:] pair_modify keyword values ... :pre one or more keyword/value pairs may be listed :ulb,l keyword = {pair} or {shift} or {mix} or {table} or {table/disp} or {tabinner} or {tabinner/disp} or {tail} or {compute} :l {pair} values = sub-style N {special} which wt1 wt2 wt3 sub-style = sub-style of "pair hybrid"_pair_hybrid.html N = which instance of sub-style (only if sub-style is used multiple times) {special} which wt1 wt2 wt3 = override {special_bonds} settings (optional) which = {lj/coul} or {lj} or {coul} w1,w2,w3 = 1-2, 1-3, and 1-4 weights from 0.0 to 1.0 inclusive {mix} value = {geometric} or {arithmetic} or {sixthpower} {shift} value = {yes} or {no} {table} value = N 2^N = # of values in table {table/disp} value = N 2^N = # of values in table {tabinner} value = cutoff cutoff = inner cutoff at which to begin table (distance units) {tabinner/disp} value = cutoff cutoff = inner cutoff at which to begin table (distance units) {tail} value = {yes} or {no} {compute} value = {yes} or {no} :pre :ule [Examples:] pair_modify shift yes mix geometric pair_modify tail yes pair_modify table 12 pair_modify pair lj/cut compute no pair_modify pair lj/cut/coul/long 1 special lj/coul 0.0 0.0 0.0 :pre [Description:] Modify the parameters of the currently defined pair style. Not all parameters are relevant to all pair styles. If used, the {pair} keyword must appear first in the list of keywords. It can only be used with the "hybrid and hybrid/overlay"_pair_hybrid.html pair styles. It means that all the following parameters will only be modified for the specified sub-style. If the sub-style is defined multiple times, then an additional numeric argument {N} must also be specified, which is a number from 1 to M where M is the number of times the sub-style was listed in the "pair_style hybrid"_pair_hybrid.html command. The extra number indicates which instance of the sub-style the remaining keywords will be applied to. Note that if the {pair} keyword is not used, and the pair style is {hybrid} or {hybrid/overlay}, then all the specified keywords will be applied to all sub-styles. The {special} keyword can only be used in conjunction with the {pair} keyword and must directly follow it. It allows to override the "special_bonds"_special_bonds.html settings for the specified sub-style. More details are given below. The {mix} keyword affects pair coefficients for interactions between atoms of type I and J, when I != J and the coefficients are not explicitly set in the input script. Note that coefficients for I = J must be set explicitly, either in the input script via the "pair_coeff" command or in the "Pair Coeffs" section of the "data file"_read_data.html. For some pair styles it is not necessary to specify coefficients when I != J, since a "mixing" rule will create them from the I,I and J,J settings. The pair_modify {mix} value determines what formulas are used to compute the mixed coefficients. In each case, the cutoff distance is mixed the same way as sigma. Note that not all pair styles support mixing. Also, some mix options are not available for certain pair styles. See the doc page for individual pair styles for those restrictions. Note also that the "pair_coeff"_pair_coeff.html command also can be to directly set coefficients for a specific I != J pairing, in which case no mixing is performed. mix {geometric} epsilon_ij = sqrt(epsilon_i * epsilon_j) sigma_ij = sqrt(sigma_i * sigma_j) :pre mix {arithmetic} epsilon_ij = sqrt(epsilon_i * epsilon_j) sigma_ij = (sigma_i + sigma_j) / 2 :pre mix {sixthpower} epsilon_ij = (2 * sqrt(epsilon_i*epsilon_j) * sigma_i^3 * sigma_j^3) / (sigma_i^6 + sigma_j^6) sigma_ij = ((sigma_i**6 + sigma_j**6) / 2) ^ (1/6) :pre The {shift} keyword determines whether a Lennard-Jones potential is shifted at its cutoff to 0.0. If so, this adds an energy term to each pairwise interaction which will be included in the thermodynamic output, but does not affect pair forces or atom trajectories. See the doc page for individual pair styles to see which ones support this option. The {table} and {table/disp} keywords apply to pair styles with a long-range Coulombic term or long-range dispersion term respectively; see the doc page for individual styles to see which potentials support these options. If N is non-zero, a table of length 2^N is pre-computed for forces and energies, which can shrink their computational cost by up to a factor of 2. The table is indexed via a bit-mapping technique "(Wolff)"_#Wolff and a linear interpolation is performed between adjacent table values. In our experiments with different table styles (lookup, linear, spline), this method typically gave the best performance in terms of speed and accuracy. The choice of table length is a tradeoff in accuracy versus speed. A larger N yields more accurate force computations, but requires more memory which can slow down the computation due to cache misses. A reasonable value of N is between 8 and 16. The default value of 12 (table of length 4096) gives approximately the same accuracy as the no-table (N = 0) option. For N = 0, forces and energies are computed directly, using a polynomial fit for the needed erfc() function evaluation, which is what earlier versions of LAMMPS did. Values greater than 16 typically slow down the simulation and will not improve accuracy; values from 1 to 8 give unreliable results. The {tabinner} and {tabinner/disp} keywords set an inner cutoff above which the pairwise computation is done by table lookup (if tables are invoked), for the corresponding Coulombic and dispersion tables discussed with the {table} and {table/disp} keywords. The smaller the cutoff is set, the less accurate the table becomes (for a given number of table values), which can require use of larger tables. The default cutoff value is sqrt(2.0) distance units which means nearly all pairwise interactions are computed via table lookup for simulations with "real" units, but some close pairs may be computed directly (non-table) for simulations with "lj" units. When the {tail} keyword is set to {yes}, certain pair styles will add a long-range VanderWaals tail "correction" to the energy and pressure. These corrections are bookkeeping terms which do not affect dynamics, unless a constant-pressure simulation is being performed. See the doc page for individual styles to see which support this option. These corrections are included in the calculation and printing of thermodynamic quantities (see the "thermo_style"_thermo_style.html command). Their effect will also be included in constant NPT or NPH simulations where the pressure influences the simulation box dimensions (e.g. the "fix npt"_fix_nh.html and "fix nph"_fix_nh.html commands). The formulas used for the long-range corrections come from equation 5 of "(Sun)"_#Sun. NOTE: The tail correction terms are computed at the beginning of each run, using the current atom counts of each atom type. If atoms are deleted (or lost) or created during a simulation, e.g. via the "fix gcmc"_fix_gcmc.html command, the correction factors are not re-computed. If you expect the counts to change dramatically, you can break a run into a series of shorter runs so that the correction factors are re-computed more frequently. Several additional assumptions are inherent in using tail corrections, including the following: The simulated system is a 3d bulk homogeneous liquid. This option should not be used for systems that are non-liquid, 2d, have a slab geometry (only 2d periodic), or inhomogeneous. :ulb,l G(r), the radial distribution function (rdf), is unity beyond the cutoff, so a fairly large cutoff should be used (i.e. 2.5 sigma for an LJ fluid), and it is probably a good idea to verify this assumption by checking the rdf. The rdf is not exactly unity beyond the cutoff for each pair of interaction types, so the tail correction is necessarily an approximation. :l The tail corrections are computed at the beginning of each simulation run. If the number of atoms changes during the run, e.g. due to atoms leaving the simulation domain, or use of the "fix gcmc"_fix_gcmc.html command, then the corrections are not updates to relect the changed atom count. If this is a large effect in your simulation, you should break the long run into several short runs, so that the correction factors are re-computed multiple times. Thermophysical properties obtained from calculations with this option enabled will not be thermodynamically consistent with the truncated force-field that was used. In other words, atoms do not feel any LJ pair interactions beyond the cutoff, but the energy and pressure reported by the simulation include an estimated contribution from those interactions. :l,ule The {compute} keyword allows pairwise computations to be turned off, even though a "pair_style"_pair_style.html is defined. This is not useful for running a real simulation, but can be useful for debugging purposes or for performing a "rerun"_rerun.html simulation, when you only wish to compute partial forces that do not include the pairwise contribution. Two examples are as follows. First, this option allows you to perform a simulation with "pair_style hybrid"_pair_hybrid.html with only a subset of the hybrid sub-styles enabled. Second, this option allows you to perform a simulation with only long-range interactions but no short-range pairwise interactions. Doing this by simply not defining a pair style will not work, because the "kspace_style"_kspace_style.html command requires a Kspace-compatible pair style be defined. :line -Use of {special} keyword :h5 - The {special} keyword allows to override the 1-2, 1-3, and 1-4 exclusion settings for individual sub-styles of a "hybrid pair style"_pair_hybrid.html. It requires 4 arguments similar to the "special_bonds"_special_bonds.html command, {which} and wt1,wt2,wt3. The {which} argument can be {lj} to change the Lennard-Jones settings, {coul} to change the Coulombic settings, or {lj/coul} to change both to the same set of 3 values. The wt1,wt2,wt3 values are numeric weights from 0.0 to 1.0 inclusive, for the 1-2, 1-3, and 1-4 bond topology neighbors, respectively. The {special} keyword can only be used in conjunction with the {pair} keyword and has to directly follow it. NOTE: The global settings specified by the "special_bonds"_special_bonds.html command affect the construction of neighbor lists. Weights of 0.0 (for 1-2, 1-3, or 1-4 neighbors) exclude those pairs from the neighbor list entirely. Weights of 1.0 store the neighbor with no weighting applied. Thus only global values different from exactly 0.0 or 1.0 can be overridden and an error is generated if the requested setting is not compatible with the global setting. Substituting 1.0e-10 for 0.0 and 0.9999999999 for 1.0 is usually a sufficient workaround in this case without causing a significant error. :line [Restrictions:] none You cannot use {shift} yes with {tail} yes, since those are conflicting options. You cannot use {tail} yes with 2d simulations. [Related commands:] "pair_style"_pair_style.html, "pair_coeff"_pair_coeff.html, "thermo_style"_thermo_style.html [Default:] The option defaults are mix = geometric, shift = no, table = 12, tabinner = sqrt(2.0), tail = no, and compute = yes. Note that some pair styles perform mixing, but only a certain style of mixing. See the doc pages for individual pair styles for details. :line :link(Wolff) [(Wolff)] Wolff and Rudd, Comp Phys Comm, 120, 200-32 (1999). :link(Sun) [(Sun)] Sun, J Phys Chem B, 102, 7338-7364 (1998). diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt index 941cabd6d..06f15df87 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/tutorial_github.txt @@ -1,214 +1,214 @@ "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line -LAMMPS GitHub tutorial :h2 -written by Stefan Paquay :h3 +LAMMPS GitHub tutorial :h3 +[written by Stefan Paquay] :line -This document briefly describes how to use GitHub to merge changes -into LAMMPS using GitHub. It assumes that you are familiar with +This document briefly describes how to use GitHub to merge changes you +make into LAMMPS, using GitHub. It assumes that you are familiar with git. You may want to have a look at the "Git book"_http://git-scm.com/book/ to reacquaint yourself. :line -Making an account :h2 +[Making an account] First of all, you need a GitHub account. This is fairly simple, just go to "GitHub"_https://github.com and create an account by clicking the ``Sign up for GitHub'' button. Once your account is created, you can sign in by clicking the button in the top left and filling in your username or e-mail address and password. :line -Forking the repository :h2 +[Forking the repository] To get changes into LAMMPS, you need to first fork the repository. At the time of writing, LAMMPS-ICMS is the preferred fork. Go to "LAMMPS on GitHub"_https://github.com/lammps/lammps and make sure branch is set to ``lammps-icms'', see the figure below. :c,image(JPG/tutorial_branch.png) Now, click on fork in the top right corner: :c,image(JPG/tutorial_fork.png) This will create your own fork of the LAMMPS repository. You can make changes in this fork and later file {pull requests} to allow the upstream repository to merge changes from your own fork into the one we just forked from. At the same time, you can set things up, so you can include changes from upstream into your repository. :line -Adding changes to your own fork :h2 +[Adding changes to your own fork] Before adding changes, it is better to first create a new branch that will contain these changes, a so-called feature branch. -Feature branches :h3 +[Feature branches] Since LAMMPS is such a big project and most user contributions come in small portions, the most ideal workflow for LAMMPS is the so-called ``Feature branch'' workflow. It is explained in great detail here: "feature branch workflow"_https://www.atlassian.com/git/tutorials/comparing-workflows/feature-branch-workflow. The idea is that every new feature for LAMMPS gets its own branch. This way, it is fairly painless to incorporate new features into the upstream repository. I will explain briefly here how to do it. In this feature branch, I will add a USER-package. I assume that git is installed on the local machine and you know how to use a command line. First of all, you need to clone your own fork of LAMMPS: $ git clone https://github.com//lammps.git :pre You can find the proper url to the right of the "HTTPS" block, see figure. :c,image(JPG/tutorial_https_block.png) The above command copies (``clones'') the git repository to your local machine. You can use this local clone to make changes and test them without interfering with the repository on github. First, however, it is recommended to make a new branch for a particular feature you would like added to LAMMPS. In this example, I will try adding a new USER-package called USER-MANIFOLD. To create a new branch, run the following git command in your repository: $ git checkout -b add-user-manifold :pre The name of this new branch is "add-user-manifold" in my case. Just name it after something that resembles the feature you want added to LAMMPS. Now that you've changed branches, you can edit the files as you see fit, add new files, and commit as much as you would like. Just remember that if halfway you decide to add another, unrelated feature, you should switch branches! After everything is done, add the files to the branch and commit them: $ git add src/USER-MANIFOLD examples/USER/manifold/ $ git add doc/fix_nv{t,e}_manifold_rattle.txt $ git add doc/fix_manifoldforce.txt doc/user_manifolds.txt :pre After the files are added, the change should be comitted: $ git commit -m 'Added user-manifold package' :pre The "-m" switch is used to add a message to the commit. Use this to indicate what type of change was commited. -Wisdom by Axel: :h4 +[Wisdom by Axel] {"Do not use "git commit -a". the -a flag will automatically include *all* modified or new files. mercurial does that and it find it hugely annoying and often leading to accidental commits of files you don't want. use git add, git rm, git mv for adding, removing, renaming and then git commit to finalize the commit. personally, i find it very convenient to use the bundled gui for commits, i.e. git gui. typically, i will do git add and other operations, but then verify and review them with git gui. git gui also allows to do line-by-line unstaging and other convenient operations."} After the commit, the changes can be pushed to the same branch on GitHub: $ git push :pre Git will ask you for your user name and password on GitHub if you have not configured anything. If you correctly type your user name and password, the change should be added to your fork on GitHub. If you want to make really sure you push to the right repository (which is good practice), you can provide it explicitly: $ git push origin :pre or using an explicit URL: $ git push git@github.com:Pakketeretet2/lammps.git :pre After that, you can file a new pull request based on this branch. GitHub will now look like this: :c,image(JPG/tutorial_pull_request_feature_branch1.png) Make sure that the current branch is set to the correct one, which, in this case, is "add-user-manifold". Now click "New pull request". If done correctly, the only changes you will see are those that were made on this branch, so in my case, I will see nothing related to $\mathrm{pair\_dzugatov}.$ This will open up a new window that lists changes made to the repository. If you are just adding new files, there is not much to do, but I suppose merge conflicts are to be resolved here if there are changes in existing files. If all changes can automatically be merged, green text at the top will say so and you can click the "Create pull request" button, see image. :c,image(JPG/tutorial_pull_request2.png) After this you have to specify a short title and a comment with details about your pull request. I guess here you write what your modifications do and why they should be incorporated upstream. After that, click the "Create pull request" button, see image below. :c,image(JPG/tutorial_pull_request3.png) Now just write some nice comments, click "Comment", and that is it. It is now up to the maintainer(s) of the upstream repository to incorporate the changes into the repository and to close the pull request. :c,image(JPG/tutorial_pull_request4.png) :line -Additional changes :h2 +[Additional changes] Before the pull request is accepted, any additional changes you push into your repository will automatically become part of the pull request. :line -After a merge :h2 +[After a merge] When everything is fine the feature branch is merged into the LAMMPS repositories: :c,image(JPG/tutorial_merged.png) Now one question remains: What to do with the feature branch that got merged into upstream? It is in principle safe to delete them from your own fork. This helps keep it a bit more tidy. Note that you first have to switch to another branch! $ git checkout lammps-icms $ git pull lammps-icms $ git branch -d add-user-manifold :pre If you do not pull first, it is not really a problem but git will warn you at the next statement that you are deleting a local branch that was not yet fully merged into HEAD. This is because git does not yet know your branch just got merged into lammps-icms upstream. If you first delete and then pull, everything should still be fine. Finally, if you delete the branch locally, you might want to push this to your remote(s) as well: $ git push origin :add-user-manifold :pre diff --git a/examples/nb3b/MOH.nb3b.harmonic b/examples/nb3b/MOH.nb3b.harmonic index b30435933..9520767a4 100644 --- a/examples/nb3b/MOH.nb3b.harmonic +++ b/examples/nb3b/MOH.nb3b.harmonic @@ -1,21 +1,44 @@ # DATE: 2013-06-28 CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none # nb3b/harmonic (nonbonded 3-body harmonic) parameters for various elements # # multiple entries can be added to this file, LAMMPS reads the ones it needs # # these entries are in LAMMPS "real" units: # k [kcal/mol/rad^2], theta_0 [degrees], cutoff [Angstroms] # # format of a single entry (one or more lines): # element 1 (central atom), element 2, element 3, # k_theta, theta_0, cutoff # # (ijj)-->determines cutoff for i-j distance # (jik)-->determines k, theta_0 for i-j-k angle term # # ielem jelem kelem k theta_0 cutoff + O O O 0.00 0.00 0.00 + O O M 0.00 0.00 0.00 + O O H 0.00 0.00 0.00 O M M 0.00 0.00 2.80 - O H H 0.00 0.00 1.20 + O M O 0.00 0.00 0.00 O M H 6.35 120.00 0.00 + O H H 0.00 0.00 1.20 + O H O 0.00 0.00 0.00 O H M 6.35 120.00 0.00 + M M M 0.00 0.00 0.00 + M M H 0.00 0.00 0.00 + M M O 0.00 0.00 0.00 + M O O 0.00 0.00 2.80 + M O M 0.00 0.00 2.80 + M O H 6.35 120.00 0.00 + M H H 0.00 0.00 0.00 + M H M 0.00 0.00 0.00 + M H O 0.00 0.00 0.00 + H H H 0.00 0.00 0.00 + H H M 0.00 0.00 0.00 + H H O 0.00 0.00 0.00 + H O O 0.00 0.00 1.20 + H O H 0.00 0.00 1.20 + H O M 6.35 120.00 0.00 + H M M 0.00 0.00 0.00 + H M O 0.00 0.00 0.00 + H M H 0.00 0.00 0.00 diff --git a/potentials/MOH.nb3b.harmonic b/potentials/MOH.nb3b.harmonic index b30435933..1ff90675c 100644 --- a/potentials/MOH.nb3b.harmonic +++ b/potentials/MOH.nb3b.harmonic @@ -1,21 +1,44 @@ -# DATE: 2013-06-28 CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none +# DATE: 2016-07-29 CONTRIBUTOR: Todd Zeitler, tzeitle@sandia.gov CITATION: none # nb3b/harmonic (nonbonded 3-body harmonic) parameters for various elements # # multiple entries can be added to this file, LAMMPS reads the ones it needs # # these entries are in LAMMPS "real" units: # k [kcal/mol/rad^2], theta_0 [degrees], cutoff [Angstroms] # # format of a single entry (one or more lines): # element 1 (central atom), element 2, element 3, # k_theta, theta_0, cutoff # # (ijj)-->determines cutoff for i-j distance # (jik)-->determines k, theta_0 for i-j-k angle term # # ielem jelem kelem k theta_0 cutoff + O O O 0.00 0.00 0.00 + O O M 0.00 0.00 0.00 + O O H 0.00 0.00 0.00 O M M 0.00 0.00 2.80 - O H H 0.00 0.00 1.20 + O M O 0.00 0.00 0.00 O M H 6.35 120.00 0.00 + O H H 0.00 0.00 1.20 + O H O 0.00 0.00 0.00 O H M 6.35 120.00 0.00 + M M M 0.00 0.00 0.00 + M M H 0.00 0.00 0.00 + M M O 0.00 0.00 0.00 + M O O 0.00 0.00 2.80 + M O M 0.00 0.00 2.80 + M O H 6.35 120.00 0.00 + M H H 0.00 0.00 0.00 + M H M 0.00 0.00 0.00 + M H O 0.00 0.00 0.00 + H H H 0.00 0.00 0.00 + H H M 0.00 0.00 0.00 + H H O 0.00 0.00 0.00 + H O O 0.00 0.00 1.20 + H O H 0.00 0.00 1.20 + H O M 6.35 120.00 0.00 + H M M 0.00 0.00 0.00 + H M O 0.00 0.00 0.00 + H M H 0.00 0.00 0.00 diff --git a/src/KSPACE/ewald_disp.cpp b/src/KSPACE/ewald_disp.cpp index d51485880..49b7cde12 100644 --- a/src/KSPACE/ewald_disp.cpp +++ b/src/KSPACE/ewald_disp.cpp @@ -1,1483 +1,1501 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing authors: Pieter in 't Veld (SNL), Stan Moore (SNL) ------------------------------------------------------------------------- */ #include #include #include #include #include #include "ewald_disp.h" #include "math_vector.h" #include "math_const.h" #include "math_special.h" #include "atom.h" #include "comm.h" #include "force.h" #include "pair.h" #include "domain.h" #include "memory.h" #include "error.h" #include "update.h" using namespace LAMMPS_NS; using namespace MathConst; using namespace MathSpecial; #define SMALL 0.00001 enum{GEOMETRIC,ARITHMETIC,SIXTHPOWER}; // same as in pair.h //#define DEBUG /* ---------------------------------------------------------------------- */ EwaldDisp::EwaldDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg) { if (narg!=1) error->all(FLERR,"Illegal kspace_style ewald/n command"); ewaldflag = dispersionflag = dipoleflag = 1; accuracy_relative = fabs(force->numeric(FLERR,arg[0])); memset(function, 0, EWALD_NFUNCS*sizeof(int)); kenergy = kvirial = NULL; cek_local = cek_global = NULL; ekr_local = NULL; hvec = NULL; kvec = NULL; B = NULL; first_output = 0; energy_self_peratom = NULL; virial_self_peratom = NULL; nmax = 0; q2 = 0; b2 = 0; M2 = 0; } /* ---------------------------------------------------------------------- */ EwaldDisp::~EwaldDisp() { deallocate(); deallocate_peratom(); delete [] ekr_local; delete [] B; } /* --------------------------------------------------------------------- */ void EwaldDisp::init() { nkvec = nkvec_max = nevec = nevec_max = 0; nfunctions = nsums = sums = 0; nbox = -1; bytes = 0.0; if (!comm->me) { if (screen) fprintf(screen,"EwaldDisp initialization ...\n"); if (logfile) fprintf(logfile,"EwaldDisp initialization ...\n"); } triclinic_check(); if (domain->dimension == 2) error->all(FLERR,"Cannot use EwaldDisp with 2d simulation"); if (slabflag == 0 && domain->nonperiodic > 0) error->all(FLERR,"Cannot use nonperiodic boundaries with EwaldDisp"); if (slabflag == 1) { if (domain->xperiodic != 1 || domain->yperiodic != 1 || domain->boundary[2][0] != 1 || domain->boundary[2][1] != 1) error->all(FLERR,"Incorrect boundaries with slab EwaldDisp"); } scale = 1.0; mumurd2e = force->qqrd2e; dielectric = force->dielectric; int tmp; Pair *pair = force->pair; int *ptr = pair ? (int *) pair->extract("ewald_order",tmp) : NULL; double *cutoff = pair ? (double *) pair->extract("cut_coul",tmp) : NULL; if (!(ptr||cutoff)) error->all(FLERR,"KSpace style is incompatible with Pair style"); int ewald_order = ptr ? *((int *) ptr) : 1<<1; int ewald_mix = ptr ? *((int *) pair->extract("ewald_mix",tmp)) : GEOMETRIC; memset(function, 0, EWALD_NFUNCS*sizeof(int)); for (int i=0; i<=EWALD_NORDER; ++i) // transcribe order if (ewald_order&(1<all(FLERR, "Unsupported mixing rule in kspace_style ewald/disp"); default: error->all(FLERR,"Unsupported order in kspace_style ewald/disp"); } nfunctions += function[k] = 1; nsums += n[k]; } if (!gewaldflag) g_ewald = 0.0; pair->init(); // so B is defined init_coeffs(); init_coeff_sums(); if (function[0]) qsum_qsq(); natoms_original = atom->natoms; // turn off coulombic if no charge if (function[0] && qsqsum == 0.0) { function[0] = 0; nfunctions -= 1; nsums -= 1; } double bsbsum = 0.0; if (function[1]) bsbsum = sum[1].x2; if (function[2]) bsbsum = sum[2].x2; if (function[3]) M2 = sum[9].x2; if (function[3] && strcmp(update->unit_style,"electron") == 0) error->all(FLERR,"Cannot (yet) use 'electron' units with dipoles"); if (qsqsum == 0.0 && bsbsum == 0.0 && M2 == 0.0) error->all(FLERR,"Cannot use Ewald/disp solver " "on system with no charge, dipole, or LJ particles"); if (fabs(qsum) > SMALL && comm->me == 0) { char str[128]; sprintf(str,"System is not charge neutral, net charge = %g",qsum); error->warning(FLERR,str); } if (!function[1] && !function[2]) dispersionflag = 0; if (!function[3]) dipoleflag = 0; pair_check(); // set accuracy (force units) from accuracy_relative or accuracy_absolute if (accuracy_absolute >= 0.0) accuracy = accuracy_absolute; else accuracy = accuracy_relative * two_charge_force; // setup K-space resolution q2 = qsqsum * force->qqrd2e; M2 *= mumurd2e; b2 = bsbsum; //Are these units right? bigint natoms = atom->natoms; if (!gewaldflag) { if (function[0]) { g_ewald = accuracy*sqrt(natoms*(*cutoff)*shape_det(domain->h)) / (2.0*q2); if (g_ewald >= 1.0) g_ewald = (1.35 - 0.15*log(accuracy))/(*cutoff); else g_ewald = sqrt(-log(g_ewald)) / (*cutoff); } else if (function[1] || function[2]) { //Try Newton Solver //Use old method to get guess g_ewald = (1.35 - 0.15*log(accuracy))/ *cutoff; double g_ewald_new = NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),b2); if (g_ewald_new > 0.0) g_ewald = g_ewald_new; else error->warning(FLERR,"Ewald/disp Newton solver failed, " "using old method to estimate g_ewald"); } else if (function[3]) { //Try Newton Solver //Use old method to get guess g_ewald = (1.35 - 0.15*log(accuracy))/ *cutoff; double g_ewald_new = NewtonSolve(g_ewald,(*cutoff),natoms,shape_det(domain->h),M2); if (g_ewald_new > 0.0) g_ewald = g_ewald_new; else error->warning(FLERR,"Ewald/disp Newton solver failed, " "using old method to estimate g_ewald"); } } if (!comm->me) { if (screen) fprintf(screen, " G vector = %g\n", g_ewald); if (logfile) fprintf(logfile, " G vector = %g\n", g_ewald); } g_ewald_6 = g_ewald; deallocate_peratom(); peratom_allocate_flag = 0; } /* ---------------------------------------------------------------------- adjust EwaldDisp coeffs, called initially and whenever volume has changed ------------------------------------------------------------------------- */ void EwaldDisp::setup() { volume = shape_det(domain->h)*slab_volfactor; memcpy(unit, domain->h_inv, sizeof(shape)); shape_scalar_mult(unit, 2.0*MY_PI); unit[2] /= slab_volfactor; // int nbox_old = nbox, nkvec_old = nkvec; if (accuracy >= 1) { nbox = 0; error->all(FLERR,"KSpace accuracy too low"); } bigint natoms = atom->natoms; double err; int kxmax = 1; int kymax = 1; int kzmax = 1; err = rms(kxmax,domain->h[0],natoms,q2,b2,M2); while (err > accuracy) { kxmax++; err = rms(kxmax,domain->h[0],natoms,q2,b2,M2); } err = rms(kymax,domain->h[1],natoms,q2,b2,M2); while (err > accuracy) { kymax++; err = rms(kymax,domain->h[1],natoms,q2,b2,M2); } err = rms(kzmax,domain->h[2]*slab_volfactor,natoms,q2,b2,M2); while (err > accuracy) { kzmax++; err = rms(kzmax,domain->h[2]*slab_volfactor,natoms,q2,b2,M2); } nbox = MAX(kxmax,kymax); nbox = MAX(nbox,kzmax); double gsqxmx = unit[0]*unit[0]*kxmax*kxmax; double gsqymx = unit[1]*unit[1]*kymax*kymax; double gsqzmx = unit[2]*unit[2]*kzmax*kzmax; gsqmx = MAX(gsqxmx,gsqymx); gsqmx = MAX(gsqmx,gsqzmx); gsqmx *= 1.00001; reallocate(); coefficients(); init_coeffs(); init_coeff_sums(); init_self(); if (!(first_output||comm->me)) { first_output = 1; if (screen) fprintf(screen, " vectors: nbox = %d, nkvec = %d\n", nbox, nkvec); if (logfile) fprintf(logfile, " vectors: nbox = %d, nkvec = %d\n", nbox, nkvec); } } /* ---------------------------------------------------------------------- compute RMS accuracy for a dimension ------------------------------------------------------------------------- */ double EwaldDisp::rms(int km, double prd, bigint natoms, double q2, double b2, double M2) { double value = 0.0; // Coulombic double g2 = g_ewald*g_ewald; value += 2.0*q2*g_ewald/prd * sqrt(1.0/(MY_PI*km*natoms)) * exp(-MY_PI*MY_PI*km*km/(g2*prd*prd)); // Lennard-Jones double g7 = g2*g2*g2*g_ewald; value += 4.0*b2*g7/3.0 * sqrt(1.0/(MY_PI*natoms)) * (exp(-MY_PI*MY_PI*km*km/(g2*prd*prd)) * (MY_PI*km/(g_ewald*prd) + 1)); // dipole value += 8.0*MY_PI*M2/volume*g_ewald * sqrt(2.0*MY_PI*km*km*km/(15.0*natoms)) * exp(-pow(MY_PI*km/(g_ewald*prd),2.0)); return value; } void EwaldDisp::reallocate() { int ix, iy, iz; int nkvec_max = nkvec; vector h; nkvec = 0; int *kflag = new int[(nbox+1)*(2*nbox+1)*(2*nbox+1)]; int *flag = kflag; for (ix=0; ix<=nbox; ++ix) for (iy=-nbox; iy<=nbox; ++iy) for (iz=-nbox; iz<=nbox; ++iz) if (!(ix||iy||iz)) *(flag++) = 0; else if ((!ix)&&(iy<0)) *(flag++) = 0; else if ((!(ix||iy))&&(iz<0)) *(flag++) = 0; // use symmetry else { h[0] = unit[0]*ix; h[1] = unit[5]*ix+unit[1]*iy; h[2] = unit[4]*ix+unit[3]*iy+unit[2]*iz; if ((*(flag++) = h[0]*h[0]+h[1]*h[1]+h[2]*h[2]<=gsqmx)) ++nkvec; } if (nkvec>nkvec_max) { deallocate(); // free memory hvec = new hvector[nkvec]; // hvec bytes += (nkvec-nkvec_max)*sizeof(hvector); kvec = new kvector[nkvec]; // kvec bytes += (nkvec-nkvec_max)*sizeof(kvector); kenergy = new double[nkvec*nfunctions]; // kenergy bytes += (nkvec-nkvec_max)*nfunctions*sizeof(double); kvirial = new double[6*nkvec*nfunctions]; // kvirial bytes += 6*(nkvec-nkvec_max)*nfunctions*sizeof(double); cek_local = new complex[nkvec*nsums]; // cek_local bytes += (nkvec-nkvec_max)*nsums*sizeof(complex); cek_global = new complex[nkvec*nsums]; // cek_global bytes += (nkvec-nkvec_max)*nsums*sizeof(complex); nkvec_max = nkvec; } flag = kflag; // create index and kvector *k = kvec; // wave vectors hvector *hi = hvec; for (ix=0; ix<=nbox; ++ix) for (iy=-nbox; iy<=nbox; ++iy) for (iz=-nbox; iz<=nbox; ++iz) if (*(flag++)) { hi->x = unit[0]*ix; hi->y = unit[5]*ix+unit[1]*iy; (hi++)->z = unit[4]*ix+unit[3]*iy+unit[2]*iz; k->x = ix+nbox; k->y = iy+nbox; (k++)->z = iz+nbox; } delete [] kflag; } +/* ---------------------------------------------------------------------- */ void EwaldDisp::reallocate_atoms() { if (eflag_atom || vflag_atom) if (atom->nmax > nmax) { deallocate_peratom(); allocate_peratom(); nmax = atom->nmax; } if ((nevec = atom->nmax*(2*nbox+1))<=nevec_max) return; delete [] ekr_local; ekr_local = new cvector[nevec]; bytes += (nevec-nevec_max)*sizeof(cvector); nevec_max = nevec; } +/* ---------------------------------------------------------------------- */ void EwaldDisp::allocate_peratom() { memory->create(energy_self_peratom, atom->nmax,EWALD_NFUNCS,"ewald/n:energy_self_peratom"); memory->create(virial_self_peratom, atom->nmax,EWALD_NFUNCS,"ewald/n:virial_self_peratom"); } +/* ---------------------------------------------------------------------- */ void EwaldDisp::deallocate_peratom() // free memory { if (energy_self_peratom) { memory->destroy(energy_self_peratom); energy_self_peratom = NULL; } if (virial_self_peratom) { memory->destroy(virial_self_peratom); virial_self_peratom = NULL; } } +/* ---------------------------------------------------------------------- */ void EwaldDisp::deallocate() // free memory { delete [] hvec; hvec = NULL; delete [] kvec; kvec = NULL; delete [] kenergy; kenergy = NULL; delete [] kvirial; kvirial = NULL; delete [] cek_local; cek_local = NULL; delete [] cek_global; cek_global = NULL; } +/* ---------------------------------------------------------------------- */ void EwaldDisp::coefficients() { vector h; hvector *hi = hvec, *nh; double eta2 = 0.25/(g_ewald*g_ewald); double b1, b2, expb2, h1, h2, c1, c2; double *ke = kenergy, *kv = kvirial; int func0 = function[0], func12 = function[1]||function[2], func3 = function[3]; for (nh = (hi = hvec)+nkvec; hintypes; if (function[1]) { // geometric 1/r^6 double **b = (double **) force->pair->extract("B",tmp); delete [] B; B = new double[n+1]; bytes += (n+1)*sizeof(double); for (int i=0; i<=n; ++i) B[i] = sqrt(fabs(b[i][i])); } if (function[2]) { // arithmetic 1/r^6 double **epsilon = (double **) force->pair->extract("epsilon",tmp); double **sigma = (double **) force->pair->extract("sigma",tmp); double eps_i, sigma_i, sigma_n, *bi = B = new double[7*n+7]; double c[7] = { 1.0, sqrt(6.0), sqrt(15.0), sqrt(20.0), sqrt(15.0), sqrt(6.0), 1.0}; if (!(epsilon&&sigma)) error->all( FLERR,"Epsilon or sigma reference not set by pair style in ewald/n"); for (int i=0; i<=n; ++i) { eps_i = sqrt(epsilon[i][i]); sigma_i = sigma[i][i]; sigma_n = 1.0; for (int j=0; j<7; ++j) { *(bi++) = sigma_n*eps_i*c[j]; sigma_n *= sigma_i; } } } } +/* ---------------------------------------------------------------------- */ + void EwaldDisp::init_coeff_sums() { if (sums) return; // calculated only once sums = 1; Sum sum_local[EWALD_MAX_NSUMS]; memset(sum_local, 0, EWALD_MAX_NSUMS*sizeof(Sum)); // now perform qsum and qsq via parent qsum_qsq() sum_local[0].x = 0.0; sum_local[0].x2 = 0.0; //if (function[0]) { // 1/r // double *q = atom->q, *qn = q+atom->nlocal; // for (double *i=q; itype, *ntype = type+atom->nlocal; for (int *i=type; itype, *ntype = type+atom->nlocal; for (int *i=type; imu) { // dipole double *mu = atom->mu[0], *nmu = mu+4*atom->nlocal; for (double *i = mu; i < nmu; i += 4) sum_local[9].x2 += i[3]*i[3]; } MPI_Allreduce(sum_local, sum, 2*EWALD_MAX_NSUMS, MPI_DOUBLE, MPI_SUM, world); } +/* ---------------------------------------------------------------------- */ void EwaldDisp::init_self() { double g1 = g_ewald, g2 = g1*g1, g3 = g1*g2; const double qscale = force->qqrd2e * scale; memset(energy_self, 0, EWALD_NFUNCS*sizeof(double)); // self energy memset(virial_self, 0, EWALD_NFUNCS*sizeof(double)); if (function[0]) { // 1/r virial_self[0] = -0.5*MY_PI*qscale/(g2*volume)*qsum*qsum; energy_self[0] = qsqsum*qscale*g1/MY_PIS-virial_self[0]; } if (function[1]) { // geometric 1/r^6 virial_self[1] = MY_PI*MY_PIS*g3/(6.0*volume)*sum[1].x*sum[1].x; energy_self[1] = -sum[1].x2*g3*g3/12.0+virial_self[1]; } if (function[2]) { // arithmetic 1/r^6 virial_self[2] = MY_PI*MY_PIS*g3/(48.0*volume)*(sum[2].x*sum[8].x+ sum[3].x*sum[7].x+sum[4].x*sum[6].x+0.5*sum[5].x*sum[5].x); energy_self[2] = -sum[2].x2*g3*g3/3.0+virial_self[2]; } if (function[3]) { // dipole virial_self[3] = 0; // in surface energy_self[3] = sum[9].x2*mumurd2e*2.0*g3/3.0/MY_PIS-virial_self[3]; } } +/* ---------------------------------------------------------------------- */ void EwaldDisp::init_self_peratom() { if (!(vflag_atom || eflag_atom)) return; double g1 = g_ewald, g2 = g1*g1, g3 = g1*g2; const double qscale = force->qqrd2e * scale; double *energy = energy_self_peratom[0]; double *virial = virial_self_peratom[0]; int nlocal = atom->nlocal; memset(energy, 0, EWALD_NFUNCS*nlocal*sizeof(double)); memset(virial, 0, EWALD_NFUNCS*nlocal*sizeof(double)); if (function[0]) { // 1/r double *ei = energy; double *vi = virial; double ce = qscale*g1/MY_PIS; double cv = -0.5*MY_PI*qscale/(g2*volume); double *qi = atom->q, *qn = qi + nlocal; for (; qi < qn; qi++, vi += EWALD_NFUNCS, ei += EWALD_NFUNCS) { double q = *qi; *vi = cv*q*qsum; *ei = ce*q*q-vi[0]; } } if (function[1]) { // geometric 1/r^6 double *ei = energy+1; double *vi = virial+1; double ce = -g3*g3/12.0; double cv = MY_PI*MY_PIS*g3/(6.0*volume); int *typei = atom->type, *typen = typei + atom->nlocal; for (; typei < typen; typei++, vi += EWALD_NFUNCS, ei += EWALD_NFUNCS) { double b = B[*typei]; *vi = cv*b*sum[1].x; *ei = ce*b*b+vi[0]; } } if (function[2]) { // arithmetic 1/r^6 double *bi; double *ei = energy+2; double *vi = virial+2; double ce = -g3*g3/3.0; double cv = 0.5*MY_PI*MY_PIS*g3/(48.0*volume); int *typei = atom->type, *typen = typei + atom->nlocal; for (; typei < typen; typei++, vi += EWALD_NFUNCS, ei += EWALD_NFUNCS) { bi = B+7*typei[0]+7; for (int k=2; k<9; ++k) *vi += cv*sum[k].x*(--bi)[0]; /* PJV 20120225: should this be this instead? above implies an inverse dependence seems to be the above way in original; i recall having tested arithmetic mixing in the conception phase, but an extra test would be prudent (pattern repeats in multiple functions below) bi = B+7*typei[0]; for (int k=2; k<9; ++k) *vi += cv*sum[k].x*(bi++)[0]; */ *ei = ce*bi[0]*bi[6]+vi[0]; } } if (function[3]&&atom->mu) { // dipole double *ei = energy+3; double *vi = virial+3; double *imu = atom->mu[0], *nmu = imu+4*atom->nlocal; double ce = mumurd2e*2.0*g3/3.0/MY_PIS; for (; imu < nmu; imu += 4, vi += EWALD_NFUNCS, ei += EWALD_NFUNCS) { *vi = 0; // in surface *ei = ce*imu[3]*imu[3]-vi[0]; } } } - /* ---------------------------------------------------------------------- compute the EwaldDisp long-range force, energy, virial ------------------------------------------------------------------------- */ void EwaldDisp::compute(int eflag, int vflag) { if (!nbox) return; // set energy/virial flags // invoke allocate_peratom() if needed for first time if (eflag || vflag) ev_setup(eflag,vflag); else evflag = eflag_global = vflag_global = eflag_atom = vflag_atom = 0; if (!peratom_allocate_flag && (eflag_atom || vflag_atom)) { allocate_peratom(); peratom_allocate_flag = 1; nmax = atom->nmax; } reallocate_atoms(); init_self_peratom(); compute_ek(); compute_force(); //compute_surface(); // assume conducting metal (tinfoil) boundary conditions // update qsum and qsqsum, if atom count has changed and energy needed if ((eflag_global || eflag_atom) && atom->natoms != natoms_original) { if (function[0]) qsum_qsq(); natoms_original = atom->natoms; } compute_energy(); compute_energy_peratom(); compute_virial(); compute_virial_dipole(); compute_virial_peratom(); } void EwaldDisp::compute_ek() { cvector *ekr = ekr_local; int lbytes = (2*nbox+1)*sizeof(cvector); hvector *h = NULL; kvector *k, *nk = kvec+nkvec; cvector *z = new cvector[2*nbox+1]; cvector z1, *zx, *zy, *zz, *zn = z+2*nbox; complex *cek, zxyz, zxy = COMPLEX_NULL, cx = COMPLEX_NULL; vector mui; double *x = atom->x[0], *xn = x+3*atom->nlocal, *q = atom->q, qi = 0.0; double bi = 0.0, ci[7]; double *mu = atom->mu ? atom->mu[0] : NULL; int i, kx, ky, n = nkvec*nsums, *type = atom->type, tri = domain->triclinic; int func[EWALD_NFUNCS]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); memset(cek_local, 0, n*sizeof(complex)); // reset sums while (xx, 1, 0); C_SET(zz->y, 1, 0); C_SET(zz->z, 1, 0); // z[0] if (tri) { // triclinic z[1] C_ANGLE(z1.x, unit[0]*x[0]+unit[5]*x[1]+unit[4]*x[2]); C_ANGLE(z1.y, unit[1]*x[1]+unit[3]*x[2]); C_ANGLE(z1.z, x[2]*unit[2]); x += 3; } else { // orthogonal z[1] C_ANGLE(z1.x, *(x++)*unit[0]); C_ANGLE(z1.y, *(x++)*unit[1]); C_ANGLE(z1.z, *(x++)*unit[2]); } for (; zzx, zz->x, z1.x); // 3D k-vector C_RMULT(zy->y, zz->y, z1.y); C_CONJ(zx->y, zy->y); C_RMULT(zy->z, zz->z, z1.z); C_CONJ(zx->z, zy->z); } kx = ky = -1; cek = cek_local; if (func[0]) qi = *(q++); if (func[1]) bi = B[*type]; if (func[2]) memcpy(ci, B+7*type[0], 7*sizeof(double)); if (func[3]) { memcpy(mui, mu, sizeof(vector)); mu += 4; h = hvec; } for (k=kvec; ky) { // based on order in if (kx!=k->x) cx = z[kx = k->x].x; // reallocate C_RMULT(zxy, z[ky = k->y].y, cx); } C_RMULT(zxyz, z[k->z].z, zxy); if (func[0]) { cek->re += zxyz.re*qi; (cek++)->im += zxyz.im*qi; } if (func[1]) { cek->re += zxyz.re*bi; (cek++)->im += zxyz.im*bi; } if (func[2]) for (i=0; i<7; ++i) { cek->re += zxyz.re*ci[i]; (cek++)->im += zxyz.im*ci[i]; } if (func[3]) { register double muk = mui[0]*h->x+mui[1]*h->y+mui[2]*h->z; ++h; cek->re += zxyz.re*muk; (cek++)->im += zxyz.im*muk; } } ekr = (cvector *) ((char *) memcpy(ekr, z, lbytes)+lbytes); ++type; } MPI_Allreduce(cek_local, cek_global, 2*n, MPI_DOUBLE, MPI_SUM, world); delete [] z; } +/* ---------------------------------------------------------------------- */ void EwaldDisp::compute_force() { kvector *k; hvector *h, *nh; cvector *z = ekr_local; vector sum[EWALD_MAX_NSUMS], mui = COMPLEX_NULL; complex *cek, zc, zx = COMPLEX_NULL, zxy = COMPLEX_NULL; complex *cek_coul; double *f = atom->f[0], *fn = f+3*atom->nlocal, *q = atom->q, *t = NULL; double *mu = atom->mu ? atom->mu[0] : NULL; const double qscale = force->qqrd2e * scale; double *ke, c[EWALD_NFUNCS] = { 8.0*MY_PI*qscale/volume, 2.0*MY_PI*MY_PIS/(12.0*volume), 2.0*MY_PI*MY_PIS/(192.0*volume), 8.0*MY_PI*mumurd2e/volume}; int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type; int func[EWALD_NFUNCS]; if (atom->torque) t = atom->torque[0]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); memset(sum, 0, EWALD_MAX_NSUMS*sizeof(vector)); // fj = -dE/dr = for (; fy) { // based on order in if (kx!=k->x) zx = z[kx = k->x].x; // reallocate C_RMULT(zxy, z[ky = k->y].y, zx); } C_CRMULT(zc, z[k->z].z, zxy); if (func[0]) { // 1/r register double im = *(ke++)*(zc.im*cek->re+cek->im*zc.re); if (func[3]) cek_coul = cek; ++cek; sum[0][0] += h->x*im; sum[0][1] += h->y*im; sum[0][2] += h->z*im; } if (func[1]) { // geometric 1/r^6 register double im = *(ke++)*(zc.im*cek->re+cek->im*zc.re); ++cek; sum[1][0] += h->x*im; sum[1][1] += h->y*im; sum[1][2] += h->z*im; } if (func[2]) { // arithmetic 1/r^6 register double im, c = *(ke++); for (i=2; i<9; ++i) { im = c*(zc.im*cek->re+cek->im*zc.re); ++cek; sum[i][0] += h->x*im; sum[i][1] += h->y*im; sum[i][2] += h->z*im; } } if (func[3]) { // dipole register double im = *(ke)*(zc.im*cek->re+ cek->im*zc.re)*(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); register double im2 = *(ke)*(zc.re*cek->re- cek->im*zc.im); sum[9][0] += h->x*im; sum[9][1] += h->y*im; sum[9][2] += h->z*im; t[0] += -mui[1]*h->z*im2 + mui[2]*h->y*im2; // torque t[1] += -mui[2]*h->x*im2 + mui[0]*h->z*im2; t[2] += -mui[0]*h->y*im2 + mui[1]*h->x*im2; if (func[0]) { // charge-dipole register double qi = *(q)*c[0]; im = - *(ke)*(zc.re*cek_coul->re - cek_coul->im*zc.im)*(mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); im += *(ke)*(zc.re*cek->re - cek->im*zc.im)*qi; sum[9][0] += h->x*im; sum[9][1] += h->y*im; sum[9][2] += h->z*im; im2 = *(ke)*(zc.re*cek_coul->im + cek_coul->re*zc.im); im2 += -*(ke)*(zc.re*cek->im - cek->im*zc.re); t[0] += -mui[1]*h->z*im2 + mui[2]*h->y*im2; // torque t[1] += -mui[2]*h->x*im2 + mui[0]*h->z*im2; t[2] += -mui[0]*h->y*im2 + mui[1]*h->x*im2; } ++cek; ke++; } } if (func[0]) { // 1/r register double qi = *(q++)*c[0]; f[0] -= sum[0][0]*qi; f[1] -= sum[0][1]*qi; f[2] -= sum[0][2]*qi; } if (func[1]) { // geometric 1/r^6 register double bi = B[*type]*c[1]; f[0] -= sum[1][0]*bi; f[1] -= sum[1][1]*bi; f[2] -= sum[1][2]*bi; } if (func[2]) { // arithmetic 1/r^6 register double *bi = B+7*type[0]+7; for (i=2; i<9; ++i) { register double c2 = (--bi)[0]*c[2]; f[0] -= sum[i][0]*c2; f[1] -= sum[i][1]*c2; f[2] -= sum[i][2]*c2; } } if (func[3]) { // dipole f[0] -= sum[9][0]; f[1] -= sum[9][1]; f[2] -= sum[9][2]; } z = (cvector *) ((char *) z+lbytes); ++type; t += 3; } } +/* ---------------------------------------------------------------------- */ void EwaldDisp::compute_surface() { // assume conducting metal (tinfoil) boundary conditions, so this function is // not called because dielectric at the boundary --> infinity, which makes all // the terms here zero. if (!function[3]) return; if (!atom->mu) return; vector sum_local = VECTOR_NULL, sum_total; memset(sum_local, 0, sizeof(vector)); double *i, *n, *mu = atom->mu[0]; for (n = (i = mu) + 4*atom->nlocal; i < n; ++i) { sum_local[0] += (i++)[0]; sum_local[1] += (i++)[0]; sum_local[2] += (i++)[0]; } MPI_Allreduce(sum_local, sum_total, 3, MPI_DOUBLE, MPI_SUM, world); virial_self[3] = mumurd2e*(2.0*MY_PI*vec_dot(sum_total,sum_total)/(2.0*dielectric+1)/volume); energy_self[3] -= virial_self[3]; if (!(vflag_atom || eflag_atom)) return; double *ei = energy_self_peratom[0]+3; double *vi = virial_self_peratom[0]+3; double cv = 2.0*mumurd2e*MY_PI/(2.0*dielectric+1)/volume; for (i = mu; i < n; i += 4, ei += EWALD_NFUNCS, vi += EWALD_NFUNCS) { *vi = cv*(i[0]*sum_total[0]+i[1]*sum_total[1]+i[2]*sum_total[2]); *ei -= *vi; } } +/* ---------------------------------------------------------------------- */ void EwaldDisp::compute_energy() { energy = 0.0; if (!eflag_global) return; complex *cek = cek_global; complex *cek_coul; double *ke = kenergy; const double qscale = force->qqrd2e * scale; double c[EWALD_NFUNCS] = { 4.0*MY_PI*qscale/volume, 2.0*MY_PI*MY_PIS/(24.0*volume), 2.0*MY_PI*MY_PIS/(192.0*volume), 4.0*MY_PI*mumurd2e/volume}; double sum[EWALD_NFUNCS]; int func[EWALD_NFUNCS]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); memset(sum, 0, EWALD_NFUNCS*sizeof(double)); // reset sums for (int k=0; kre*cek->re+cek->im*cek->im); if (func[3]) cek_coul = cek; ++cek; } if (func[1]) { // geometric 1/r^6 sum[1] += *(ke++)*(cek->re*cek->re+cek->im*cek->im); ++cek; } if (func[2]) { // arithmetic 1/r^6 register double r = (cek[0].re*cek[6].re+cek[0].im*cek[6].im)+ (cek[1].re*cek[5].re+cek[1].im*cek[5].im)+ (cek[2].re*cek[4].re+cek[2].im*cek[4].im)+ 0.5*(cek[3].re*cek[3].re+cek[3].im*cek[3].im); cek += 7; sum[2] += *(ke++)*r; } if (func[3]) { // dipole sum[3] += *(ke)*(cek->re*cek->re+cek->im*cek->im); if (func[0]) { // charge-dipole sum[3] += *(ke)*2.0*(cek->re*cek_coul->im - cek->im*cek_coul->re); } ke++; ++cek; } } for (int k=0; kq; double *eatomj = eatom; double *mu = atom->mu ? atom->mu[0] : NULL; const double qscale = force->qqrd2e * scale; double *ke = kenergy; double c[EWALD_NFUNCS] = { 4.0*MY_PI*qscale/volume, 2.0*MY_PI*MY_PIS/(24.0*volume), 2.0*MY_PI*MY_PIS/(192.0*volume), 4.0*MY_PI*mumurd2e/volume}; int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type; int func[EWALD_NFUNCS]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); for (int j = 0; j < atom->nlocal; j++, ++eatomj) { k = kvec; kx = ky = -1; ke = kenergy; cek = cek_global; memset(sum, 0, EWALD_MAX_NSUMS*sizeof(double)); if (func[3]) { register double di = c[3]; mui[0] = di*(mu++)[0]; mui[1] = di*(mu++)[0]; mui[2] = di*(mu++)[0]; mu++; } for (nh = (h = hvec)+nkvec; hy) { // based on order in if (kx!=k->x) zx = z[kx = k->x].x; // reallocate C_RMULT(zxy, z[ky = k->y].y, zx); } C_CRMULT(zc, z[k->z].z, zxy); if (func[0]) { // 1/r sum[0] += *(ke++)*(cek->re*zc.re - cek->im*zc.im); if (func[3]) cek_coul = cek; ++cek; } if (func[1]) { // geometric 1/r^6 sum[1] += *(ke++)*(cek->re*zc.re - cek->im*zc.im); ++cek; } if (func[2]) { // arithmetic 1/r^6 register double im, c = *(ke++); for (i=2; i<9; ++i) { im = c*(cek->re*zc.re - cek->im*zc.im); ++cek; sum[i] += im; } } if (func[3]) { // dipole double muk = (mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); sum[9] += *(ke)*(cek->re*zc.re - cek->im*zc.im)*muk; if (func[0]) { // charge-dipole register double qj = *(q)*c[0]; sum[9] += *(ke)*(cek_coul->im*zc.re + cek_coul->re*zc.im)*muk; sum[9] -= *(ke)*(cek->re*zc.im + cek->im*zc.re)*qj; } ++cek; ke++; } } if (func[0]) { // 1/r register double qj = *(q++)*c[0]; *eatomj += sum[0]*qj - energy_self_peratom[j][0]; } if (func[1]) { // geometric 1/r^6 register double bj = B[*type]*c[1]; *eatomj += sum[1]*bj - energy_self_peratom[j][1]; } if (func[2]) { // arithmetic 1/r^6 register double *bj = B+7*type[0]+7; for (i=2; i<9; ++i) { register double c2 = (--bj)[0]*c[2]; *eatomj += 0.5*sum[i]*c2; } *eatomj -= energy_self_peratom[j][2]; } if (func[3]) { // dipole *eatomj += sum[9] - energy_self_peratom[j][3]; } z = (cvector *) ((char *) z+lbytes); ++type; } } +/* ---------------------------------------------------------------------- */ #define swap(a, b) { register double t = a; a= b; b = t; } void EwaldDisp::compute_virial() { memset(virial, 0, sizeof(shape)); if (!vflag_global) return; complex *cek = cek_global; complex *cek_coul; double *kv = kvirial; const double qscale = force->qqrd2e * scale; double c[EWALD_NFUNCS] = { 4.0*MY_PI*qscale/volume, 2.0*MY_PI*MY_PIS/(24.0*volume), 2.0*MY_PI*MY_PIS/(192.0*volume), 4.0*MY_PI*mumurd2e/volume}; shape sum[EWALD_NFUNCS]; int func[EWALD_NFUNCS]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); memset(sum, 0, EWALD_NFUNCS*sizeof(shape)); for (int k=0; kre*cek->re+cek->im*cek->im; if (func[3]) cek_coul = cek; ++cek; sum[0][0] += *(kv++)*r; sum[0][1] += *(kv++)*r; sum[0][2] += *(kv++)*r; sum[0][3] += *(kv++)*r; sum[0][4] += *(kv++)*r; sum[0][5] += *(kv++)*r; } if (func[1]) { // geometric 1/r^6 register double r = cek->re*cek->re+cek->im*cek->im; ++cek; sum[1][0] += *(kv++)*r; sum[1][1] += *(kv++)*r; sum[1][2] += *(kv++)*r; sum[1][3] += *(kv++)*r; sum[1][4] += *(kv++)*r; sum[1][5] += *(kv++)*r; } if (func[2]) { // arithmetic 1/r^6 register double r = (cek[0].re*cek[6].re+cek[0].im*cek[6].im)+ (cek[1].re*cek[5].re+cek[1].im*cek[5].im)+ (cek[2].re*cek[4].re+cek[2].im*cek[4].im)+ 0.5*(cek[3].re*cek[3].re+cek[3].im*cek[3].im); cek += 7; sum[2][0] += *(kv++)*r; sum[2][1] += *(kv++)*r; sum[2][2] += *(kv++)*r; sum[2][3] += *(kv++)*r; sum[2][4] += *(kv++)*r; sum[2][5] += *(kv++)*r; } if (func[3]) { register double r = cek->re*cek->re+cek->im*cek->im; sum[3][0] += *(kv++)*r; sum[3][1] += *(kv++)*r; sum[3][2] += *(kv++)*r; sum[3][3] += *(kv++)*r; sum[3][4] += *(kv++)*r; sum[3][5] += *(kv++)*r; if (func[0]) { // charge-dipole kv -= 6; register double r = 2.0*(cek->re*cek_coul->im - cek->im*cek_coul->re); sum[3][0] += *(kv++)*r; sum[3][1] += *(kv++)*r; sum[3][2] += *(kv++)*r; sum[3][3] += *(kv++)*r; sum[3][4] += *(kv++)*r; sum[3][5] += *(kv++)*r; } ++cek; } } for (int k=0; kmu ? atom->mu[0] : NULL; double *vatomj = NULL; if (vflag_atom && vatom) vatomj = vatom[0]; const double qscale = force->qqrd2e * scale; double *ke, c[EWALD_NFUNCS] = { 8.0*MY_PI*qscale/volume, 2.0*MY_PI*MY_PIS/(12.0*volume), 2.0*MY_PI*MY_PIS/(192.0*volume), 8.0*MY_PI*mumurd2e/volume}; int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type; int func[EWALD_NFUNCS]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); memset(&sum[0], 0, 6*sizeof(double)); memset(&sum_total[0], 0, 6*sizeof(double)); for (int j = 0; j < atom->nlocal; j++) { k = kvec; kx = ky = -1; ke = kenergy; cek = cek_global; memset(&sum[0], 0, 6*sizeof(double)); if (func[3]) { register double di = c[3]; mui[0] = di*(mu++)[0]; mui[1] = di*(mu++)[0]; mui[2] = di*(mu++)[0]; mu++; } for (nh = (h = hvec)+nkvec; hy) { // based on order in if (kx!=k->x) zx = z[kx = k->x].x; // reallocate C_RMULT(zxy, z[ky = k->y].y, zx); } C_CRMULT(zc, z[k->z].z, zxy); double im = 0.0; if (func[0]) { // 1/r ke++; if (func[3]) cek_coul = cek; ++cek; } if (func[1]) { // geometric 1/r^6 ke++; ++cek; } if (func[2]) { // arithmetic 1/r^6 ke++; for (i=2; i<9; ++i) { ++cek; } } if (func[3]) { // dipole im = *(ke)*(zc.re*cek->re - cek->im*zc.im); if (func[0]) { // charge-dipole im += *(ke)*(zc.im*cek_coul->re + cek_coul->im*zc.re); } sum[0] -= mui[0]*h->x*im; sum[1] -= mui[1]*h->y*im; sum[2] -= mui[2]*h->z*im; sum[3] -= mui[0]*h->y*im; sum[4] -= mui[0]*h->z*im; sum[5] -= mui[1]*h->z*im; ++cek; ke++; } } if (vflag_global) for (int n = 0; n < 6; n++) sum_total[n] -= sum[n]; if (vflag_atom) for (int n = 0; n < 6; n++) vatomj[n] -= sum[n]; z = (cvector *) ((char *) z+lbytes); ++type; if (vflag_atom) vatomj += 6; } if (vflag_global) { MPI_Allreduce(&sum_total[0],&sum[0],6,MPI_DOUBLE,MPI_SUM,world); for (int n = 0; n < 6; n++) virial[n] += sum[n]; } } +/* ---------------------------------------------------------------------- */ + void EwaldDisp::compute_virial_peratom() { if (!vflag_atom) return; kvector *k; hvector *h, *nh; cvector *z = ekr_local; vector mui = VECTOR_NULL; complex *cek, zc = COMPLEX_NULL, zx = COMPLEX_NULL, zxy = COMPLEX_NULL; complex *cek_coul; double *kv; double *q = atom->q; double *vatomj = vatom ? vatom[0] : NULL; double *mu = atom->mu ? atom->mu[0] : NULL; const double qscale = force->qqrd2e * scale; double c[EWALD_NFUNCS] = { 4.0*MY_PI*qscale/volume, 2.0*MY_PI*MY_PIS/(24.0*volume), 2.0*MY_PI*MY_PIS/(192.0*volume), 4.0*MY_PI*mumurd2e/volume}; shape sum[EWALD_MAX_NSUMS]; int func[EWALD_NFUNCS]; memcpy(func, function, EWALD_NFUNCS*sizeof(int)); int i, kx, ky, lbytes = (2*nbox+1)*sizeof(cvector), *type = atom->type; for (int j = 0; j < atom->nlocal; j++) { k = kvec; kx = ky = -1; kv = kvirial; cek = cek_global; memset(sum, 0, EWALD_MAX_NSUMS*sizeof(shape)); if (func[3]) { register double di = c[3]; mui[0] = di*(mu++)[0]; mui[1] = di*(mu++)[0]; mui[2] = di*(mu++)[0]; mu++; } for (nh = (h = hvec)+nkvec; hy) { // based on order in if (kx!=k->x) zx = z[kx = k->x].x; // reallocate C_RMULT(zxy, z[ky = k->y].y, zx); } C_CRMULT(zc, z[k->z].z, zxy); if (func[0]) { // 1/r if (func[3]) cek_coul = cek; register double r = cek->re*zc.re - cek->im*zc.im; ++cek; sum[0][0] += *(kv++)*r; sum[0][1] += *(kv++)*r; sum[0][2] += *(kv++)*r; sum[0][3] += *(kv++)*r; sum[0][4] += *(kv++)*r; sum[0][5] += *(kv++)*r; } if (func[1]) { // geometric 1/r^6 register double r = cek->re*zc.re - cek->im*zc.im; ++cek; sum[1][0] += *(kv++)*r; sum[1][1] += *(kv++)*r; sum[1][2] += *(kv++)*r; sum[1][3] += *(kv++)*r; sum[1][4] += *(kv++)*r; sum[1][5] += *(kv++)*r; } if (func[2]) { // arithmetic 1/r^6 register double r; for (i=2; i<9; ++i) { r = cek->re*zc.re - cek->im*zc.im; ++cek; sum[i][0] += *(kv++)*r; sum[i][1] += *(kv++)*r; sum[i][2] += *(kv++)*r; sum[i][3] += *(kv++)*r; sum[i][4] += *(kv++)*r; sum[i][5] += *(kv++)*r; kv -= 6; } kv += 6; } if (func[3]) { // dipole double muk = (mui[0]*h->x+mui[1]*h->y+mui[2]*h->z); register double r = (cek->re*zc.re - cek->im*zc.im)*muk; sum[9][0] += *(kv++)*r; sum[9][1] += *(kv++)*r; sum[9][2] += *(kv++)*r; sum[9][3] += *(kv++)*r; sum[9][4] += *(kv++)*r; sum[9][5] += *(kv++)*r; if (func[0]) { // charge-dipole kv -= 6; register double qj = *(q)*c[0]; r = (cek_coul->im*zc.re + cek_coul->re*zc.im)*muk; r += -(cek->re*zc.im + cek->im*zc.re)*qj; sum[9][0] += *(kv++)*r; sum[9][1] += *(kv++)*r; sum[9][2] += *(kv++)*r; sum[9][3] += *(kv++)*r; sum[9][4] += *(kv++)*r; sum[9][5] += *(kv++)*r; } ++cek; } } if (func[0]) { // 1/r register double qi = *(q++)*c[0]; for (int n = 0; n < 6; n++) vatomj[n] += sum[0][n]*qi; } if (func[1]) { // geometric 1/r^6 register double bi = B[*type]*c[1]; for (int n = 0; n < 6; n++) vatomj[n] += sum[1][n]*bi; } if (func[2]) { // arithmetic 1/r^6 register double *bj = B+7*type[0]+7; for (i=2; i<9; ++i) { register double c2 = (--bj)[0]*c[2]; for (int n = 0; n < 6; n++) vatomj[n] += 0.5*sum[i][n]*c2; } } if (func[3]) { // dipole for (int n = 0; n < 6; n++) vatomj[n] += sum[9][n]; } for (int k=0; kq; double **x = atom->x; double zprd = domain->zprd; int nlocal = atom->nlocal; double dipole = 0.0; for (int i = 0; i < nlocal; i++) dipole += q[i]*x[i][2]; if (function[3] && atom->mu) { double **mu = atom->mu; for (int i = 0; i < nlocal; i++) dipole += mu[i][2]; } // sum local contributions to get global dipole moment double dipole_all; MPI_Allreduce(&dipole,&dipole_all,1,MPI_DOUBLE,MPI_SUM,world); // need to make non-neutral systems and/or // per-atom energy translationally invariant double dipole_r2 = 0.0; if (eflag_atom || fabs(qsum) > SMALL) { if (function[3] && atom->mu) error->all(FLERR,"Cannot (yet) use kspace slab correction with " "long-range dipoles and non-neutral systems or per-atom energy"); for (int i = 0; i < nlocal; i++) dipole_r2 += q[i]*x[i][2]*x[i][2]; // sum local contributions double tmp; MPI_Allreduce(&dipole_r2,&tmp,1,MPI_DOUBLE,MPI_SUM,world); dipole_r2 = tmp; } // compute corrections const double e_slabcorr = MY_2PI*(dipole_all*dipole_all - qsum*dipole_r2 - qsum*qsum*zprd*zprd/12.0)/volume; const double qscale = force->qqrd2e * scale; if (eflag_global) energy += qscale * e_slabcorr; // per-atom energy if (eflag_atom) { double efact = qscale * MY_2PI/volume; for (int i = 0; i < nlocal; i++) eatom[i] += efact * q[i]*(x[i][2]*dipole_all - 0.5*(dipole_r2 + qsum*x[i][2]*x[i][2]) - qsum*zprd*zprd/12.0); } // add on force corrections double ffact = qscale * (-4.0*MY_PI/volume); double **f = atom->f; for (int i = 0; i < nlocal; i++) f[i][2] += ffact * q[i]*(dipole_all - qsum*x[i][2]); // add on torque corrections if (function[3] && atom->mu && atom->torque) { double **mu = atom->mu; double **torque = atom->torque; for (int i = 0; i < nlocal; i++) { torque[i][0] += ffact * dipole_all * mu[i][1]; torque[i][1] += -ffact * dipole_all * mu[i][0]; } } } /* ---------------------------------------------------------------------- Newton solver used to find g_ewald for LJ systems ------------------------------------------------------------------------- */ double EwaldDisp::NewtonSolve(double x, double Rc, bigint natoms, double vol, double b2) { double dx,tol; int maxit; maxit = 10000; //Maximum number of iterations tol = 0.00001; //Convergence tolerance //Begin algorithm for (int i = 0; i < maxit; i++) { dx = f(x,Rc,natoms,vol,b2) / derivf(x,Rc,natoms,vol,b2); x = x - dx; //Update x if (fabs(dx) < tol) return x; if (x < 0 || x != x) // solver failed return -1; } return -1; } /* ---------------------------------------------------------------------- Calculate f(x) ------------------------------------------------------------------------- */ double EwaldDisp::f(double x, double Rc, bigint natoms, double vol, double b2) { double a = Rc*x; double f = 0.0; if (function[1] || function[2]) { // LJ f = (4.0*MY_PI*b2*powint(x,4)/vol/sqrt((double)natoms)*erfc(a) * (6.0*powint(a,-5) + 6.0*powint(a,-3) + 3.0/a + a) - accuracy); } else { // dipole double rg2 = a*a; double rg4 = rg2*rg2; double rg6 = rg4*rg2; double Cc = 4.0*rg4 + 6.0*rg2 + 3.0; double Dc = 8.0*rg6 + 20.0*rg4 + 30.0*rg2 + 15.0; f = (b2/(sqrt(vol*powint(x,4)*powint(Rc,9)*natoms)) * sqrt(13.0/6.0*Cc*Cc + 2.0/15.0*Dc*Dc - 13.0/15.0*Cc*Dc) * exp(-rg2)) - accuracy; } return f; } /* ---------------------------------------------------------------------- Calculate numerical derivative f'(x) ------------------------------------------------------------------------- */ double EwaldDisp::derivf(double x, double Rc, bigint natoms, double vol, double b2) { double h = 0.000001; //Derivative step-size return (f(x + h,Rc,natoms,vol,b2) - f(x,Rc,natoms,vol,b2)) / h; } diff --git a/src/MANYBODY/pair_nb3b_harmonic.cpp b/src/MANYBODY/pair_nb3b_harmonic.cpp index ae0282293..231119fe2 100644 --- a/src/MANYBODY/pair_nb3b_harmonic.cpp +++ b/src/MANYBODY/pair_nb3b_harmonic.cpp @@ -1,499 +1,499 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing author: Todd R. Zeitler (SNL) (based on Stillinger-Weber pair style) ------------------------------------------------------------------------- */ #include #include #include #include #include "pair_nb3b_harmonic.h" #include "atom.h" #include "neighbor.h" #include "neigh_request.h" #include "force.h" #include "comm.h" #include "memory.h" #include "neighbor.h" #include "neigh_list.h" #include "memory.h" #include "error.h" using namespace LAMMPS_NS; #define MAXLINE 1024 #define DELTA 4 #define SMALL 0.001 #define PI 3.141592653589793238462643383279 /* ---------------------------------------------------------------------- */ PairNb3bHarmonic::PairNb3bHarmonic(LAMMPS *lmp) : Pair(lmp) { single_enable = 0; one_coeff = 1; manybody_flag = 1; nelements = 0; elements = NULL; nparams = maxparam = 0; params = NULL; elem2param = NULL; map = NULL; } /* ---------------------------------------------------------------------- check if allocated, since class can be destructed when incomplete ------------------------------------------------------------------------- */ PairNb3bHarmonic::~PairNb3bHarmonic() { if (elements) for (int i = 0; i < nelements; i++) delete [] elements[i]; delete [] elements; memory->destroy(params); memory->destroy(elem2param); if (allocated) { memory->destroy(setflag); memory->destroy(cutsq); delete [] map; } } /* ---------------------------------------------------------------------- */ void PairNb3bHarmonic::compute(int eflag, int vflag) { int i,j,k,ii,jj,kk,inum,jnum,jnumm1; int itype,jtype,ktype,ijparam,ikparam,ijkparam; double xtmp,ytmp,ztmp,evdwl; double rsq1,rsq2; double delr1[3],delr2[3],fj[3],fk[3]; int *ilist,*jlist,*numneigh,**firstneigh; evdwl = 0.0; if (eflag || vflag) ev_setup(eflag,vflag); else evflag = vflag_fdotr = 0; double **x = atom->x; double **f = atom->f; int *type = atom->type; inum = list->inum; ilist = list->ilist; numneigh = list->numneigh; firstneigh = list->firstneigh; // loop over full neighbor list of my atoms for (ii = 0; ii < inum; ii++) { i = ilist[ii]; itype = map[type[i]]; xtmp = x[i][0]; ytmp = x[i][1]; ztmp = x[i][2]; jlist = firstneigh[i]; jnum = numneigh[i]; jnumm1 = jnum - 1; for (jj = 0; jj < jnumm1; jj++) { j = jlist[jj]; j &= NEIGHMASK; jtype = map[type[j]]; ijparam = elem2param[itype][jtype][jtype]; delr1[0] = x[j][0] - xtmp; delr1[1] = x[j][1] - ytmp; delr1[2] = x[j][2] - ztmp; rsq1 = delr1[0]*delr1[0] + delr1[1]*delr1[1] + delr1[2]*delr1[2]; if (rsq1 > params[ijparam].cutsq) continue; for (kk = jj+1; kk < jnum; kk++) { k = jlist[kk]; k &= NEIGHMASK; ktype = map[type[k]]; ikparam = elem2param[itype][ktype][ktype]; ijkparam = elem2param[itype][jtype][ktype]; delr2[0] = x[k][0] - xtmp; delr2[1] = x[k][1] - ytmp; delr2[2] = x[k][2] - ztmp; rsq2 = delr2[0]*delr2[0] + delr2[1]*delr2[1] + delr2[2]*delr2[2]; if (rsq2 > params[ikparam].cutsq) continue; threebody(¶ms[ijparam],¶ms[ikparam],¶ms[ijkparam], rsq1,rsq2,delr1,delr2,fj,fk,eflag,evdwl); f[i][0] -= fj[0] + fk[0]; f[i][1] -= fj[1] + fk[1]; f[i][2] -= fj[2] + fk[2]; f[j][0] += fj[0]; f[j][1] += fj[1]; f[j][2] += fj[2]; f[k][0] += fk[0]; f[k][1] += fk[1]; f[k][2] += fk[2]; if (evflag) ev_tally3(i,j,k,evdwl,0.0,fj,fk,delr1,delr2); } } } if (vflag_fdotr) virial_fdotr_compute(); } /* ---------------------------------------------------------------------- */ void PairNb3bHarmonic::allocate() { allocated = 1; int n = atom->ntypes; memory->create(setflag,n+1,n+1,"pair:setflag"); memory->create(cutsq,n+1,n+1,"pair:cutsq"); map = new int[n+1]; } /* ---------------------------------------------------------------------- global settings ------------------------------------------------------------------------- */ void PairNb3bHarmonic::settings(int narg, char **arg) { if (narg != 0) error->all(FLERR,"Illegal pair_style command"); } /* ---------------------------------------------------------------------- set coeffs for one or more type pairs ------------------------------------------------------------------------- */ void PairNb3bHarmonic::coeff(int narg, char **arg) { int i,j,n; if (!allocated) allocate(); if (narg != 3 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); // insure I,J args are * * if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0) error->all(FLERR,"Incorrect args for pair coefficients"); // read args that map atom types to elements in potential file // map[i] = which element the Ith atom type is, -1 if NULL // nelements = # of unique elements // elements = list of element names if (elements) { for (i = 0; i < nelements; i++) delete [] elements[i]; delete [] elements; } elements = new char*[atom->ntypes]; for (i = 0; i < atom->ntypes; i++) elements[i] = NULL; nelements = 0; for (i = 3; i < narg; i++) { if (strcmp(arg[i],"NULL") == 0) { map[i-2] = -1; continue; } for (j = 0; j < nelements; j++) if (strcmp(arg[i],elements[j]) == 0) break; map[i-2] = j; if (j == nelements) { n = strlen(arg[i]) + 1; elements[j] = new char[n]; strcpy(elements[j],arg[i]); nelements++; } } // read potential file and initialize potential parameters read_file(arg[2]); setup_params(); // clear setflag since coeff() called once with I,J = * * n = atom->ntypes; for (int i = 1; i <= n; i++) for (int j = i; j <= n; j++) setflag[i][j] = 0; // set setflag i,j for type pairs where both are mapped to elements int count = 0; for (int i = 1; i <= n; i++) for (int j = i; j <= n; j++) if (map[i] >= 0 && map[j] >= 0) { setflag[i][j] = 1; count++; } if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients"); } /* ---------------------------------------------------------------------- init specific to this pair style ------------------------------------------------------------------------- */ void PairNb3bHarmonic::init_style() { if (atom->tag_enable == 0) error->all(FLERR,"Pair style nb3b/harmonic requires atom IDs"); if (force->newton_pair == 0) error->all(FLERR,"Pair style nb3b/harmonic requires newton pair on"); // need a full neighbor list int irequest = neighbor->request(this,instance_me); neighbor->requests[irequest]->half = 0; neighbor->requests[irequest]->full = 1; } /* ---------------------------------------------------------------------- init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ double PairNb3bHarmonic::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); return cutmax; } /* ---------------------------------------------------------------------- */ void PairNb3bHarmonic::read_file(char *file) { int params_per_line = 6; char **words = new char*[params_per_line+1]; memory->sfree(params); params = NULL; nparams = maxparam = 0; // open file on proc 0 FILE *fp = NULL; if (comm->me == 0) { fp = force->open_potential(file); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open nb3b/harmonic potential file %s",file); error->one(FLERR,str); } } // read each set of params from potential file // one set of params can span multiple lines // store params if all 3 element tags are in element list int n,nwords,ielement,jelement,kelement; char line[MAXLINE],*ptr; int eof = 0; while (1) { if (comm->me == 0) { ptr = fgets(line,MAXLINE,fp); if (ptr == NULL) { eof = 1; fclose(fp); } else n = strlen(line) + 1; } MPI_Bcast(&eof,1,MPI_INT,0,world); if (eof) break; MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); // strip comment, skip line if blank if ((ptr = strchr(line,'#'))) *ptr = '\0'; nwords = atom->count_words(line); if (nwords == 0) continue; // concatenate additional lines until have params_per_line words while (nwords < params_per_line) { n = strlen(line); if (comm->me == 0) { ptr = fgets(&line[n],MAXLINE-n,fp); if (ptr == NULL) { eof = 1; fclose(fp); } else n = strlen(line) + 1; } MPI_Bcast(&eof,1,MPI_INT,0,world); if (eof) break; MPI_Bcast(&n,1,MPI_INT,0,world); MPI_Bcast(line,n,MPI_CHAR,0,world); if ((ptr = strchr(line,'#'))) *ptr = '\0'; nwords = atom->count_words(line); } if (nwords != params_per_line) error->all(FLERR,"Incorrect format in nb3b/harmonic potential file"); // words = ptrs to all words in line nwords = 0; words[nwords++] = strtok(line," \t\n\r\f"); while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue; // ielement,jelement,kelement = 1st args // if all 3 args are in element list, then parse this line // else skip to next entry in file for (ielement = 0; ielement < nelements; ielement++) if (strcmp(words[0],elements[ielement]) == 0) break; if (ielement == nelements) continue; for (jelement = 0; jelement < nelements; jelement++) if (strcmp(words[1],elements[jelement]) == 0) break; if (jelement == nelements) continue; for (kelement = 0; kelement < nelements; kelement++) if (strcmp(words[2],elements[kelement]) == 0) break; if (kelement == nelements) continue; // load up parameter settings and error check their values if (nparams == maxparam) { maxparam += DELTA; params = (Param *) memory->srealloc(params,maxparam*sizeof(Param), "pair:params"); } params[nparams].ielement = ielement; params[nparams].jelement = jelement; params[nparams].kelement = kelement; params[nparams].k_theta = atof(words[3]); params[nparams].theta0 = atof(words[4]); params[nparams].cutoff = atof(words[5]); if (params[nparams].k_theta < 0.0 || params[nparams].theta0 < 0.0 || params[nparams].cutoff < 0.0) error->all(FLERR,"Illegal nb3b/harmonic parameter"); nparams++; } delete [] words; } /* ---------------------------------------------------------------------- */ void PairNb3bHarmonic::setup_params() { int i,j,k,m,n; double rtmp; // set elem2param for all triplet combinations // must be a single exact match to lines read from file // do not allow for ACB in place of ABC memory->destroy(elem2param); memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param"); for (i = 0; i < nelements; i++) for (j = 0; j < nelements; j++) for (k = 0; k < nelements; k++) { n = -1; for (m = 0; m < nparams; m++) { if (i == params[m].ielement && j == params[m].jelement && k == params[m].kelement) { if (n >= 0) error->all(FLERR,"Potential file has duplicate entry"); n = m; } } -// if (n < 0) error->all(FLERR,"Potential file is missing an entry"); + if (n < 0) error->all(FLERR,"Potential file is missing an entry"); elem2param[i][j][k] = n; } // compute parameter values derived from inputs // set cutsq using shortcut to reduce neighbor list for accelerated // calculations. cut must remain unchanged as it is a potential parameter // (cut = a*sigma) for (m = 0; m < nparams; m++) { params[m].cut = params[m].cutoff; params[m].cutsq = params[m].cut * params[m].cut; params[m].theta0 = params[m].theta0 / 180.0 * PI; } // set cutmax to max of all params cutmax = 0.0; for (m = 0; m < nparams; m++) { rtmp = sqrt(params[m].cutsq); if (rtmp > cutmax) cutmax = rtmp; } } /* ---------------------------------------------------------------------- */ void PairNb3bHarmonic::threebody(Param *paramij, Param *paramik, Param *paramijk, double rsq1, double rsq2, double *delr1, double *delr2, double *fj, double *fk, int eflag, double &eng) { double dtheta,tk; double r1,r2,c,s,a,a11,a12,a22; // angle (cos and sin) r1 = sqrt(rsq1); r2 = sqrt(rsq2); c = delr1[0]*delr2[0] + delr1[1]*delr2[1] + delr1[2]*delr2[2]; c /= r1*r2; if (c > 1.0) c = 1.0; if (c < -1.0) c = -1.0; s = sqrt(1.0 - c*c); if (s < SMALL) s = SMALL; s = 1.0/s; // force & energy dtheta = acos(c) - paramijk->theta0; tk = paramijk->k_theta * dtheta; if (eflag) eng = tk*dtheta; a = -2.0 * tk * s; a11 = a*c / rsq1; a12 = -a / (r1*r2); a22 = a*c / rsq2; fj[0] = a11*delr1[0] + a12*delr2[0]; fj[1] = a11*delr1[1] + a12*delr2[1]; fj[2] = a11*delr1[2] + a12*delr2[2]; fk[0] = a22*delr2[0] + a12*delr1[0]; fk[1] = a22*delr2[1] + a12*delr1[1]; fk[2] = a22*delr2[2] + a12*delr1[2]; } diff --git a/src/USER-QMMM/fix_qmmm.cpp b/src/USER-QMMM/fix_qmmm.cpp index 4db40fe84..4ee472cfa 100644 --- a/src/USER-QMMM/fix_qmmm.cpp +++ b/src/USER-QMMM/fix_qmmm.cpp @@ -1,847 +1,847 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing author: Axel Kohlmeyer (ICTP) ------------------------------------------------------------------------- */ #include "fix_qmmm.h" #include "atom.h" #include "domain.h" #include "comm.h" #include "update.h" #include "force.h" #include "error.h" #include "group.h" #include "memory.h" #include #include #include "libqmmm.h" // message tags for QM/MM inter communicator communication // have to match with those from the QM code enum {QMMM_TAG_OTHER=0, QMMM_TAG_SIZE=1, QMMM_TAG_COORD=2, QMMM_TAG_FORCE=3, QMMM_TAG_FORCE2=4, QMMM_TAG_CELL=5, QMMM_TAG_RADII=6, QMMM_TAG_CHARGE=7, QMMM_TAG_TYPE=8, QMMM_TAG_MASS=9}; using namespace LAMMPS_NS; using namespace FixConst; // prototypes for local helper functions static int match_element(double mass, int search_isotopes, double &delta); /****************************************************************************/ /* re-usable integer hash table code with static linkage. */ /** hash table top level data structure */ typedef struct taginthash_t { struct taginthash_node_t **bucket; /* array of hash nodes */ tagint size; /* size of the array */ tagint entries; /* number of entries in table */ tagint downshift; /* shift cound, used in hash function */ tagint mask; /* used to select bits for hashing */ } taginthash_t; /** hash table node data structure */ typedef struct taginthash_node_t { tagint data; /* data in hash node */ tagint key; /* key for hash lookup */ struct taginthash_node_t *next; /* next node in hash chain */ } taginthash_node_t; #define HASH_FAIL -1 #define HASH_LIMIT 0.5 /* initialize new hash table */ static void taginthash_init(taginthash_t *tptr, tagint buckets); /* lookup entry in hash table */ static tagint taginthash_lookup(const taginthash_t *tptr, tagint key); /* generate list of keys for reverse lookups. */ static tagint *taginthash_keys(taginthash_t *tptr); /* insert an entry into hash table. */ static tagint taginthash_insert(taginthash_t *tptr, tagint key, tagint data); /* delete the hash table */ static void taginthash_destroy(taginthash_t *tptr); /* adapted sort for in-place sorting of map indices. */ static void id_sort(tagint *idmap, tagint left, tagint right); /************************************************************************ * integer hash code: ************************************************************************/ /* taginthash() - Hash function returns a hash number for a given key. * tptr: Pointer to a hash table, key: The key to create a hash number for */ static tagint taginthash(const taginthash_t *tptr, tagint key) { tagint hashvalue; hashvalue = (((key*1103515249)>>tptr->downshift) & tptr->mask); if (hashvalue < 0) { hashvalue = 0; } return hashvalue; } /* * rebuild_table_tagint() - Create new hash table when old one fills up. * * tptr: Pointer to a hash table */ static void rebuild_table_tagint(taginthash_t *tptr) { taginthash_node_t **old_bucket, *old_hash, *tmp; tagint old_size, h, i; old_bucket=tptr->bucket; old_size=tptr->size; /* create a new table and rehash old buckets */ taginthash_init(tptr, old_size<<1); for (i=0; inext; h=taginthash(tptr, tmp->key); tmp->next=tptr->bucket[h]; tptr->bucket[h]=tmp; tptr->entries++; } /* while */ } /* for */ /* free memory used by old table */ free(old_bucket); return; } /* * taginthash_init() - Initialize a new hash table. * * tptr: Pointer to the hash table to initialize * buckets: The number of initial buckets to create */ void taginthash_init(taginthash_t *tptr, tagint buckets) { /* make sure we allocate something */ if (buckets==0) buckets=16; /* initialize the table */ tptr->entries=0; tptr->size=2; tptr->mask=1; tptr->downshift=29; /* ensure buckets is a power of 2 */ while (tptr->sizesize<<=1; tptr->mask=(tptr->mask<<1)+1; tptr->downshift--; } /* while */ /* allocate memory for table */ tptr->bucket=(taginthash_node_t **) calloc(tptr->size, sizeof(taginthash_node_t *)); return; } /* * taginthash_lookup() - Lookup an entry in the hash table and return a pointer to * it or HASH_FAIL if it wasn't found. * * tptr: Pointer to the hash table * key: The key to lookup */ tagint taginthash_lookup(const taginthash_t *tptr, tagint key) { tagint h; taginthash_node_t *node; /* find the entry in the hash table */ h=taginthash(tptr, key); for (node=tptr->bucket[h]; node!=NULL; node=node->next) { if (node->key == key) break; } /* return the entry if it exists, or HASH_FAIL */ return(node ? node->data : HASH_FAIL); } /* * taginthash_keys() - Return a list of keys. * NOTE: the returned list must be freed with free(3). */ tagint *taginthash_keys(taginthash_t *tptr) { tagint *keys; taginthash_node_t *node; keys = (tagint *)calloc(tptr->entries, sizeof(tagint)); for (tagint i=0; i < tptr->size; ++i) { for (node=tptr->bucket[i]; node != NULL; node=node->next) { keys[node->data] = node->key; } } return keys; } /* * taginthash_insert() - Insert an entry into the hash table. If the entry already * exists return a pointer to it, otherwise return HASH_FAIL. * * tptr: A pointer to the hash table * key: The key to insert into the hash table * data: A pointer to the data to insert into the hash table */ tagint taginthash_insert(taginthash_t *tptr, tagint key, tagint data) { tagint tmp; taginthash_node_t *node; tagint h; /* check to see if the entry exists */ if ((tmp=taginthash_lookup(tptr, key)) != HASH_FAIL) return(tmp); /* expand the table if needed */ while (tptr->entries>=HASH_LIMIT*tptr->size) rebuild_table_tagint(tptr); /* insert the new entry */ h=taginthash(tptr, key); node=(struct taginthash_node_t *) malloc(sizeof(taginthash_node_t)); node->data=data; node->key=key; node->next=tptr->bucket[h]; tptr->bucket[h]=node; tptr->entries++; return HASH_FAIL; } /* * taginthash_destroy() - Delete the entire table, and all remaining entries. * */ void taginthash_destroy(taginthash_t *tptr) { taginthash_node_t *node, *last; tagint i; for (i=0; isize; i++) { node = tptr->bucket[i]; while (node != NULL) { last = node; node = node->next; free(last); } } /* free the entire array of buckets */ if (tptr->bucket != NULL) { free(tptr->bucket); memset(tptr, 0, sizeof(taginthash_t)); } } /************************************************************************ * integer list sort code: ************************************************************************/ /* sort for integer map. initial call id_sort(idmap, 0, natoms - 1); */ static void id_sort(tagint *idmap, tagint left, tagint right) { tagint pivot, l_hold, r_hold; l_hold = left; r_hold = right; pivot = idmap[left]; while (left < right) { while ((idmap[right] >= pivot) && (left < right)) right--; if (left != right) { idmap[left] = idmap[right]; left++; } while ((idmap[left] <= pivot) && (left < right)) left++; if (left != right) { idmap[right] = idmap[left]; right--; } } idmap[left] = pivot; pivot = left; left = l_hold; right = r_hold; if (left < pivot) id_sort(idmap, left, pivot-1); if (right > pivot) id_sort(idmap, pivot+1, right); } /****************************************************************************/ /* struct for packed data communication of coordinates and forces. */ struct commdata { tagint tag; float x,y,z; float q; }; /*************************************************************** * create class and parse arguments in LAMMPS script. Syntax: * fix ID group-ID qmmm [couple ] ***************************************************************/ FixQMMM::FixQMMM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { if (narg > 5) error->all(FLERR,"Illegal fix qmmm command"); if (strcmp(update->unit_style,"metal") == 0) { qmmm_fscale = 1.0/23.0609; } else if (strcmp(update->unit_style,"real") == 0) { qmmm_fscale = 1.0; } else error->all(FLERR,"Fix qmmm requires real or metal units"); if (atom->tag_enable == 0) error->all(FLERR,"Fix qmmm requires atom IDs"); if (atom->tag_consecutive() == 0) error->all(FLERR,"Fix qmmm requires consecutive atom IDs"); /* define ec coupling group */ mm_group = group->find("all"); if ((narg == 5) && (0 == strcmp(arg[0],"couple"))) { #if 0 /* ignore ES coupling group for now */ mm_group = group->find(arg[4]); #endif } else if (narg != 3) error->all(FLERR,"Illegal fix qmmm command"); if (mm_group == -1) error->all(FLERR,"Could not find fix qmmm couple group ID"); /* retrieve settings from global QM/MM configuration struct */ comm_mode = qmmmcfg.comm_mode; qmmm_mode = qmmmcfg.qmmm_mode; qmmm_role = qmmmcfg.role; verbose = qmmmcfg.verbose; if (comm_mode != QMMM_COMM_MPI) error->all(FLERR,"Only MPI communication mode is currently supported"); if ((qmmm_role != QMMM_ROLE_MASTER) && (qmmm_role != QMMM_ROLE_SLAVE)) error->all(FLERR,"LAMMPS can only function as MM master or MM slave"); qm_comm = MPI_Comm_f2c(qmmmcfg.qm_comm); mm_comm = MPI_Comm_f2c(qmmmcfg.mm_comm); /* initialize storage */ qm_idmap = mm_idmap = NULL; qm_remap = mm_remap = NULL; qm_coord = mm_coord = qm_force = mm_force = NULL; qm_charge =NULL; mm_type = NULL; do_init = 1; /* storage required to communicate a single coordinate or force. */ size_one = sizeof(struct commdata); maxbuf = -1; } /********************************* * Clean up on deleting the fix. * *********************************/ FixQMMM::~FixQMMM() { if (qm_idmap) { taginthash_t *hashtable = (taginthash_t *)qm_idmap; taginthash_destroy(hashtable); delete hashtable; free(qm_remap); } memory->destroy(comm_buf); memory->destroy(qm_coord); memory->destroy(qm_force); memory->destroy(qm_charge); } /* ---------------------------------------------------------------------- */ int FixQMMM::setmask() { int mask = 0; mask |= POST_INTEGRATE; mask |= POST_FORCE; return mask; } /* ---------------------------------------------------------------------- */ void FixQMMM::exchange_positions() { double **x = atom->x; double *charge = atom->q; - const int * const mask = atom->mask; - const int * const type = atom->type; + int * const mask = atom->mask; + int * const type = atom->type; double * const mass = atom->mass; tagint * const tag = atom->tag; const int nlocal = atom->nlocal; const int ntypes = atom->ntypes; const int natoms = (int) atom->natoms; if (atom->natoms > MAXSMALLINT) error->all(FLERR,"Too many MM atoms for fix qmmmm"); /* * CHECK * AK: this is not good. atom->natoms can be huge. instead: - collect list of atom tags (from local and remoted full MM procs) that match fix qmmm group - sort list -> master list of QM/MM interacting atoms - create hash table that connects master list index with tag - collect necessary data and get master list index via hash table */ if (comm->me == 0) { // Pack various cell dimension properties into one chunk. double celldata[9]; celldata[0] = domain->boxlo[0]; celldata[1] = domain->boxlo[1]; celldata[2] = domain->boxlo[2]; celldata[3] = domain->boxhi[0]; celldata[4] = domain->boxhi[1]; celldata[5] = domain->boxhi[2]; celldata[6] = domain->xy; celldata[7] = domain->xz; celldata[8] = domain->yz; if (qmmm_role == QMMM_ROLE_MASTER) { int isend_buf[4]; isend_buf[0] = natoms; isend_buf[1] = num_qm; isend_buf[2] = num_mm; isend_buf[3] = ntypes; MPI_Send(isend_buf, 4, MPI_INT, 1, QMMM_TAG_SIZE, qm_comm); MPI_Send(celldata, 9, MPI_DOUBLE, 1, QMMM_TAG_CELL, qm_comm); } if (verbose > 0) { if (screen) fputs("QMMM: exchange positions\n",screen); if (logfile) fputs("QMMM: exchange positions\n",logfile); } } if (qmmm_role == QMMM_ROLE_MASTER) { int i; double *mm_coord_all = (double *) calloc(3*natoms, sizeof(double)); double *mm_charge_all = (double *) calloc(natoms, sizeof(double)); int *mm_mask_all = (int *) calloc(natoms, sizeof(int)); /* check and potentially grow local communication buffers. */ if (atom->nmax*size_one > maxbuf) { memory->destroy(comm_buf); maxbuf = atom->nmax*size_one; comm_buf = memory->smalloc(maxbuf,"qmmm:comm_buf"); } if (comm->me == 0) { // insert local atoms into comm buffer and global arrays for (i=0; ione(FLERR,"Cannot handle parallel MM (yet)"); } } else if (qmmm_role == QMMM_ROLE_SLAVE) { MPI_Recv(qm_coord, 3*num_qm, MPI_DOUBLE, 0, QMMM_TAG_COORD, mm_comm, MPI_STATUS_IGNORE); // not needed for as long as we allow only one MPI task as slave MPI_Bcast(qm_coord, 3*num_qm, MPI_DOUBLE,0,world); /* update coordinates of (QM) atoms */ for (int i=0; i < nlocal; ++i) { if (mask[i] & groupbit) { for (int j=0; j < num_qm; ++j) { if (tag[i] == qm_remap[j]) { x[i][0] = qm_coord[3*j]; x[i][1] = qm_coord[3*j+1]; x[i][2] = qm_coord[3*j+2]; } } } } } return; } /* ---------------------------------------------------------------------- */ void FixQMMM::exchange_forces() { double **f = atom->f; const int * const mask = atom->mask; const tagint * const tag = atom->tag; const int nlocal = atom->nlocal; const int natoms = (int) atom->natoms; if ((comm->me) == 0 && (verbose > 0)) { if (screen) fputs("QMMM: exchange forces\n",screen); if (logfile) fputs("QMMM: exchange forces\n",logfile); } if (qmmm_role == QMMM_ROLE_MASTER) { struct commdata *buf = static_cast(comm_buf); double *mm_force_all = (double *) calloc(natoms*3, sizeof(double)); double *mm_force_on_qm_atoms = qm_coord; // use qm_coord as a buffer if (comm->me == 0) { // receive QM forces from QE MPI_Recv(qm_force,3*num_qm,MPI_DOUBLE,1,QMMM_TAG_FORCE,qm_comm,MPI_STATUS_IGNORE); // receive ec contribution to MM forces from QE MPI_Recv(mm_force_all,3*natoms,MPI_DOUBLE,1,QMMM_TAG_FORCE2,qm_comm,MPI_STATUS_IGNORE); // receive MM forces from LAMMPS MPI_Recv( mm_force_on_qm_atoms, 3*num_qm,MPI_DOUBLE,1,QMMM_TAG_FORCE,mm_comm,MPI_STATUS_IGNORE); // subtract MM forces from QM forces to get the delta // NOTE: QM forces are always sent in "real" units, // so we need to apply the scaling factor to get to the // supported internal units ("metal" or "real") for (int i=0; i < num_qm; ++i) { if (verbose > 1) { const char fmt[] = "[" TAGINT_FORMAT "]: QM(%g %g %g) MM(%g %g %g) /\\(%g %g %g)\n"; if (screen) fprintf(screen, fmt, qm_remap[i], qmmm_fscale*qm_force[3*i+0], qmmm_fscale*qm_force[3*i+1], qmmm_fscale*qm_force[3*i+2], mm_force_on_qm_atoms[3*i+0], mm_force_on_qm_atoms[3*i+1], mm_force_on_qm_atoms[3*i+2], qmmm_fscale*qm_force[3*i+0] - mm_force_on_qm_atoms[3*i+0], qmmm_fscale*qm_force[3*i+1] - mm_force_on_qm_atoms[3*i+1], qmmm_fscale*qm_force[3*i+2] - mm_force_on_qm_atoms[3*i+2]); if (logfile) fprintf(logfile, fmt, qm_remap[i], qmmm_fscale*qm_force[3*i+0], qmmm_fscale*qm_force[3*i+1], qmmm_fscale*qm_force[3*i+2], mm_force_on_qm_atoms[3*i+0], mm_force_on_qm_atoms[3*i+1], mm_force_on_qm_atoms[3*i+2], qmmm_fscale*qm_force[3*i+0] - mm_force_on_qm_atoms[3*i+0], qmmm_fscale*qm_force[3*i+1] - mm_force_on_qm_atoms[3*i+1], qmmm_fscale*qm_force[3*i+2] - mm_force_on_qm_atoms[3*i+2]); } buf[i].tag = qm_remap[i]; buf[i].x = qmmm_fscale*qm_force[3*i+0] - mm_force_on_qm_atoms[3*i+0]; buf[i].y = qmmm_fscale*qm_force[3*i+1] - mm_force_on_qm_atoms[3*i+1]; buf[i].z = qmmm_fscale*qm_force[3*i+2] - mm_force_on_qm_atoms[3*i+2]; } } MPI_Bcast(comm_buf,num_qm*size_one,MPI_BYTE,0,world); // Inefficient... use buffers. MPI_Bcast(mm_force_all,natoms*3,MPI_DOUBLE,0,world); /* apply forces resulting from QM/MM coupling */ if (qmmm_mode == QMMM_MODE_MECH) { for (int i=0; i < nlocal; ++i) { if (mask[i] & groupbit) { for (int j=0; j < num_qm; ++j) { if (tag[i] == buf[j].tag) { f[i][0] += buf[j].x; f[i][1] += buf[j].y; f[i][2] += buf[j].z; } } } } } else if (qmmm_mode == QMMM_MODE_ELEC) { for (int i=0; i < nlocal; ++i) { if (mask[i] & groupbit) { for (int j=0; j < num_qm; ++j) { if (tag[i] == buf[j].tag) { f[i][0] += buf[j].x; f[i][1] += buf[j].y; f[i][2] += buf[j].z; } } } else { const int k = (int) tag[i]-1; f[i][0] += qmmm_fscale * mm_force_all[ 3*k + 0 ]; f[i][1] += qmmm_fscale * mm_force_all[ 3*k + 1 ]; f[i][2] += qmmm_fscale * mm_force_all[ 3*k + 2 ]; } } } free(mm_force_all); } else if (qmmm_role == QMMM_ROLE_SLAVE) { // use qm_force and qm_coord as communication buffer double * mm_force_on_qm_atoms = qm_force; double * reduced_mm_force_on_qm_atoms = qm_coord; memset( mm_force_on_qm_atoms, 0, 3*num_qm*sizeof(double) ); for (int i=0; i < nlocal; ++i) { if (mask[i] & groupbit) { const int j = 3*taginthash_lookup((taginthash_t *)qm_idmap, tag[i]); if (j != 3*HASH_FAIL) { mm_force_on_qm_atoms[j] = f[i][0]; mm_force_on_qm_atoms[j+1] = f[i][1]; mm_force_on_qm_atoms[j+2] = f[i][2]; } } } // collect and send MM slave forces to MM master // the reduction is not really needed with only one rank (for now) MPI_Reduce(mm_force_on_qm_atoms, reduced_mm_force_on_qm_atoms, 3*num_qm, MPI_DOUBLE, MPI_SUM, 0, world); // use qm_coord array as a communication buffer MPI_Send(reduced_mm_force_on_qm_atoms, 3*num_qm, MPI_DOUBLE, 0, QMMM_TAG_FORCE, mm_comm); } return; } /* ---------------------------------------------------------------------- */ void FixQMMM::init() { if (strstr(update->integrate_style,"respa")) error->all(FLERR,"Fix qmmm does not currently support r-RESPA"); if (do_init) { int me = comm->me; do_init = 0; if (qmmm_role == QMMM_ROLE_MASTER) { MPI_Request req[2]; int nat[2]; if (me == 0) { // receive number of QM atoms from QE MPI_Irecv(nat, 1, MPI_INT, 1, QMMM_TAG_SIZE, qm_comm, req); // receive number of QM atoms from MM slave MPI_Irecv(nat+1, 1, MPI_INT, 1, QMMM_TAG_SIZE, mm_comm, req+1); MPI_Waitall(2,req,MPI_STATUS_IGNORE); } // broadcast across MM master processes MPI_Bcast(nat, 2, MPI_INT, 0, world); num_qm = group->count(igroup); num_mm = group->count(mm_group); // consistency check. the fix group and the QM and MM slave if ((num_qm != nat[0]) || (num_qm != nat[1])) error->all(FLERR,"Inconsistent number of QM/MM atoms"); memory->create(qm_coord,3*num_qm,"qmmm:qm_coord"); memory->create(qm_charge,num_qm,"qmmm:qm_charge"); memory->create(qm_force,3*num_qm,"qmmm:qm_force"); const char fmt1[] = "Initializing QM/MM master with %d QM atoms\n"; const char fmt2[] = "Initializing QM/MM master with %d MM atoms\n"; const char fmt3[] = "Electrostatic coupling with %d atoms\n"; if (screen) { fprintf(screen,fmt1,num_qm); fprintf(screen,fmt2,num_mm); if (qmmm_mode == QMMM_MODE_ELEC) fprintf(screen,fmt3,num_mm-num_qm); } if (logfile) { fprintf(logfile,fmt1,num_qm); fprintf(logfile,fmt2,num_mm); if (qmmm_mode == QMMM_MODE_ELEC) fprintf(logfile,fmt3,num_mm-num_qm); } } else if (qmmm_role == QMMM_ROLE_SLAVE) { num_qm = group->count(igroup); if (me == 0) { /* send number of QM atoms to MM-master for confirmation */ MPI_Send(&num_qm, 1, MPI_INT, 0, QMMM_TAG_SIZE, mm_comm); } memory->create(qm_coord,3*num_qm,"qmmm:qm_coord"); memory->create(qm_force,3*num_qm,"qmmm:qm_force"); const char fmt[] = "Initializing QM/MM slave with %d QM atoms\n"; if (screen) fprintf(screen,fmt,num_qm); if (logfile) fprintf(logfile,fmt,num_qm); } // communication buffer maxbuf = atom->nmax*size_one; comm_buf = (void *) memory->smalloc(maxbuf,"qmmm:comm_buf"); /* initialize and build hashtable to map QM atoms */ taginthash_t *qm_hash=new taginthash_t; taginthash_init(qm_hash, num_qm); qm_idmap = (void *)qm_hash; const int nlocal = atom->nlocal; int i, j, tmp, ndata, qm_ntag; tagint *tag = atom->tag; int *mask = atom->mask; struct commdata *buf = static_cast(comm_buf); if (me == 0) { MPI_Status status; MPI_Request request; tagint *qm_taglist = new tagint[num_qm]; qm_ntag = 0; for (i=0; i < nlocal; ++i) { if (mask[i] & groupbit) qm_taglist[qm_ntag++] = tag[i]; } /* loop over procs to receive remote data */ for (i=1; i < comm->nprocs; ++i) { MPI_Irecv(comm_buf, maxbuf, MPI_BYTE, i, 0, world, &request); MPI_Send(&tmp, 0, MPI_INT, i, 0, world); MPI_Wait(&request, &status); MPI_Get_count(&status, MPI_BYTE, &ndata); ndata /= size_one; for (j=0; j < ndata; ++j) { qm_taglist[qm_ntag++] = buf[j].tag; } } /* sort list of tags by value to have consistently the * same list when running in parallel and build hash table. */ id_sort(qm_taglist, 0, num_qm-1); for (i=0; i < num_qm; ++i) { taginthash_insert(qm_hash, qm_taglist[i], i); } delete[] qm_taglist; /* generate reverse index-to-tag map for communicating * qm/mm forces back to the proper atoms */ qm_remap=taginthash_keys(qm_hash); if (verbose > 1) { const char fmt[] = "qm_remap[%d]=" TAGINT_FORMAT " qm_hash[" TAGINT_FORMAT "]=" TAGINT_FORMAT "\n"; // print hashtable and reverse mapping for (i=0; i < num_qm; ++i) { if (screen) fprintf(screen,fmt,i,qm_remap[i],qm_remap[i], taginthash_lookup(qm_hash, qm_remap[i])); if (logfile) fprintf(logfile,fmt,i,qm_remap[i],qm_remap[i], taginthash_lookup(qm_hash, qm_remap[i])); } } } else { j = 0; for (i=0; i < nlocal; ++i) { if (mask[i] & groupbit) { buf[j].x = -1.0; buf[j].tag = tag[i]; ++j; } } /* blocking receive to wait until it is our turn to send data. */ MPI_Recv(&tmp, 0, MPI_INT, 0, 0, world, MPI_STATUS_IGNORE); MPI_Rsend(comm_buf, j*size_one, MPI_BYTE, 0, 0, world); } // finally, after all is set up, do a first position synchronization exchange_positions(); } } /* ---------------------------------------------------------------------- */ void FixQMMM::post_integrate() { exchange_positions(); } /* ---------------------------------------------------------------------- */ void FixQMMM::setup(int) { exchange_forces(); } /* ---------------------------------------------------------------------- */ void FixQMMM::post_force(int vflag) { exchange_forces(); } /* ---------------------------------------------------------------------- */ /* local memory usage. approximately. */ double FixQMMM::memory_usage(void) { double bytes; bytes = sizeof(FixQMMM); bytes += maxbuf; bytes += 6*num_qm*sizeof(double); return bytes; } // Local Variables: // mode: c++ // compile-command: "make -j4 openmpi" // c-basic-offset: 2 // fill-column: 76 // indent-tabs-mode: nil // End: diff --git a/src/fix_ave_histo.cpp b/src/fix_ave_histo.cpp index 9123a8561..1255aade3 100644 --- a/src/fix_ave_histo.cpp +++ b/src/fix_ave_histo.cpp @@ -1,1074 +1,1074 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include #include #include #include "fix_ave_histo.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute.h" #include "group.h" #include "input.h" #include "variable.h" #include "memory.h" #include "error.h" #include "force.h" using namespace LAMMPS_NS; using namespace FixConst; enum{X,V,F,COMPUTE,FIX,VARIABLE}; enum{ONE,RUNNING}; enum{SCALAR,VECTOR,WINDOW}; enum{GLOBAL,PERATOM,LOCAL}; enum{IGNORE,END,EXTRA}; #define INVOKED_SCALAR 1 #define INVOKED_VECTOR 2 #define INVOKED_ARRAY 4 #define INVOKED_PERATOM 8 #define INVOKED_LOCAL 16 #define BIG 1.0e20 /* ---------------------------------------------------------------------- */ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg) { if (narg < 10) error->all(FLERR,"Illegal fix ave/histo command"); MPI_Comm_rank(world,&me); nevery = force->inumeric(FLERR,arg[3]); nrepeat = force->inumeric(FLERR,arg[4]); nfreq = force->inumeric(FLERR,arg[5]); global_freq = nfreq; vector_flag = 1; size_vector = 4; extvector = 0; array_flag = 1; size_array_cols = 3; extarray = 0; dynamic_group_allow = 1; lo = force->numeric(FLERR,arg[6]); hi = force->numeric(FLERR,arg[7]); nbins = force->inumeric(FLERR,arg[8]); // scan values to count them // then read options so know mode = SCALAR/VECTOR before re-reading values nvalues = 0; int iarg = 9; while (iarg < narg) { if (strcmp(arg[iarg],"x") == 0 || strcmp(arg[iarg],"y") == 0 || strcmp(arg[iarg],"z") == 0 || strcmp(arg[iarg],"vx") == 0 || strcmp(arg[iarg],"vy") == 0 || strcmp(arg[iarg],"vz") == 0 || strcmp(arg[iarg],"fx") == 0 || strcmp(arg[iarg],"fy") == 0 || strcmp(arg[iarg],"fz") == 0 || strncmp(arg[iarg],"c_",2) == 0 || strncmp(arg[iarg],"f_",2) == 0 || strncmp(arg[iarg],"v_",2) == 0) { nvalues++; iarg++; } else break; } options(narg,arg); // parse values until one isn't recognized // if mode = VECTOR and value is a global array: // expand it as if columns listed one by one // adjust nvalues accordingly via maxvalues which = argindex = value2index = NULL; ids = NULL; int maxvalues = nvalues; allocate_values(maxvalues); nvalues = 0; iarg = 9; while (iarg < narg) { if (strcmp(arg[iarg],"x") == 0) { which[nvalues] = X; argindex[nvalues] = 0; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"y") == 0) { which[nvalues] = X; argindex[nvalues] = 1; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"z") == 0) { which[nvalues] = X; argindex[nvalues] = 2; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"vx") == 0) { which[nvalues] = V; argindex[nvalues] = 0; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"vy") == 0) { which[nvalues] = V; argindex[nvalues] = 1; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"vz") == 0) { which[nvalues] = V; argindex[nvalues] = 2; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"fx") == 0) { which[nvalues] = F; argindex[nvalues] = 0; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"fy") == 0) { which[nvalues] = F; argindex[nvalues] = 1; ids[nvalues] = NULL; nvalues++; iarg++; } else if (strcmp(arg[iarg],"fz") == 0) { which[nvalues] = F; argindex[nvalues] = 2; ids[nvalues] = NULL; nvalues++; iarg++; } else if ((strncmp(arg[iarg],"c_",2) == 0) || (strncmp(arg[iarg],"f_",2) == 0) || (strncmp(arg[iarg],"v_",2) == 0)) { if (arg[iarg][0] == 'c') which[nvalues] = COMPUTE; else if (arg[iarg][0] == 'f') which[nvalues] = FIX; else if (arg[iarg][0] == 'v') which[nvalues] = VARIABLE; int n = strlen(arg[iarg]); char *suffix = new char[n]; strcpy(suffix,&arg[iarg][2]); char *ptr = strchr(suffix,'['); if (ptr) { if (suffix[strlen(suffix)-1] != ']') error->all(FLERR,"Illegal fix ave/histo command"); argindex[nvalues] = atoi(ptr+1); *ptr = '\0'; } else argindex[nvalues] = 0; n = strlen(suffix) + 1; ids[nvalues] = new char[n]; strcpy(ids[nvalues],suffix); delete [] suffix; if (mode == VECTOR && which[nvalues] == COMPUTE && argindex[nvalues] == 0) { int icompute = modify->find_compute(ids[nvalues]); if (icompute < 0) error->all(FLERR,"Compute ID for fix ave/histo does not exist"); if (modify->compute[icompute]->array_flag) { int ncols = modify->compute[icompute]->size_array_cols; maxvalues += ncols-1; allocate_values(maxvalues); argindex[nvalues] = 1; for (int icol = 1; icol < ncols; icol++) { which[nvalues+icol] = which[nvalues]; argindex[nvalues+icol] = icol+1; n = strlen(ids[nvalues]) + 1; ids[nvalues+icol] = new char[n]; strcpy(ids[nvalues+icol],ids[nvalues]); } nvalues += ncols-1; } } else if (mode == VECTOR && which[nvalues] == FIX && argindex[nvalues] == 0) { int ifix = modify->find_fix(ids[nvalues]); if (ifix < 0) error->all(FLERR,"Fix ID for fix ave/histo does not exist"); if (modify->fix[ifix]->array_flag) { int ncols = modify->fix[ifix]->size_array_cols; maxvalues += ncols-1; allocate_values(maxvalues); argindex[nvalues] = 1; for (int icol = 1; icol < ncols; icol++) { which[nvalues+icol] = which[nvalues]; argindex[nvalues+icol] = icol+1; n = strlen(ids[nvalues]) + 1; ids[nvalues+icol] = new char[n]; strcpy(ids[nvalues+icol],ids[nvalues]); } nvalues += ncols-1; } } nvalues++; iarg++; } else break; } // setup and error check // kind = inputs are all global, or all per-atom, or all local // for fix inputs, check that fix frequency is acceptable if (nevery <= 0 || nrepeat <= 0 || nfreq <= 0) error->all(FLERR,"Illegal fix ave/histo command"); if (nfreq % nevery || nrepeat*nevery > nfreq) error->all(FLERR,"Illegal fix ave/histo command"); if (lo >= hi) error->all(FLERR,"Illegal fix ave/histo command"); if (nbins <= 0) error->all(FLERR,"Illegal fix ave/histo command"); if (ave != RUNNING && overwrite) error->all(FLERR,"Illegal fix ave/histo command"); int kindflag; for (int i = 0; i < nvalues; i++) { if (which[i] == X || which[i] == V || which[i] == F) kindflag = PERATOM; else if (which[i] == COMPUTE) { Compute *compute = modify->compute[modify->find_compute(ids[0])]; if (compute->scalar_flag || compute->vector_flag || compute->array_flag) kindflag = GLOBAL; else if (compute->peratom_flag) kindflag = PERATOM; else if (compute->local_flag) kindflag = LOCAL; else error->all(FLERR,"Fix ave/histo input is invalid compute"); } else if (which[i] == FIX) { Fix *fix = modify->fix[modify->find_fix(ids[0])]; if (fix->scalar_flag || fix->vector_flag || fix->array_flag) kindflag = GLOBAL; else if (fix->peratom_flag) kindflag = PERATOM; else if (fix->local_flag) kindflag = LOCAL; else error->all(FLERR,"Fix ave/histo input is invalid fix"); } else if (which[i] == VARIABLE) { int ivariable = input->variable->find(ids[i]); if (input->variable->equalstyle(ivariable)) kindflag = GLOBAL; else if (input->variable->atomstyle(ivariable)) kindflag = PERATOM; else error->all(FLERR,"Fix ave/histo input is invalid variable"); } if (i == 0) kind = kindflag; else if (kindflag != kind) error->all(FLERR, "Fix ave/histo inputs are not all global, peratom, or local"); } if (kind == PERATOM && mode == SCALAR) error->all(FLERR, "Fix ave/histo cannot input per-atom values in scalar mode"); if (kind == LOCAL && mode == SCALAR) error->all(FLERR,"Fix ave/histo cannot input local values in scalar mode"); for (int i = 0; i < nvalues; i++) { if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) { int icompute = modify->find_compute(ids[i]); if (icompute < 0) error->all(FLERR,"Compute ID for fix ave/histo does not exist"); if (argindex[i] == 0 && modify->compute[icompute]->scalar_flag == 0) error->all(FLERR, "Fix ave/histo compute does not calculate a global scalar"); if (argindex[i] && modify->compute[icompute]->vector_flag == 0) error->all(FLERR, "Fix ave/histo compute does not calculate a global vector"); if (argindex[i] && argindex[i] > modify->compute[icompute]->size_vector) error->all(FLERR, "Fix ave/histo compute vector is accessed out-of-range"); } else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) { int icompute = modify->find_compute(ids[i]); if (icompute < 0) error->all(FLERR,"Compute ID for fix ave/histo does not exist"); if (argindex[i] == 0 && modify->compute[icompute]->vector_flag == 0) error->all(FLERR, "Fix ave/histo compute does not calculate a global vector"); if (argindex[i] && modify->compute[icompute]->array_flag == 0) error->all(FLERR, "Fix ave/histo compute does not calculate a global array"); if (argindex[i] && argindex[i] > modify->compute[icompute]->size_array_cols) error->all(FLERR, "Fix ave/histo compute array is accessed out-of-range"); } else if (which[i] == COMPUTE && kind == PERATOM) { int icompute = modify->find_compute(ids[i]); if (icompute < 0) error->all(FLERR,"Compute ID for fix ave/histo does not exist"); if (modify->compute[icompute]->peratom_flag == 0) error->all(FLERR, "Fix ave/histo compute does not calculate per-atom values"); if (argindex[i] == 0 && modify->compute[icompute]->size_peratom_cols != 0) error->all(FLERR,"Fix ave/histo compute does not " "calculate a per-atom vector"); if (argindex[i] && modify->compute[icompute]->size_peratom_cols == 0) error->all(FLERR,"Fix ave/histo compute does not " "calculate a per-atom array"); if (argindex[i] && argindex[i] > modify->compute[icompute]->size_peratom_cols) error->all(FLERR, "Fix ave/histo compute array is accessed out-of-range"); } else if (which[i] == COMPUTE && kind == LOCAL) { int icompute = modify->find_compute(ids[i]); if (icompute < 0) error->all(FLERR,"Compute ID for fix ave/histo does not exist"); if (modify->compute[icompute]->local_flag == 0) error->all(FLERR, "Fix ave/histo compute does not calculate local values"); if (argindex[i] == 0 && modify->compute[icompute]->size_local_cols != 0) error->all(FLERR,"Fix ave/histo compute does not " "calculate a local vector"); if (argindex[i] && modify->compute[icompute]->size_local_cols == 0) error->all(FLERR,"Fix ave/histo compute does not " "calculate a local array"); if (argindex[i] && argindex[i] > modify->compute[icompute]->size_local_cols) error->all(FLERR, "Fix ave/histo compute array is accessed out-of-range"); } else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) { int ifix = modify->find_fix(ids[i]); if (ifix < 0) error->all(FLERR,"Fix ID for fix ave/histo does not exist"); if (argindex[i] == 0 && modify->fix[ifix]->scalar_flag == 0) error->all(FLERR, "Fix ave/histo fix does not calculate a global scalar"); if (argindex[i] && modify->fix[ifix]->vector_flag == 0) error->all(FLERR, "Fix ave/histo fix does not calculate a global vector"); if (argindex[i] && argindex[i] > modify->fix[ifix]->size_vector) error->all(FLERR,"Fix ave/histo fix vector is accessed out-of-range"); if (nevery % modify->fix[ifix]->global_freq) error->all(FLERR, "Fix for fix ave/histo not computed at compatible time"); } else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) { int ifix = modify->find_fix(ids[i]); if (ifix < 0) error->all(FLERR,"Fix ID for fix ave/histo does not exist"); if (argindex[i] == 0 && modify->fix[ifix]->vector_flag == 0) error->all(FLERR, "Fix ave/histo fix does not calculate a global vector"); if (argindex[i] && modify->fix[ifix]->array_flag == 0) error->all(FLERR,"Fix ave/histo fix does not calculate a global array"); if (argindex[i] && argindex[i] > modify->fix[ifix]->size_array_cols) error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range"); if (nevery % modify->fix[ifix]->global_freq) error->all(FLERR, "Fix for fix ave/histo not computed at compatible time"); } else if (which[i] == FIX && kind == PERATOM) { int ifix = modify->find_fix(ids[i]); if (ifix < 0) error->all(FLERR,"Fix ID for fix ave/histo does not exist"); if (modify->fix[ifix]->peratom_flag == 0) error->all(FLERR, "Fix ave/histo fix does not calculate per-atom values"); if (argindex[i] == 0 && modify->fix[ifix]->size_peratom_cols != 0) error->all(FLERR,"Fix ave/histo fix does not " "calculate a per-atom vector"); if (argindex[i] && modify->fix[ifix]->size_peratom_cols == 0) error->all(FLERR,"Fix ave/histo fix does not " "calculate a per-atom array"); if (argindex[i] && argindex[i] > modify->fix[ifix]->size_peratom_cols) error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range"); if (nevery % modify->fix[ifix]->global_freq) error->all(FLERR, "Fix for fix ave/histo not computed at compatible time"); } else if (which[i] == FIX && kind == LOCAL) { int ifix = modify->find_fix(ids[i]); if (ifix < 0) error->all(FLERR,"Fix ID for fix ave/histo does not exist"); if (modify->fix[ifix]->local_flag == 0) error->all(FLERR,"Fix ave/histo fix does not calculate local values"); if (argindex[i] == 0 && modify->fix[ifix]->size_local_cols != 0) error->all(FLERR,"Fix ave/histo fix does not " "calculate a local vector"); if (argindex[i] && modify->fix[ifix]->size_local_cols == 0) error->all(FLERR,"Fix ave/histo fix does not " "calculate a local array"); if (argindex[i] && argindex[i] > modify->fix[ifix]->size_local_cols) error->all(FLERR,"Fix ave/histo fix array is accessed out-of-range"); if (nevery % modify->fix[ifix]->global_freq) error->all(FLERR, "Fix for fix ave/histo not computed at compatible time"); } else if (which[i] == VARIABLE && kind == GLOBAL && mode == SCALAR) { int ivariable = input->variable->find(ids[i]); if (ivariable < 0) error->all(FLERR,"Variable name for fix ave/histo does not exist"); if (argindex[i] == 0 && input->variable->equalstyle(ivariable) == 0) error->all(FLERR,"Fix ave/histo variable is not equal-style variable"); if (argindex[i] && input->variable->vectorstyle(ivariable) == 0) error->all(FLERR,"Fix ave/histo variable is not vector-style variable"); } else if (which[i] == VARIABLE && kind == GLOBAL && mode == VECTOR) { int ivariable = input->variable->find(ids[i]); if (ivariable < 0) error->all(FLERR,"Variable name for fix ave/histo does not exist"); if (argindex[i] == 0 && input->variable->vectorstyle(ivariable) == 0) error->all(FLERR,"Fix ave/histo variable is not vector-style variable"); if (argindex[i]) error->all(FLERR,"Fix ave/histo variable cannot be indexed"); } else if (which[i] == VARIABLE && kind == PERATOM) { int ivariable = input->variable->find(ids[i]); if (ivariable < 0) error->all(FLERR,"Variable name for fix ave/histo does not exist"); if (argindex[i] == 0 && input->variable->atomstyle(ivariable) == 0) error->all(FLERR,"Fix ave/histo variable is not atom-style variable"); if (argindex[i]) error->all(FLERR,"Fix ave/histo variable cannot be indexed"); } } // print file comment lines if (fp && me == 0) { clearerr(fp); if (title1) fprintf(fp,"%s\n",title1); else fprintf(fp,"# Histogrammed data for fix %s\n",id); if (title2) fprintf(fp,"%s\n",title2); else fprintf(fp,"# TimeStep Number-of-bins " "Total-counts Missing-counts Min-value Max-value\n"); if (title3) fprintf(fp,"%s\n",title3); else fprintf(fp,"# Bin Coord Count Count/Total\n"); if (ferror(fp)) error->one(FLERR,"Error writing file header"); filepos = ftell(fp); } delete [] title1; delete [] title2; delete [] title3; // allocate and initialize memory for averaging if (beyond == EXTRA) nbins += 2; size_array_rows = nbins; bin = new double[nbins]; bin_total = new double[nbins]; bin_all = new double[nbins]; coord = new double[nbins]; stats_list = NULL; bin_list = NULL; vector = NULL; maxatom = 0; if (ave == WINDOW) { - memory->create(stats_list,nwindow,4,"histo:stats_list"); + memory->create(stats_list,nwindow,4,"ave/histo:stats_list"); memory->create(bin_list,nwindow,nbins,"ave/histo:bin_list"); } // initializations // set coord to bin centers if (beyond == EXTRA) { binsize = (hi-lo)/(nbins-2); bininv = 1.0/binsize; } else { binsize = (hi-lo)/nbins; bininv = 1.0/binsize; } if (beyond == EXTRA) { coord[0] = lo; coord[nbins-1] = hi; for (int i = 1; i < nbins-1; i++) coord[i] = lo + (i-1+0.5)*binsize; } else { for (int i = 0; i < nbins; i++) coord[i] = lo + (i+0.5)*binsize; } irepeat = 0; iwindow = window_limit = 0; stats_total[0] = stats_total[1] = stats_total[2] = stats_total[3] = 0.0; for (int i = 0; i < nbins; i++) bin_total[i] = 0.0; // nvalid = next step on which end_of_step does something // add nvalid to all computes that store invocation times // since don't know a priori which are invoked by this fix // once in end_of_step() can set timestep for ones actually invoked nvalid_last = -1; nvalid = nextvalid(); modify->addstep_compute_all(nvalid); } /* ---------------------------------------------------------------------- */ FixAveHisto::~FixAveHisto() { memory->destroy(which); memory->destroy(argindex); memory->destroy(value2index); for (int i = 0; i < nvalues; i++) delete [] ids[i]; memory->sfree(ids); if (fp && me == 0) fclose(fp); delete [] bin; delete [] bin_total; delete [] bin_all; delete [] coord; memory->destroy(stats_list); memory->destroy(bin_list); memory->destroy(vector); } /* ---------------------------------------------------------------------- */ int FixAveHisto::setmask() { int mask = 0; mask |= END_OF_STEP; return mask; } /* ---------------------------------------------------------------------- */ void FixAveHisto::init() { // set current indices for all computes,fixes,variables for (int i = 0; i < nvalues; i++) { if (which[i] == COMPUTE) { int icompute = modify->find_compute(ids[i]); if (icompute < 0) error->all(FLERR,"Compute ID for fix ave/histo does not exist"); value2index[i] = icompute; } else if (which[i] == FIX) { int ifix = modify->find_fix(ids[i]); if (ifix < 0) error->all(FLERR,"Fix ID for fix ave/histo does not exist"); value2index[i] = ifix; } else if (which[i] == VARIABLE) { int ivariable = input->variable->find(ids[i]); if (ivariable < 0) error->all(FLERR,"Variable name for fix ave/histo does not exist"); value2index[i] = ivariable; } } // need to reset nvalid if nvalid < ntimestep b/c minimize was performed if (nvalid < update->ntimestep) { irepeat = 0; nvalid = nextvalid(); modify->addstep_compute_all(nvalid); } } /* ---------------------------------------------------------------------- only does something if nvalid = current timestep ------------------------------------------------------------------------- */ void FixAveHisto::setup(int vflag) { end_of_step(); } /* ---------------------------------------------------------------------- */ void FixAveHisto::end_of_step() { int i,j,m; // skip if not step which requires doing something // error check if timestep was reset in an invalid manner bigint ntimestep = update->ntimestep; if (ntimestep < nvalid_last || ntimestep > nvalid) error->all(FLERR,"Invalid timestep reset for fix ave/histo"); if (ntimestep != nvalid) return; nvalid_last = nvalid; // zero if first step if (irepeat == 0) { stats[0] = stats[1] = 0.0; stats[2] = BIG; stats[3] = -BIG; for (i = 0; i < nbins; i++) bin[i] = 0.0; } // accumulate results of computes,fixes,variables to local copy // compute/fix/variable may invoke computes so wrap with clear/add modify->clearstep_compute(); for (i = 0; i < nvalues; i++) { m = value2index[i]; j = argindex[i]; // atom attributes if (which[i] == X) bin_atoms(&atom->x[0][j],3); else if (which[i] == V) bin_atoms(&atom->v[0][j],3); else if (which[i] == F) bin_atoms(&atom->f[0][j],3); // invoke compute if not previously invoked if (which[i] == COMPUTE) { Compute *compute = modify->compute[m]; if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_SCALAR)) { compute->compute_scalar(); compute->invoked_flag |= INVOKED_SCALAR; } bin_one(compute->scalar); } else { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } bin_one(compute->vector[j-1]); } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } bin_vector(compute->size_vector,compute->vector,1); } else { if (!(compute->invoked_flag & INVOKED_ARRAY)) { compute->compute_array(); compute->invoked_flag |= INVOKED_ARRAY; } if (compute->array) bin_vector(compute->size_array_rows,&compute->array[0][j-1], compute->size_array_cols); } } else if (kind == PERATOM) { if (!(compute->invoked_flag & INVOKED_PERATOM)) { compute->compute_peratom(); compute->invoked_flag |= INVOKED_PERATOM; } if (j == 0) bin_atoms(compute->vector_atom,1); else if (compute->array_atom) bin_atoms(&compute->array_atom[0][j-1],compute->size_peratom_cols); } else if (kind == LOCAL) { if (!(compute->invoked_flag & INVOKED_LOCAL)) { compute->compute_local(); compute->invoked_flag |= INVOKED_LOCAL; } if (j == 0) bin_vector(compute->size_local_rows,compute->vector_local,1); else if (compute->array_local) bin_vector(compute->size_local_rows,&compute->array_local[0][j-1], compute->size_local_cols); } // access fix fields, guaranteed to be ready } else if (which[i] == FIX) { Fix *fix = modify->fix[m]; if (kind == GLOBAL && mode == SCALAR) { if (j == 0) bin_one(fix->compute_scalar()); else bin_one(fix->compute_vector(j-1)); } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { int n = fix->size_vector; for (i = 0; i < n; i++) bin_one(fix->compute_vector(i)); } else { int n = fix->size_vector; for (i = 0; i < n; i++) bin_one(fix->compute_array(i,j-1)); } } else if (kind == PERATOM) { if (j == 0) bin_atoms(fix->vector_atom,1); else if (fix->array_atom) bin_atoms(fix->array_atom[j-1],fix->size_peratom_cols); } else if (kind == LOCAL) { if (j == 0) bin_vector(fix->size_local_rows,fix->vector_local,1); else if (fix->array_local) bin_vector(fix->size_local_rows,&fix->array_local[0][j-1], fix->size_local_cols); } // evaluate equal-style or vector-style or atom-style variable } else if (which[i] == VARIABLE) { if (kind == GLOBAL && mode == SCALAR) { if (j == 0) bin_one(input->variable->compute_equal(m)); else { double *varvec; int nvec = input->variable->compute_vector(m,&varvec); if (nvec < j) bin_one(0.0); else bin_one(varvec[j-1]); } } else if (kind == GLOBAL && mode == VECTOR) { double *varvec; int nvec = input->variable->compute_vector(m,&varvec); bin_vector(nvec,varvec,1); } else if (which[i] == VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo:vector"); } input->variable->compute_atom(m,igroup,vector,1,0); bin_atoms(vector,1); } } } // done if irepeat < nrepeat // else reset irepeat and nvalid irepeat++; if (irepeat < nrepeat) { nvalid += nevery; modify->addstep_compute(nvalid); return; } irepeat = 0; nvalid = ntimestep + nfreq - (nrepeat-1)*nevery; modify->addstep_compute(nvalid); // merge histogram stats across procs if necessary if (kind == PERATOM || kind == LOCAL) { MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world); MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world); MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world); stats[0] = stats_all[0]; stats[1] = stats_all[1]; stats[2] = stats_all[2]; stats[3] = stats_all[3]; for (i = 0; i < nbins; i++) bin[i] = bin_all[i]; } // if ave = ONE, only single Nfreq timestep value is needed // if ave = RUNNING, combine with all previous Nfreq timestep values // if ave = WINDOW, combine with nwindow most recent Nfreq timestep values if (ave == ONE) { stats_total[0] = stats[0]; stats_total[1] = stats[1]; stats_total[2] = stats[2]; stats_total[3] = stats[3]; for (i = 0; i < nbins; i++) bin_total[i] = bin[i]; } else if (ave == RUNNING) { stats_total[0] += stats[0]; stats_total[1] += stats[1]; stats_total[2] = MIN(stats_total[2],stats[2]); stats_total[3] = MAX(stats_total[3],stats[3]); for (i = 0; i < nbins; i++) bin_total[i] += bin[i]; } else if (ave == WINDOW) { stats_total[0] += stats[0]; if (window_limit) stats_total[0] -= stats_list[iwindow][0]; stats_list[iwindow][0] = stats[0]; stats_total[1] += stats[1]; if (window_limit) stats_total[1] -= stats_list[iwindow][1]; stats_list[iwindow][1] = stats[1]; if (window_limit) m = nwindow; else m = iwindow+1; stats_list[iwindow][2] = stats[2]; stats_total[2] = stats_list[0][2]; for (i = 1; i < m; i++) stats_total[2] = MIN(stats_total[2],stats_list[i][2]); stats_list[iwindow][3] = stats[3]; stats_total[3] = stats_list[0][3]; for (i = 1; i < m; i++) stats_total[3] = MAX(stats_total[3],stats_list[i][3]); for (i = 0; i < nbins; i++) { bin_total[i] += bin[i]; if (window_limit) bin_total[i] -= bin_list[iwindow][i]; bin_list[iwindow][i] = bin[i]; } iwindow++; if (iwindow == nwindow) { iwindow = 0; window_limit = 1; } } // output result to file if (fp && me == 0) { clearerr(fp); if (overwrite) fseek(fp,filepos,SEEK_SET); fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins, stats_total[0],stats_total[1],stats_total[2],stats_total[3]); if (stats_total[0] != 0.0) for (i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n", i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]); else for (i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0); if (ferror(fp)) error->one(FLERR,"Error writing out histogram data"); fflush(fp); if (overwrite) { long fileend = ftell(fp); if (fileend > 0) ftruncate(fileno(fp),fileend); } } } /* ---------------------------------------------------------------------- return Ith vector value ------------------------------------------------------------------------- */ double FixAveHisto::compute_vector(int i) { return stats_total[i]; } /* ---------------------------------------------------------------------- return I,J array value ------------------------------------------------------------------------- */ double FixAveHisto::compute_array(int i, int j) { if (j == 0) return coord[i]; else if (j == 1) return bin_total[i]; else if (stats_total[0] != 0.0) return bin_total[i]/stats_total[0]; return 0.0; } /* ---------------------------------------------------------------------- bin a single value ------------------------------------------------------------------------- */ void FixAveHisto::bin_one(double value) { stats[2] = MIN(stats[2],value); stats[3] = MAX(stats[3],value); if (value < lo) { if (beyond == IGNORE) { stats[1] += 1.0; return; } else bin[0] += 1.0; } else if (value > hi) { if (beyond == IGNORE) { stats[1] += 1.0; return; } else bin[nbins-1] += 1.0; } else { int ibin = static_cast ((value-lo)*bininv); ibin = MIN(ibin,nbins-1); if (beyond == EXTRA) ibin++; bin[ibin] += 1.0; } stats[0] += 1.0; } /* ---------------------------------------------------------------------- bin a vector of values with stride ------------------------------------------------------------------------- */ void FixAveHisto::bin_vector(int n, double *values, int stride) { int m = 0; for (int i = 0; i < n; i++) { bin_one(values[m]); m += stride; } } /* ---------------------------------------------------------------------- bin a per-atom vector of values with stride only bin if atom is in group ------------------------------------------------------------------------- */ void FixAveHisto::bin_atoms(double *values, int stride) { int *mask = atom->mask; int nlocal = atom->nlocal; int m = 0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) bin_one(values[m]); m += stride; } } /* ---------------------------------------------------------------------- parse optional args ------------------------------------------------------------------------- */ void FixAveHisto::options(int narg, char **arg) { // option defaults fp = NULL; ave = ONE; startstep = 0; mode = SCALAR; beyond = IGNORE; overwrite = 0; title1 = NULL; title2 = NULL; title3 = NULL; // optional args int iarg = 9 + nvalues; while (iarg < narg) { if (strcmp(arg[iarg],"file") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); if (me == 0) { fp = fopen(arg[iarg+1],"w"); if (fp == NULL) { char str[128]; sprintf(str,"Cannot open fix ave/histo file %s",arg[iarg+1]); error->one(FLERR,str); } } iarg += 2; } else if (strcmp(arg[iarg],"ave") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); if (strcmp(arg[iarg+1],"one") == 0) ave = ONE; else if (strcmp(arg[iarg+1],"running") == 0) ave = RUNNING; else if (strcmp(arg[iarg+1],"window") == 0) ave = WINDOW; else error->all(FLERR,"Illegal fix ave/histo command"); if (ave == WINDOW) { if (iarg+3 > narg) error->all(FLERR,"Illegal fix ave/histo command"); nwindow = force->inumeric(FLERR,arg[iarg+2]); if (nwindow <= 0) error->all(FLERR,"Illegal fix ave/histo command"); } iarg += 2; if (ave == WINDOW) iarg++; } else if (strcmp(arg[iarg],"start") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); startstep = force->inumeric(FLERR,arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"mode") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); if (strcmp(arg[iarg+1],"scalar") == 0) mode = SCALAR; else if (strcmp(arg[iarg+1],"vector") == 0) mode = VECTOR; else error->all(FLERR,"Illegal fix ave/histo command"); iarg += 2; } else if (strcmp(arg[iarg],"beyond") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); if (strcmp(arg[iarg+1],"ignore") == 0) beyond = IGNORE; else if (strcmp(arg[iarg+1],"end") == 0) beyond = END; else if (strcmp(arg[iarg+1],"extra") == 0) beyond = EXTRA; else error->all(FLERR,"Illegal fix ave/histo command"); iarg += 2; } else if (strcmp(arg[iarg],"overwrite") == 0) { overwrite = 1; iarg += 1; } else if (strcmp(arg[iarg],"title1") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); delete [] title1; int n = strlen(arg[iarg+1]) + 1; title1 = new char[n]; strcpy(title1,arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title2") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); delete [] title2; int n = strlen(arg[iarg+1]) + 1; title2 = new char[n]; strcpy(title2,arg[iarg+1]); iarg += 2; } else if (strcmp(arg[iarg],"title3") == 0) { if (iarg+2 > narg) error->all(FLERR,"Illegal fix ave/histo command"); delete [] title3; int n = strlen(arg[iarg+1]) + 1; title3 = new char[n]; strcpy(title3,arg[iarg+1]); iarg += 2; } else error->all(FLERR,"Illegal fix ave/histo command"); } } /* ---------------------------------------------------------------------- reallocate vectors for each input value, of length N ------------------------------------------------------------------------- */ void FixAveHisto::allocate_values(int n) { - memory->grow(which,n,"ave/time:which"); - memory->grow(argindex,n,"ave/time:argindex"); - memory->grow(value2index,n,"ave/time:value2index"); - ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/time:ids"); + memory->grow(which,n,"ave/hsito:which"); + memory->grow(argindex,n,"ave/histo:argindex"); + memory->grow(value2index,n,"ave/histo:value2index"); + ids = (char **) memory->srealloc(ids,n*sizeof(char *),"ave/histo:ids"); } /* ---------------------------------------------------------------------- calculate nvalid = next step on which end_of_step does something can be this timestep if multiple of nfreq and nrepeat = 1 else backup from next multiple of nfreq startstep is lower bound on nfreq multiple ------------------------------------------------------------------------- */ bigint FixAveHisto::nextvalid() { bigint nvalid = (update->ntimestep/nfreq)*nfreq + nfreq; while (nvalid < startstep) nvalid += nfreq; if (nvalid-nfreq == update->ntimestep && nrepeat == 1) nvalid = update->ntimestep; else nvalid -= (nrepeat-1)*nevery; if (nvalid < update->ntimestep) nvalid += nfreq; return nvalid; } diff --git a/src/fix_ave_histo_weight.cpp b/src/fix_ave_histo_weight.cpp index 8671a38a9..277a57a48 100644 --- a/src/fix_ave_histo_weight.cpp +++ b/src/fix_ave_histo_weight.cpp @@ -1,571 +1,570 @@ /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- Contributing author: Shawn Coleman (ARL) ------------------------------------------------------------------------- */ #include #include #include #include "fix_ave_histo_weight.h" #include "atom.h" #include "update.h" #include "modify.h" #include "compute.h" #include "group.h" #include "input.h" #include "variable.h" #include "memory.h" #include "error.h" #include "force.h" using namespace LAMMPS_NS; using namespace FixConst; enum{X,V,F,COMPUTE,FIX,VARIABLE}; enum{ONE,RUNNING}; enum{SCALAR,VECTOR,WINDOW}; enum{GLOBAL,PERATOM,LOCAL}; enum{IGNORE,END,EXTRA}; enum{SINGLE,VALUE}; #define INVOKED_SCALAR 1 #define INVOKED_VECTOR 2 #define INVOKED_ARRAY 4 #define INVOKED_PERATOM 8 #define INVOKED_LOCAL 16 #define BIG 1.0e20 /* ---------------------------------------------------------------------- */ FixAveHistoWeight::FixAveHistoWeight(LAMMPS *lmp, int narg, char **arg) : FixAveHisto(lmp, narg, arg) { // nvalues = 2 required for histo/weight if (nvalues != 2) error->all(FLERR,"Illegal fix ave/histo/weight command"); // check that length of 2 values is the same int size[2]; for (int i = 0; i < nvalues; i++) { if (which[i] == X || which[i] == V || which[i] == F) { size[i] = atom->nlocal; } else if (which[i] == COMPUTE && kind == GLOBAL && mode == SCALAR) { int icompute = modify->find_compute(ids[i]); size[i] = modify->compute[icompute]->size_vector; } else if (which[i] == COMPUTE && kind == GLOBAL && mode == VECTOR) { int icompute = modify->find_compute(ids[i]); size[i] = modify->compute[icompute]->size_array_rows; } else if (which[i] == COMPUTE && kind == PERATOM) { size[i] = atom->nlocal; } else if (which[i] == COMPUTE && kind == LOCAL) { int icompute = modify->find_compute(ids[i]); size[i] = modify->compute[icompute]->size_local_rows; } else if (which[i] == FIX && kind == GLOBAL && mode == SCALAR) { int ifix = modify->find_fix(ids[i]); size[i] = modify->fix[ifix]->size_vector; } else if (which[i] == FIX && kind == GLOBAL && mode == VECTOR) { int ifix = modify->find_fix(ids[i]); size[i]= modify->fix[ifix]->size_array_rows; } else if (which[i] == FIX && kind == PERATOM) { size[i] = atom->nlocal; } else if (which[i] == FIX && kind == LOCAL) { int ifix = modify->find_fix(ids[i]); size[i] = modify->fix[ifix]->size_local_rows; } else if (which[i] == VARIABLE && kind == PERATOM) { size[i] = atom->nlocal; } } if (size[0] != size[1]) error->all(FLERR,"Fix ave/histo/weight value and weight vector " "lengths do not match"); } /* ---------------------------------------------------------------------- */ void FixAveHistoWeight::end_of_step() { int i,j,m; // skip if not step which requires doing something // error check if timestep was reset in an invalid manner bigint ntimestep = update->ntimestep; if (ntimestep < nvalid_last || ntimestep > nvalid) error->all(FLERR,"Invalid timestep reset for fix ave/histo"); if (ntimestep != nvalid) return; nvalid_last = nvalid; // zero if first step if (irepeat == 0) { stats[0] = stats[1] = 0.0; stats[2] = BIG; stats[3] = -BIG; for (i = 0; i < nbins; i++) bin[i] = 0.0; } // first calculate weight factors, then bin single value // accumulate results of computes,fixes,variables to local copy // compute/fix/variable may invoke computes so wrap with clear/add modify->clearstep_compute(); // calcualte weight factors which are 2nd value (i = 1) double weight = 0.0; double *weights = NULL; int stride = 0; i = 1; m = value2index[i]; j = argindex[i]; // atom attributes if (which[i] == X) { weights = &atom->x[0][j]; stride = 3; } else if (which[i] == V){ weights = &atom->v[0][j]; stride = 3; bin_atoms(&atom->v[0][j],3); } else if (which[i] == F) { weights = &atom->f[0][j]; stride = 3; } // invoke compute if not previously invoked if (which[i] == COMPUTE) { + Compute *compute = modify->compute[m]; + if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_SCALAR)) { compute->compute_scalar(); compute->invoked_flag |= INVOKED_SCALAR; } weight = compute->scalar; } else { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } weight = compute->vector[j-1]; } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } weights = compute->vector; stride = 1; } else { if (!(compute->invoked_flag & INVOKED_ARRAY)) { compute->compute_array(); compute->invoked_flag |= INVOKED_ARRAY; } if (compute->array) weights = &compute->array[0][j-1]; stride = compute->size_array_cols; } } else if (kind == PERATOM) { if (!(compute->invoked_flag & INVOKED_PERATOM)) { compute->compute_peratom(); compute->invoked_flag |= INVOKED_PERATOM; } if (j == 0) { weights = compute->vector_atom; stride = 1; } else if (compute->array_atom) { weights = &compute->array_atom[0][j-1]; stride = compute->size_peratom_cols; } } else if (kind == LOCAL) { if (!(compute->invoked_flag & INVOKED_LOCAL)) { compute->compute_local(); compute->invoked_flag |= INVOKED_LOCAL; } if (j == 0) { weights = compute->vector_local; stride = 1; } else if (compute->array_local) { weights = &compute->array_local[0][j-1]; stride = compute->size_local_cols; } } // access fix fields, guaranteed to be ready } else if (which[i] == FIX) { Fix *fix = modify->fix[m]; if (kind == GLOBAL && mode == SCALAR) { if (j == 0) weight = fix->compute_scalar(); else weight = fix->compute_vector(j-1); - } else if (kind == GLOBAL && mode == VECTOR) { - - error->all(FLERR,"Illegal fix ave/spatial command"); - + error->all(FLERR,"Fix ave/histo/weight option not yet supported"); + // NOTE: need to allocate local storage if (j == 0) { int n = fix->size_vector; for (i = 0; i < n; i++) weights[n] = fix->compute_vector(i); } else { int n = fix->size_vector; for (i = 0; i < n; i++) weights[n] = fix->compute_array(i,j-1); } - } else if (kind == PERATOM) { if (j == 0) { weights = fix->vector_atom; stride = 1; } else if (fix->array_atom) { weights = fix->array_atom[j-1]; stride = fix->size_peratom_cols; } } else if (kind == LOCAL) { if (j == 0) { weights = fix->vector_local; stride = 1; } else if (fix->array_local) { weights = &fix->array_local[0][j-1]; stride = fix->size_local_cols; } } // evaluate equal-style variable } else if (which[i] == VARIABLE && kind == GLOBAL) { weight = input->variable->compute_equal(m); } else if (which[i] == VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } input->variable->compute_atom(m,igroup,vector,1,0); weights = vector; stride = 1; } // bin values using weights, values are 1st value (i = 0) i = 0; m = value2index[i]; j = argindex[i]; // atom attributes if (which[i] == X && weights != NULL) bin_atoms_weights(&atom->x[0][j],3,weights,stride); else if (which[i] == V && weights != NULL) bin_atoms_weights(&atom->v[0][j],3,weights,stride); else if (which[i] == F && weights != NULL) bin_atoms_weights(&atom->f[0][j],3,weights,stride); // invoke compute if not previously invoked if (which[i] == COMPUTE) { Compute *compute = modify->compute[m]; if (kind == GLOBAL && mode == SCALAR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_SCALAR)) { compute->compute_scalar(); compute->invoked_flag |= INVOKED_SCALAR; } bin_one_weights(compute->scalar,weight); } else { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } bin_one_weights(compute->vector[j-1],weight); } } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { if (!(compute->invoked_flag & INVOKED_VECTOR)) { compute->compute_vector(); compute->invoked_flag |= INVOKED_VECTOR; } bin_vector_weights(compute->size_vector,compute->vector,1, weights,stride); } else { if (!(compute->invoked_flag & INVOKED_ARRAY)) { compute->compute_array(); compute->invoked_flag |= INVOKED_ARRAY; } if (compute->array) bin_vector_weights(compute->size_array_rows,&compute->array[0][j-1], compute->size_array_cols,weights,stride); } } else if (kind == PERATOM) { if (!(compute->invoked_flag & INVOKED_PERATOM)) { compute->compute_peratom(); compute->invoked_flag |= INVOKED_PERATOM; } if (j == 0) bin_atoms_weights(compute->vector_atom,1,weights, stride); else if (compute->array_atom) bin_atoms_weights(&compute->array_atom[0][j-1], compute->size_peratom_cols,weights,stride); } else if (kind == LOCAL) { if (!(compute->invoked_flag & INVOKED_LOCAL)) { compute->compute_local(); compute->invoked_flag |= INVOKED_LOCAL; } if (j == 0) bin_vector_weights(compute->size_local_rows, compute->vector_local,1,weights,stride); else if (compute->array_local) bin_vector_weights(compute->size_local_rows, &compute->array_local[0][j-1], compute->size_local_cols,weights,stride); } // access fix fields, guaranteed to be ready } else if (which[i] == FIX) { Fix *fix = modify->fix[m]; if (kind == GLOBAL && mode == SCALAR) { if (j == 0) bin_one_weights(fix->compute_scalar(),weight); else bin_one_weights(fix->compute_vector(j-1),weight); } else if (kind == GLOBAL && mode == VECTOR) { if (j == 0) { int n = fix->size_vector; for (i = 0; i < n; i++) bin_one_weights(fix->compute_vector(i),weights[i*stride]); } else { int n = fix->size_vector; for (i = 0; i < n; i++) bin_one_weights(fix->compute_array(i,j-1),weights[i*stride]); } } else if (kind == PERATOM) { if (j == 0) bin_atoms_weights(fix->vector_atom,1,weights,stride); else if (fix->array_atom) bin_atoms_weights(fix->array_atom[j-1],fix->size_peratom_cols, weights,stride); } else if (kind == LOCAL) { if (j == 0) bin_vector_weights(fix->size_local_rows,fix->vector_local,1, weights,stride); else if (fix->array_local) bin_vector_weights(fix->size_local_rows,&fix->array_local[0][j-1], fix->size_local_cols,weights,stride); } // evaluate equal-style variable } else if (which[i] == VARIABLE && kind == GLOBAL) { bin_one_weights(input->variable->compute_equal(m),weight); } else if (which[i] == VARIABLE && kind == PERATOM) { if (atom->nmax > maxatom) { memory->destroy(vector); maxatom = atom->nmax; memory->create(vector,maxatom,"ave/histo/weight:vector"); } input->variable->compute_atom(m,igroup,vector,1,0); bin_atoms_weights(vector,1,weights,stride); } // code beyond this point is identical to FixAveHisto // done if irepeat < nrepeat // else reset irepeat and nvalid irepeat++; if (irepeat < nrepeat) { nvalid += nevery; modify->addstep_compute(nvalid); return; } irepeat = 0; nvalid = ntimestep + nfreq - (nrepeat-1)*nevery; modify->addstep_compute(nvalid); // merge histogram stats across procs if necessary if (kind == PERATOM || kind == LOCAL) { MPI_Allreduce(stats,stats_all,2,MPI_DOUBLE,MPI_SUM,world); MPI_Allreduce(&stats[2],&stats_all[2],1,MPI_DOUBLE,MPI_MIN,world); MPI_Allreduce(&stats[3],&stats_all[3],1,MPI_DOUBLE,MPI_MAX,world); MPI_Allreduce(bin,bin_all,nbins,MPI_DOUBLE,MPI_SUM,world); stats[0] = stats_all[0]; stats[1] = stats_all[1]; stats[2] = stats_all[2]; stats[3] = stats_all[3]; for (i = 0; i < nbins; i++) bin[i] = bin_all[i]; } // if ave = ONE, only single Nfreq timestep value is needed // if ave = RUNNING, combine with all previous Nfreq timestep values // if ave = WINDOW, combine with nwindow most recent Nfreq timestep values if (ave == ONE) { stats_total[0] = stats[0]; stats_total[1] = stats[1]; stats_total[2] = stats[2]; stats_total[3] = stats[3]; for (i = 0; i < nbins; i++) bin_total[i] = bin[i]; } else if (ave == RUNNING) { stats_total[0] += stats[0]; stats_total[1] += stats[1]; stats_total[2] = MIN(stats_total[2],stats[2]); stats_total[3] = MAX(stats_total[3],stats[3]); for (i = 0; i < nbins; i++) bin_total[i] += bin[i]; } else if (ave == WINDOW) { stats_total[0] += stats[0]; if (window_limit) stats_total[0] -= stats_list[iwindow][0]; stats_list[iwindow][0] = stats[0]; stats_total[1] += stats[1]; if (window_limit) stats_total[1] -= stats_list[iwindow][1]; stats_list[iwindow][1] = stats[1]; if (window_limit) m = nwindow; else m = iwindow+1; stats_list[iwindow][2] = stats[2]; stats_total[2] = stats_list[0][2]; for (i = 1; i < m; i++) stats_total[2] = MIN(stats_total[2],stats_list[i][2]); stats_list[iwindow][3] = stats[3]; stats_total[3] = stats_list[0][3]; for (i = 1; i < m; i++) stats_total[3] = MAX(stats_total[3],stats_list[i][3]); for (i = 0; i < nbins; i++) { bin_total[i] += bin[i]; if (window_limit) bin_total[i] -= bin_list[iwindow][i]; bin_list[iwindow][i] = bin[i]; } iwindow++; if (iwindow == nwindow) { iwindow = 0; window_limit = 1; } } // output result to file if (fp && me == 0) { clearerr(fp); if (overwrite) fseek(fp,filepos,SEEK_SET); fprintf(fp,BIGINT_FORMAT " %d %g %g %g %g\n",ntimestep,nbins, stats_total[0],stats_total[1],stats_total[2],stats_total[3]); if (stats_total[0] != 0.0) for (i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n", i+1,coord[i],bin_total[i],bin_total[i]/stats_total[0]); else for (i = 0; i < nbins; i++) fprintf(fp,"%d %g %g %g\n",i+1,coord[i],0.0,0.0); if (ferror(fp)) error->one(FLERR,"Error writing out histogram data"); fflush(fp); if (overwrite) { long fileend = ftell(fp); if (fileend > 0) ftruncate(fileno(fp),fileend); } } } /* ---------------------------------------------------------------------- bin a single value with weight) ------------------------------------------------------------------------- */ void FixAveHistoWeight::bin_one_weights(double value, double weight) { stats[2] = MIN(stats[2],value); stats[3] = MAX(stats[3],value); if (value < lo) { if (beyond == IGNORE) { stats[1] += weight; return; } else bin[0] += weight; } else if (value > hi) { if (beyond == IGNORE) { stats[1] += weight; return; } else bin[nbins-1] += weight; } else { int ibin = static_cast ((value-lo)*bininv); ibin = MIN(ibin,nbins-1); if (beyond == EXTRA) ibin++; bin[ibin] += weight; } stats[0] += weight; } /* ---------------------------------------------------------------------- bin a vector of values with weights values and weights each have a stride ------------------------------------------------------------------------- */ void FixAveHistoWeight::bin_vector_weights(int n, double *values, int stride, double *weights, int stridewt) { int m = 0; int m2 = 0; for (int i = 0; i < n; i++) { bin_one_weights(values[m],weights[m2]); m += stride; m2 += stridewt; } } /* ---------------------------------------------------------------------- bin a per-atom vector of values with weights values and weights each have a stride only bin if atom is in group ------------------------------------------------------------------------- */ void FixAveHistoWeight::bin_atoms_weights(double *values, int stride, double *weights, int stridewt) { int *mask = atom->mask; int nlocal = atom->nlocal; int m = 0; int m2 = 0; for (int i = 0; i < nlocal; i++) { if (mask[i] & groupbit) bin_one_weights(values[m],weights[m2]); m += stride; m2 += stridewt; } } diff --git a/src/version.h b/src/version.h index 9aa19faf5..bcce3d4e3 100644 --- a/src/version.h +++ b/src/version.h @@ -1 +1 @@ -#define LAMMPS_VERSION "28 Jul 2016" +#define LAMMPS_VERSION "30 Jul 2016"