diff --git a/doc/src/Eqs/fix_rhok.jpg b/doc/src/Eqs/fix_rhok.jpg new file mode 100644 index 000000000..829a866be Binary files /dev/null and b/doc/src/Eqs/fix_rhok.jpg differ diff --git a/doc/src/Eqs/fix_rhok.tex b/doc/src/Eqs/fix_rhok.tex new file mode 100644 index 000000000..a468dfedc --- /dev/null +++ b/doc/src/Eqs/fix_rhok.tex @@ -0,0 +1,11 @@ +\documentclass[12pt]{article} + +\begin{document} + +\begin{eqnarray*} + U &=& \frac{1}{2} K (|\rho_{\vec{k}}| - a)^2 \\ + \rho_{\vec{k}} &=& \sum_j^N \exp(-i\vec{k} \cdot \vec{r}_j )/\sqrt{N} \\ + \vec{k} &=& (2\pi n_x /L_x , 2\pi n_y /L_y , 2\pi n_z/L_z ) +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 8eed777e4..40527dabb 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -1,1250 +1,1251 @@ "Previous Section"_Section_start.html - "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Section_packages.html :c :link(lws,http://lammps.sandia.gov) :link(ld,Manual.html) :link(lc,Section_commands.html#comm) :line 3. Commands :h3 This section describes how a LAMMPS input script is formatted and the input script commands used to define a LAMMPS simulation. 3.1 "LAMMPS input script"_#cmd_1 3.2 "Parsing rules"_#cmd_2 3.3 "Input script structure"_#cmd_3 3.4 "Commands listed by category"_#cmd_4 3.5 "Commands listed alphabetically"_#cmd_5 :all(b) :line :line 3.1 LAMMPS input script :link(cmd_1),h4 LAMMPS executes by reading commands from a input script (text file), one line at a time. When the input script ends, LAMMPS exits. Each command causes LAMMPS to take some action. It may set an internal variable, read in a file, or run a simulation. Most commands have default settings, which means you only need to use the command if you wish to change the default. In many cases, the ordering of commands in an input script is not important. However the following rules apply: (1) LAMMPS does not read your entire input script and then perform a simulation with all the settings. Rather, the input script is read one line at a time and each command takes effect when it is read. Thus this sequence of commands: timestep 0.5 run 100 run 100 :pre does something different than this sequence: run 100 timestep 0.5 run 100 :pre In the first case, the specified timestep (0.5 fmsec) is used for two simulations of 100 timesteps each. In the 2nd case, the default timestep (1.0 fmsec) is used for the 1st 100 step simulation and a 0.5 fmsec timestep is used for the 2nd one. (2) Some commands are only valid when they follow other commands. For example you cannot set the temperature of a group of atoms until atoms have been defined and a group command is used to define which atoms belong to the group. (3) Sometimes command B will use values that can be set by command A. This means command A must precede command B in the input script if it is to have the desired effect. For example, the "read_data"_read_data.html command initializes the system by setting up the simulation box and assigning atoms to processors. If default values are not desired, the "processors"_processors.html and "boundary"_boundary.html commands need to be used before read_data to tell LAMMPS how to map processors to the simulation box. Many input script errors are detected by LAMMPS and an ERROR or WARNING message is printed. "This section"_Section_errors.html gives more information on what errors mean. The documentation for each command lists restrictions on how the command can be used. :line 3.2 Parsing rules :link(cmd_2),h4 Each non-blank line in the input script is treated as a command. LAMMPS commands are case sensitive. Command names are lower-case, as are specified command arguments. Upper case letters may be used in file names or user-chosen ID strings. Here is how each line in the input script is parsed by LAMMPS: (1) If the last printable character on the line is a "&" character, the command is assumed to continue on the next line. The next line is concatenated to the previous line by removing the "&" character and line break. This allows long commands to be continued across two or more lines. See the discussion of triple quotes in (6) for how to continue a command across multiple line without using "&" characters. (2) All characters from the first "#" character onward are treated as comment and discarded. See an exception in (6). Note that a comment after a trailing "&" character will prevent the command from continuing on the next line. Also note that for multi-line commands a single leading "#" will comment out the entire command. (3) The line is searched repeatedly for $ characters, which indicate variables that are replaced with a text string. See an exception in (6). If the $ is followed by curly brackets, then the variable name is the text inside the curly brackets. If no curly brackets follow the $, then the variable name is the single character immediately following the $. Thus $\{myTemp\} and $x refer to variable names "myTemp" and "x". How the variable is converted to a text string depends on what style of variable it is; see the "variable"_variable.html doc page for details. It can be a variable that stores multiple text strings, and return one of them. The returned text string can be multiple "words" (space separated) which will then be interpreted as multiple arguments in the input command. The variable can also store a numeric formula which will be evaluated and its numeric result returned as a string. As a special case, if the $ is followed by parenthesis, then the text inside the parenthesis is treated as an "immediate" variable and evaluated as an "equal-style variable"_variable.html. This is a way to use numeric formulas in an input script without having to assign them to variable names. For example, these 3 input script lines: variable X equal (xlo+xhi)/2+sqrt(v_area) region 1 block $X 2 INF INF EDGE EDGE variable X delete :pre can be replaced by region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre so that you do not have to define (or discard) a temporary variable X. Note that neither the curly-bracket or immediate form of variables can contain nested $ characters for other variables to substitute for. Thus you cannot do this: variable a equal 2 variable b2 equal 4 print "B2 = $\{b$a\}" :pre Nor can you specify this $($x-1.0) for an immediate variable, but you could use $(v_x-1.0), since the latter is valid syntax for an "equal-style variable"_variable.html. See the "variable"_variable.html command for more details of how strings are assigned to variables and evaluated, and how they can be used in input script commands. (4) The line is broken into "words" separated by whitespace (tabs, spaces). Note that words can thus contain letters, digits, underscores, or punctuation characters. (5) The first word is the command name. All successive words in the line are arguments. (6) If you want text with spaces to be treated as a single argument, it can be enclosed in either single or double or triple quotes. A long single argument enclosed in single or double quotes can span multiple lines if the "&" character is used, as described above. When the lines are concatenated together (and the "&" characters and line breaks removed), the text will become a single line. If you want multiple lines of an argument to retain their line breaks, the text can be enclosed in triple quotes, in which case "&" characters are not needed. For example: print "Volume = $v" print 'Volume = $v' if "$\{steps\} > 1000" then quit variable a string "red green blue & purple orange cyan" print """ System volume = $v System temperature = $t """ :pre In each case, the single, double, or triple quotes are removed when the single argument they enclose is stored internally. See the "dump modify format"_dump_modify.html, "print"_print.html, "if"_if.html, and "python"_python.html commands for examples. A "#" or "$" character that is between quotes will not be treated as a comment indicator in (2) or substituted for as a variable in (3). NOTE: If the argument is itself a command that requires a quoted argument (e.g. using a "print"_print.html command as part of an "if"_if.html or "run every"_run.html command), then single, double, or triple quotes can be nested in the usual manner. See the doc pages for those commands for examples. Only one of level of nesting is allowed, but that should be sufficient for most use cases. :line 3.3 Input script structure :h4,link(cmd_3) This section describes the structure of a typical LAMMPS input script. The "examples" directory in the LAMMPS distribution contains many sample input scripts; the corresponding problems are discussed in "Section 7"_Section_example.html, and animated on the "LAMMPS WWW Site"_lws. A LAMMPS input script typically has 4 parts: Initialization Atom definition Settings Run a simulation :ol The last 2 parts can be repeated as many times as desired. I.e. run a simulation, change some settings, run some more, etc. Each of the 4 parts is now described in more detail. Remember that almost all the commands need only be used if a non-default value is desired. (1) Initialization Set parameters that need to be defined before atoms are created or read-in from a file. The relevant commands are "units"_units.html, "dimension"_dimension.html, "newton"_newton.html, "processors"_processors.html, "boundary"_boundary.html, "atom_style"_atom_style.html, "atom_modify"_atom_modify.html. If force-field parameters appear in the files that will be read, these commands tell LAMMPS what kinds of force fields are being used: "pair_style"_pair_style.html, "bond_style"_bond_style.html, "angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html, "improper_style"_improper_style.html. (2) Atom definition There are 3 ways to define atoms in LAMMPS. Read them in from a data or restart file via the "read_data"_read_data.html or "read_restart"_read_restart.html commands. These files can contain molecular topology information. Or create atoms on a lattice (with no molecular topology), using these commands: "lattice"_lattice.html, "region"_region.html, "create_box"_create_box.html, "create_atoms"_create_atoms.html. The entire set of atoms can be duplicated to make a larger simulation using the "replicate"_replicate.html command. (3) Settings Once atoms and molecular topology are defined, a variety of settings can be specified: force field coefficients, simulation parameters, output options, etc. Force field coefficients are set by these commands (they can also be set in the read-in files): "pair_coeff"_pair_coeff.html, "bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html, "dihedral_coeff"_dihedral_coeff.html, "improper_coeff"_improper_coeff.html, "kspace_style"_kspace_style.html, "dielectric"_dielectric.html, "special_bonds"_special_bonds.html. Various simulation parameters are set by these commands: "neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html, "group"_group.html, "timestep"_timestep.html, "reset_timestep"_reset_timestep.html, "run_style"_run_style.html, "min_style"_min_style.html, "min_modify"_min_modify.html. Fixes impose a variety of boundary conditions, time integration, and diagnostic options. The "fix"_fix.html command comes in many flavors. Various computations can be specified for execution during a simulation using the "compute"_compute.html, "compute_modify"_compute_modify.html, and "variable"_variable.html commands. Output options are set by the "thermo"_thermo.html, "dump"_dump.html, and "restart"_restart.html commands. (4) Run a simulation A molecular dynamics simulation is run using the "run"_run.html command. Energy minimization (molecular statics) is performed using the "minimize"_minimize.html command. A parallel tempering (replica-exchange) simulation can be run using the "temper"_temper.html command. :line 3.4 Commands listed by category :link(cmd_4),h4 This section lists core LAMMPS commands, grouped by category. The "next section"_#cmd_5 lists all commands alphabetically. The next section also includes (long) lists of style options for entries that appear in the following categories as a single command (fix, compute, pair, etc). Commands that are added by user packages are not included in the categories here, but they are in the next section. Initialization: "newton"_newton.html, "package"_package.html, "processors"_processors.html, "suffix"_suffix.html, "units"_units.html Setup simulation box: "boundary"_boundary.html, "box"_box.html, "change_box"_change_box.html, "create_box"_create_box.html, "dimension"_dimension.html, "lattice"_lattice.html, "region"_region.html Setup atoms: "atom_modify"_atom_modify.html, "atom_style"_atom_style.html, "balance"_balance.html, "create_atoms"_create_atoms.html, "create_bonds"_create_bonds.html, "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "displace_atoms"_displace_atoms.html, "group"_group.html, "mass"_mass.html, "molecule"_molecule.html, "read_data"_read_data.html, "read_dump"_read_dump.html, "read_restart"_read_restart.html, "replicate"_replicate.html, "set"_set.html, "velocity"_velocity.html Force fields: "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, "bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html, "bond_write"_bond_write.html, "dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html, "dihedral_style"_dihedral_style.html, "improper_coeff"_improper_coeff.html, "improper_style"_improper_style.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html, "pair_style"_pair_style.html, "pair_write"_pair_write.html, "special_bonds"_special_bonds.html Settings: "comm_modify"_comm_modify.html, "comm_style"_comm_style.html, "info"_info.html, "min_modify"_min_modify.html, "min_style"_min_style.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "partition"_partition.html, "reset_timestep"_reset_timestep.html, "run_style"_run_style.html, "timer"_timer.html, "timestep"_timestep.html Operations within timestepping (fixes) and diagnostics (computes): "compute"_compute.html, "compute_modify"_compute_modify.html, "fix"_fix.html, "fix_modify"_fix_modify.html, "uncompute"_uncompute.html, "unfix"_unfix.html Output: "dump image"_dump_image.html, "dump movie"_dump_image.html, "dump"_dump.html, "dump_modify"_dump_modify.html, "restart"_restart.html, "thermo"_thermo.html, "thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, "undump"_undump.html, "write_coeff"_write_coeff.html, "write_data"_write_data.html, "write_dump"_write_dump.html, "write_restart"_write_restart.html Actions: "minimize"_minimize.html, "neb"_neb.html, "prd"_prd.html, "rerun"_rerun.html, "run"_run.html, "tad"_tad.html, "temper"_temper.html Input script control: "clear"_clear.html, "echo"_echo.html, "if"_if.html, "include"_include.html, "jump"_jump.html, "label"_label.html, "log"_log.html, "next"_next.html, "print"_print.html, "python"_python.html, "quit"_quit.html, "shell"_shell.html, "variable"_variable.html :line 3.5 Individual commands :h4,link(cmd_5),link(comm) This section lists all LAMMPS commands alphabetically, with a separate listing below of styles within certain commands. The "previous section"_#cmd_4 lists the same commands, grouped by category. Note that some style options for some commands are part of specific LAMMPS packages, which means they cannot be used unless the package was included when LAMMPS was built. Not all packages are included in a default LAMMPS build. These dependencies are listed as Restrictions in the command's documentation. "angle_coeff"_angle_coeff.html, "angle_style"_angle_style.html, "atom_modify"_atom_modify.html, "atom_style"_atom_style.html, "balance"_balance.html, "bond_coeff"_bond_coeff.html, "bond_style"_bond_style.html, "bond_write"_bond_write.html, "boundary"_boundary.html, "box"_box.html, "change_box"_change_box.html, "clear"_clear.html, "comm_modify"_comm_modify.html, "comm_style"_comm_style.html, "compute"_compute.html, "compute_modify"_compute_modify.html, "create_atoms"_create_atoms.html, "create_bonds"_create_bonds.html, "create_box"_create_box.html, "delete_atoms"_delete_atoms.html, "delete_bonds"_delete_bonds.html, "dielectric"_dielectric.html, "dihedral_coeff"_dihedral_coeff.html, "dihedral_style"_dihedral_style.html, "dimension"_dimension.html, "displace_atoms"_displace_atoms.html, "dump"_dump.html, "dump image"_dump_image.html, "dump_modify"_dump_modify.html, "dump movie"_dump_image.html, "echo"_echo.html, "fix"_fix.html, "fix_modify"_fix_modify.html, "group"_group.html, "if"_if.html, "info"_info.html, "improper_coeff"_improper_coeff.html, "improper_style"_improper_style.html, "include"_include.html, "jump"_jump.html, "kspace_modify"_kspace_modify.html, "kspace_style"_kspace_style.html, "label"_label.html, "lattice"_lattice.html, "log"_log.html, "mass"_mass.html, "minimize"_minimize.html, "min_modify"_min_modify.html, "min_style"_min_style.html, "molecule"_molecule.html, "neb"_neb.html, "neigh_modify"_neigh_modify.html, "neighbor"_neighbor.html, "newton"_newton.html, "next"_next.html, "package"_package.html, "pair_coeff"_pair_coeff.html, "pair_modify"_pair_modify.html, "pair_style"_pair_style.html, "pair_write"_pair_write.html, "partition"_partition.html, "prd"_prd.html, "print"_print.html, "processors"_processors.html, "python"_python.html, "quit"_quit.html, "read_data"_read_data.html, "read_dump"_read_dump.html, "read_restart"_read_restart.html, "region"_region.html, "replicate"_replicate.html, "rerun"_rerun.html, "reset_timestep"_reset_timestep.html, "restart"_restart.html, "run"_run.html, "run_style"_run_style.html, "set"_set.html, "shell"_shell.html, "special_bonds"_special_bonds.html, "suffix"_suffix.html, "tad"_tad.html, "temper"_temper.html, "thermo"_thermo.html, "thermo_modify"_thermo_modify.html, "thermo_style"_thermo_style.html, "timer"_timer.html, "timestep"_timestep.html, "uncompute"_uncompute.html, "undump"_undump.html, "unfix"_unfix.html, "units"_units.html, "variable"_variable.html, "velocity"_velocity.html, "write_coeff"_write_coeff.html, "write_data"_write_data.html, "write_dump"_write_dump.html, "write_restart"_write_restart.html :tb(c=6,ea=c) These are additional commands in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "dump netcdf"_dump_netcdf.html, "dump netcdf/mpiio"_dump_netcdf.html, "dump vtk"_dump_vtk.html, "group2ndx"_group2ndx.html, "ndx2group"_group2ndx.html, "temper/grem"_temper_grem.html, "temper/npt"_temper_npt.html :tb(c=3,ea=c) :line Fix styles :h4 See the "fix"_fix.html command for one-line descriptions of each style or click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "adapt"_fix_adapt.html, "addforce"_fix_addforce.html, "append/atoms"_fix_append_atoms.html, "atom/swap"_fix_atom_swap.html, "aveforce"_fix_aveforce.html, "ave/atom"_fix_ave_atom.html, "ave/chunk"_fix_ave_chunk.html, "ave/correlate"_fix_ave_correlate.html, "ave/histo"_fix_ave_histo.html, "ave/histo/weight"_fix_ave_histo.html, "ave/time"_fix_ave_time.html, "balance"_fix_balance.html, "bond/break"_fix_bond_break.html, "bond/create"_fix_bond_create.html, "bond/swap"_fix_bond_swap.html, "box/relax"_fix_box_relax.html, "cmap"_fix_cmap.html, "controller"_fix_controller.html, "deform (k)"_fix_deform.html, "deposit"_fix_deposit.html, "drag"_fix_drag.html, "dt/reset"_fix_dt_reset.html, "efield"_fix_efield.html, "ehex"_fix_ehex.html, "enforce2d"_fix_enforce2d.html, "evaporate"_fix_evaporate.html, "external"_fix_external.html, "freeze"_fix_freeze.html, "gcmc"_fix_gcmc.html, "gld"_fix_gld.html, "gravity (o)"_fix_gravity.html, "halt"_fix_halt.html, "heat"_fix_heat.html, "indent"_fix_indent.html, "latte"_fix_latte.html, "langevin (k)"_fix_langevin.html, "lineforce"_fix_lineforce.html, "momentum (k)"_fix_momentum.html, "move"_fix_move.html, "mscg"_fix_mscg.html, "msst"_fix_msst.html, "neb"_fix_neb.html, "nph (ko)"_fix_nh.html, "nphug (o)"_fix_nphug.html, "nph/asphere (o)"_fix_nph_asphere.html, "nph/body"_fix_nph_body.html, "nph/sphere (o)"_fix_nph_sphere.html, "npt (kio)"_fix_nh.html, "npt/asphere (o)"_fix_npt_asphere.html, "npt/body"_fix_npt_body.html, "npt/sphere (o)"_fix_npt_sphere.html, "nve (kio)"_fix_nve.html, "nve/asphere (i)"_fix_nve_asphere.html, "nve/asphere/noforce"_fix_nve_asphere_noforce.html, "nve/body"_fix_nve_body.html, "nve/limit"_fix_nve_limit.html, "nve/line"_fix_nve_line.html, "nve/noforce"_fix_nve_noforce.html, "nve/sphere (o)"_fix_nve_sphere.html, "nve/tri"_fix_nve_tri.html, "nvt (iko)"_fix_nh.html, "nvt/asphere (o)"_fix_nvt_asphere.html, "nvt/body"_fix_nvt_body.html, "nvt/sllod (io)"_fix_nvt_sllod.html, "nvt/sphere (o)"_fix_nvt_sphere.html, "oneway"_fix_oneway.html, "orient/bcc"_fix_orient.html, "orient/fcc"_fix_orient.html, "planeforce"_fix_planeforce.html, "poems"_fix_poems.html, "pour"_fix_pour.html, "press/berendsen"_fix_press_berendsen.html, "print"_fix_print.html, "property/atom"_fix_property_atom.html, "python"_fix_python.html, "qeq/comb (o)"_fix_qeq_comb.html, "qeq/dynamic"_fix_qeq.html, "qeq/fire"_fix_qeq.html, "qeq/point"_fix_qeq.html, "qeq/shielded"_fix_qeq.html, "qeq/slater"_fix_qeq.html, "rattle"_fix_shake.html, "reax/bonds"_fix_reax_bonds.html, "recenter"_fix_recenter.html, "restrain"_fix_restrain.html, "rigid (o)"_fix_rigid.html, "rigid/nph (o)"_fix_rigid.html, "rigid/npt (o)"_fix_rigid.html, "rigid/nve (o)"_fix_rigid.html, "rigid/nvt (o)"_fix_rigid.html, "rigid/small (o)"_fix_rigid.html, "rigid/small/nph (o)"_fix_rigid.html, "rigid/small/npt (o)"_fix_rigid.html, "rigid/small/nve (o)"_fix_rigid.html, "rigid/small/nvt (o)"_fix_rigid.html, "setforce (k)"_fix_setforce.html, "shake"_fix_shake.html, "spring"_fix_spring.html, "spring/chunk"_fix_spring_chunk.html, "spring/rg"_fix_spring_rg.html, "spring/self"_fix_spring_self.html, "srd"_fix_srd.html, "store/force"_fix_store_force.html, "store/state"_fix_store_state.html, "temp/berendsen"_fix_temp_berendsen.html, "temp/csld"_fix_temp_csvr.html, "temp/csvr"_fix_temp_csvr.html, "temp/rescale"_fix_temp_rescale.html, "tfmc"_fix_tfmc.html, "thermal/conductivity"_fix_thermal_conductivity.html, "tmd"_fix_tmd.html, "ttm"_fix_ttm.html, "tune/kspace"_fix_tune_kspace.html, "vector"_fix_vector.html, "viscosity"_fix_viscosity.html, "viscous"_fix_viscous.html, "wall/colloid"_fix_wall.html, "wall/gran"_fix_wall_gran.html, "wall/gran/region"_fix_wall_gran_region.html, "wall/harmonic"_fix_wall.html, "wall/lj1043"_fix_wall.html, "wall/lj126"_fix_wall.html, "wall/lj93"_fix_wall.html, "wall/piston"_fix_wall_piston.html, "wall/reflect (k)"_fix_wall_reflect.html, "wall/region"_fix_wall_region.html, "wall/srd"_fix_wall_srd.html :tb(c=8,ea=c) These are additional fix styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "adapt/fep"_fix_adapt_fep.html, "addtorque"_fix_addtorque.html, "atc"_fix_atc.html, "ave/correlate/long"_fix_ave_correlate_long.html, "colvars"_fix_colvars.html, "dpd/energy"_fix_dpd_energy.html, "drude"_fix_drude.html, "drude/transform/direct"_fix_drude_transform.html, "drude/transform/reverse"_fix_drude_transform.html, "edpd/source"_fix_dpd_source.html, "eos/cv"_fix_eos_cv.html, "eos/table"_fix_eos_table.html, "eos/table/rx"_fix_eos_table_rx.html, "filter/corotate"_fix_filter_corotate.html, "flow/gauss"_fix_flow_gauss.html, "gle"_fix_gle.html, "grem"_fix_grem.html, "imd"_fix_imd.html, "ipi"_fix_ipi.html, "langevin/drude"_fix_langevin_drude.html, "langevin/eff"_fix_langevin_eff.html, "lb/fluid"_fix_lb_fluid.html, "lb/momentum"_fix_lb_momentum.html, "lb/pc"_fix_lb_pc.html, "lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html, "lb/viscous"_fix_lb_viscous.html, "meso"_fix_meso.html, "manifoldforce"_fix_manifoldforce.html, "meso/stationary"_fix_meso_stationary.html, "mvv/dpd"_fix_mvv_dpd.html, "mvv/edpd"_fix_mvv_dpd.html, "mvv/tdpd"_fix_mvv_dpd.html, "nve/dot"_fix_nve_dot.html, "nve/dotc/langevin"_fix_nve_dotc_langevin.html, "nve/manifold/rattle"_fix_nve_manifold_rattle.html, "nvk"_fix_nvk.html, "nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "nph/eff"_fix_nh_eff.html, "npt/eff"_fix_nh_eff.html, "nve/eff"_fix_nve_eff.html, "nvt/eff"_fix_nh_eff.html, "nvt/sllod/eff"_fix_nvt_sllod_eff.html, "phonon"_fix_phonon.html, "pimd"_fix_pimd.html, "qbmsst"_fix_qbmsst.html, "qeq/reax (ko)"_fix_qeq_reax.html, "qmmm"_fix_qmmm.html, "qtb"_fix_qtb.html, "reax/c/bonds"_fix_reax_bonds.html, "reax/c/species"_fix_reaxc_species.html, +"rhok"_fix_rhok.html, "rx"_fix_rx.html, "saed/vtk"_fix_saed_vtk.html, "shardlow"_fix_shardlow.html, "smd"_fix_smd.html, "smd/adjust/dt"_fix_smd_adjust_dt.html, "smd/integrate/tlsph"_fix_smd_integrate_tlsph.html, "smd/integrate/ulsph"_fix_smd_integrate_ulsph.html, "smd/move/triangulated/surface"_fix_smd_move_triangulated_surface.html, "smd/setvel"_fix_smd_setvel.html, "smd/wall/surface"_fix_smd_wall_surface.html, "tdpd/source"_fix_dpd_source.html, "temp/rescale/eff"_fix_temp_rescale_eff.html, "ti/spring"_fix_ti_spring.html, "ttm/mod"_fix_ttm.html, "wall/ees"_fix_wall_ees.html, "wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c) :line Compute styles :h4 See the "compute"_compute.html command for one-line descriptions of each style or click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "aggregate/atom"_compute_cluster_atom.html, "angle"_compute_angle.html, "angle/local"_compute_angle_local.html, "angmom/chunk"_compute_angmom_chunk.html, "body/local"_compute_body_local.html, "bond"_compute_bond.html, "bond/local"_compute_bond_local.html, "centro/atom"_compute_centro_atom.html, "chunk/atom"_compute_chunk_atom.html, "cluster/atom"_compute_cluster_atom.html, "cna/atom"_compute_cna_atom.html, "com"_compute_com.html, "com/chunk"_compute_com_chunk.html, "contact/atom"_compute_contact_atom.html, "coord/atom"_compute_coord_atom.html, "damage/atom"_compute_damage_atom.html, "dihedral"_compute_dihedral.html, "dihedral/local"_compute_dihedral_local.html, "dilatation/atom"_compute_dilatation_atom.html, "dipole/chunk"_compute_dipole_chunk.html, "displace/atom"_compute_displace_atom.html, "erotate/asphere"_compute_erotate_asphere.html, "erotate/rigid"_compute_erotate_rigid.html, "erotate/sphere"_compute_erotate_sphere.html, "erotate/sphere/atom"_compute_erotate_sphere_atom.html, "event/displace"_compute_event_displace.html, "fragment/atom"_compute_cluster_atom.html, "global/atom"_compute_global_atom.html, "group/group"_compute_group_group.html, "gyration"_compute_gyration.html, "gyration/chunk"_compute_gyration_chunk.html, "heat/flux"_compute_heat_flux.html, "hexorder/atom"_compute_hexorder_atom.html, "improper"_compute_improper.html, "improper/local"_compute_improper_local.html, "inertia/chunk"_compute_inertia_chunk.html, "ke"_compute_ke.html, "ke/atom"_compute_ke_atom.html, "ke/rigid"_compute_ke_rigid.html, "msd"_compute_msd.html, "msd/chunk"_compute_msd_chunk.html, "msd/nongauss"_compute_msd_nongauss.html, "omega/chunk"_compute_omega_chunk.html, "orientorder/atom"_compute_orientorder_atom.html, "pair"_compute_pair.html, "pair/local"_compute_pair_local.html, "pe"_compute_pe.html, "pe/atom"_compute_pe_atom.html, "plasticity/atom"_compute_plasticity_atom.html, "pressure"_compute_pressure.html, "property/atom"_compute_property_atom.html, "property/local"_compute_property_local.html, "property/chunk"_compute_property_chunk.html, "rdf"_compute_rdf.html, "reduce"_compute_reduce.html, "reduce/region"_compute_reduce.html, "rigid/local"_compute_rigid_local.html, "slice"_compute_slice.html, "sna/atom"_compute_sna_atom.html, "snad/atom"_compute_sna_atom.html, "snav/atom"_compute_sna_atom.html, "stress/atom"_compute_stress_atom.html, "temp (k)"_compute_temp.html, "temp/asphere"_compute_temp_asphere.html, "temp/body"_compute_temp_body.html, "temp/chunk"_compute_temp_chunk.html, "temp/com"_compute_temp_com.html, "temp/deform"_compute_temp_deform.html, "temp/partial"_compute_temp_partial.html, "temp/profile"_compute_temp_profile.html, "temp/ramp"_compute_temp_ramp.html, "temp/region"_compute_temp_region.html, "temp/sphere"_compute_temp_sphere.html, "ti"_compute_ti.html, "torque/chunk"_compute_torque_chunk.html, "vacf"_compute_vacf.html, "vcm/chunk"_compute_vcm_chunk.html, "voronoi/atom"_compute_voronoi_atom.html :tb(c=6,ea=c) These are additional compute styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "ackland/atom"_compute_ackland_atom.html, "basal/atom"_compute_basal_atom.html, "cnp/atom"_compute_cnp_atom.html, "dpd"_compute_dpd.html, "dpd/atom"_compute_dpd_atom.html, "edpd/temp/atom"_compute_edpd_temp_atom.html, "fep"_compute_fep.html, "force/tally"_compute_tally.html, "heat/flux/tally"_compute_tally.html, "ke/eff"_compute_ke_eff.html, "ke/atom/eff"_compute_ke_atom_eff.html, "meso/e/atom"_compute_meso_e_atom.html, "meso/rho/atom"_compute_meso_rho_atom.html, "meso/t/atom"_compute_meso_t_atom.html, "pe/tally"_compute_tally.html, "pe/mol/tally"_compute_tally.html, "saed"_compute_saed.html, "smd/contact/radius"_compute_smd_contact_radius.html, "smd/damage"_compute_smd_damage.html, "smd/hourglass/error"_compute_smd_hourglass_error.html, "smd/internal/energy"_compute_smd_internal_energy.html, "smd/plastic/strain"_compute_smd_plastic_strain.html, "smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html, "smd/rho"_compute_smd_rho.html, "smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html, "smd/tlsph/dt"_compute_smd_tlsph_dt.html, "smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html, "smd/tlsph/shape"_compute_smd_tlsph_shape.html, "smd/tlsph/strain"_compute_smd_tlsph_strain.html, "smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html, "smd/tlsph/stress"_compute_smd_tlsph_stress.html, "smd/triangle/mesh/vertices"_compute_smd_triangle_mesh_vertices.html, "smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html, "smd/ulsph/strain"_compute_smd_ulsph_strain.html, "smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html, "smd/ulsph/stress"_compute_smd_ulsph_stress.html, "smd/vol"_compute_smd_vol.html, "stress/tally"_compute_tally.html, "tdpd/cc/atom"_compute_tdpd_cc_atom.html, "temp/drude"_compute_temp_drude.html, "temp/eff"_compute_temp_eff.html, "temp/deform/eff"_compute_temp_deform_eff.html, "temp/region/eff"_compute_temp_region_eff.html, "temp/rotate"_compute_temp_rotate.html, "xrd"_compute_xrd.html :tb(c=6,ea=c) :line Pair_style potentials :h4 See the "pair_style"_pair_style.html command for an overview of pair potentials. Click on the style itself for a full description. Many of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "none"_pair_none.html, "zero"_pair_zero.html, "hybrid"_pair_hybrid.html, "hybrid/overlay"_pair_hybrid.html, "adp (o)"_pair_adp.html, "airebo (oi)"_pair_airebo.html, "airebo/morse (oi)"_pair_airebo.html, "beck (go)"_pair_beck.html, "body"_pair_body.html, "bop"_pair_bop.html, "born (go)"_pair_born.html, "born/coul/dsf"_pair_born.html, "born/coul/dsf/cs"_pair_born.html, "born/coul/long (go)"_pair_born.html, "born/coul/long/cs"_pair_born.html, "born/coul/msm (o)"_pair_born.html, "born/coul/wolf (go)"_pair_born.html, "brownian (o)"_pair_brownian.html, "brownian/poly (o)"_pair_brownian.html, "buck (giko)"_pair_buck.html, "buck/coul/cut (giko)"_pair_buck.html, "buck/coul/long (giko)"_pair_buck.html, "buck/coul/long/cs"_pair_buck.html, "buck/coul/msm (o)"_pair_buck.html, "buck/long/coul/long (o)"_pair_buck_long.html, "colloid (go)"_pair_colloid.html, "comb (o)"_pair_comb.html, "comb3"_pair_comb.html, "coul/cut (gko)"_pair_coul.html, "coul/debye (gko)"_pair_coul.html, "coul/dsf (gko)"_pair_coul.html, "coul/long (gko)"_pair_coul.html, "coul/long/cs"_pair_coul.html, "coul/msm"_pair_coul.html, "coul/streitz"_pair_coul.html, "coul/wolf (ko)"_pair_coul.html, "dpd (gio)"_pair_dpd.html, "dpd/tstat (go)"_pair_dpd.html, "dsmc"_pair_dsmc.html, "eam (gikot)"_pair_eam.html, "eam/alloy (gikot)"_pair_eam.html, "eam/fs (gikot)"_pair_eam.html, "eim (o)"_pair_eim.html, "gauss (go)"_pair_gauss.html, "gayberne (gio)"_pair_gayberne.html, "gran/hertz/history (o)"_pair_gran.html, "gran/hooke (o)"_pair_gran.html, "gran/hooke/history (o)"_pair_gran.html, "gw"_pair_gw.html, "gw/zbl"_pair_gw.html, "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, "kim"_pair_kim.html, "lcbop"_pair_lcbop.html, "line/lj"_pair_line_lj.html, "lj/charmm/coul/charmm (iko)"_pair_charmm.html, "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, "lj/charmm/coul/long (giko)"_pair_charmm.html, "lj/charmm/coul/msm"_pair_charmm.html, "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html, "lj/charmmfsw/coul/long"_pair_charmm.html, "lj/class2 (gko)"_pair_class2.html, "lj/class2/coul/cut (ko)"_pair_class2.html, "lj/class2/coul/long (gko)"_pair_class2.html, "lj/cubic (go)"_pair_lj_cubic.html, "lj/cut (gikot)"_pair_lj.html, "lj/cut/coul/cut (gko)"_pair_lj.html, "lj/cut/coul/debye (gko)"_pair_lj.html, "lj/cut/coul/dsf (gko)"_pair_lj.html, "lj/cut/coul/long (gikot)"_pair_lj.html, "lj/cut/coul/long/cs"_pair_lj.html, "lj/cut/coul/msm (go)"_pair_lj.html, "lj/cut/dipole/cut (go)"_pair_dipole.html, "lj/cut/dipole/long"_pair_dipole.html, "lj/cut/tip4p/cut (o)"_pair_lj.html, "lj/cut/tip4p/long (ot)"_pair_lj.html, "lj/expand (gko)"_pair_lj_expand.html, "lj/gromacs (gko)"_pair_gromacs.html, "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, "lj/long/coul/long (io)"_pair_lj_long.html, "lj/long/dipole/long"_pair_dipole.html, "lj/long/tip4p/long"_pair_lj_long.html, "lj/smooth (o)"_pair_lj_smooth.html, "lj/smooth/linear (o)"_pair_lj_smooth_linear.html, "lj96/cut (go)"_pair_lj96.html, "lubricate (o)"_pair_lubricate.html, "lubricate/poly (o)"_pair_lubricate.html, "lubricateU"_pair_lubricateU.html, "lubricateU/poly"_pair_lubricateU.html, "meam"_pair_meam.html, "mie/cut (o)"_pair_mie.html, "morse (gkot)"_pair_morse.html, "nb3b/harmonic (o)"_pair_nb3b_harmonic.html, "nm/cut (o)"_pair_nm.html, "nm/cut/coul/cut (o)"_pair_nm.html, "nm/cut/coul/long (o)"_pair_nm.html, "peri/eps"_pair_peri.html, "peri/lps (o)"_pair_peri.html, "peri/pmb (o)"_pair_peri.html, "peri/ves"_pair_peri.html, "polymorphic"_pair_polymorphic.html, "python"_pair_python.html, "reax"_pair_reax.html, "rebo (oi)"_pair_airebo.html, "resquared (go)"_pair_resquared.html, "snap"_pair_snap.html, "soft (go)"_pair_soft.html, "sw (giko)"_pair_sw.html, "table (gko)"_pair_table.html, "tersoff (giko)"_pair_tersoff.html, "tersoff/mod (gko)"_pair_tersoff_mod.html, "tersoff/mod/c (o)"_pair_tersoff_mod.html, "tersoff/zbl (gko)"_pair_tersoff_zbl.html, "tip4p/cut (o)"_pair_coul.html, "tip4p/long (o)"_pair_coul.html, "tri/lj"_pair_tri_lj.html, "vashishta (ko)"_pair_vashishta.html, "vashishta/table (o)"_pair_vashishta.html, "yukawa (go)"_pair_yukawa.html, "yukawa/colloid (go)"_pair_yukawa_colloid.html, "zbl (go)"_pair_zbl.html :tb(c=4,ea=c) These are additional pair styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "agni (o)"_pair_agni.html, "awpmd/cut"_pair_awpmd.html, "buck/mdf"_pair_mdf.html, "coul/cut/soft (o)"_pair_lj_soft.html, "coul/diel (o)"_pair_coul_diel.html, "coul/long/soft (o)"_pair_lj_soft.html, "dpd/fdt"_pair_dpd_fdt.html, "dpd/fdt/energy"_pair_dpd_fdt.html, "eam/cd (o)"_pair_eam.html, "edip (o)"_pair_edip.html, "edip/multi"_pair_edip.html, "edpd"_pair_meso.html, "eff/cut"_pair_eff.html, "exp6/rx"_pair_exp6_rx.html, "gauss/cut"_pair_gauss.html, "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html, "lennard/mdf"_pair_mdf.html, "list"_pair_list.html, "lj/charmm/coul/long/soft (o)"_pair_charmm.html, "lj/cut/coul/cut/soft (o)"_pair_lj_soft.html, "lj/cut/coul/long/soft (o)"_pair_lj_soft.html, "lj/cut/dipole/sf (go)"_pair_dipole.html, "lj/cut/soft (o)"_pair_lj_soft.html, "lj/cut/thole/long (o)"_pair_thole.html, "lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html, "lj/mdf"_pair_mdf.html, "lj/sdk (gko)"_pair_sdk.html, "lj/sdk/coul/long (go)"_pair_sdk.html, "lj/sdk/coul/msm (o)"_pair_sdk.html, "mdpd"_pair_meso.html, "mdpd/rhosum"_pair_meso.html, "meam/c"_pair_meam.html, "meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, "mgpt"_pair_mgpt.html, "momb"_pair_momb.html, "morse/smooth/linear"_pair_morse.html, "morse/soft"_pair_morse.html, "multi/lucy"_pair_multi_lucy.html, "multi/lucy/rx"_pair_multi_lucy_rx.html, "oxdna/coaxstk"_pair_oxdna.html, "oxdna/excv"_pair_oxdna.html, "oxdna/hbond"_pair_oxdna.html, "oxdna/stk"_pair_oxdna.html, "oxdna/xstk"_pair_oxdna.html, "oxdna2/coaxstk"_pair_oxdna2.html, "oxdna2/dh"_pair_oxdna2.html, "oxdna2/excv"_pair_oxdna2.html, "oxdna2/stk"_pair_oxdna2.html, "quip"_pair_quip.html, "reax/c (ko)"_pair_reaxc.html, "smd/hertz"_pair_smd_hertz.html, "smd/tlsph"_pair_smd_tlsph.html, "smd/triangulated/surface"_pair_smd_triangulated_surface.html, "smd/ulsph"_pair_smd_ulsph.html, "smtbq"_pair_smtbq.html, "sph/heatconduction"_pair_sph_heatconduction.html, "sph/idealgas"_pair_sph_idealgas.html, "sph/lj"_pair_sph_lj.html, "sph/rhosum"_pair_sph_rhosum.html, "sph/taitwater"_pair_sph_taitwater.html, "sph/taitwater/morris"_pair_sph_taitwater_morris.html, "srp"_pair_srp.html, "table/rx"_pair_table_rx.html, "tdpd"_pair_meso.html, "tersoff/table (o)"_pair_tersoff.html, "thole"_pair_thole.html, "tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) :line Bond_style potentials :h4 See the "bond_style"_bond_style.html command for an overview of bond potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "none"_bond_none.html, "zero"_bond_zero.html, "hybrid"_bond_hybrid.html, "class2 (ko)"_bond_class2.html, "fene (iko)"_bond_fene.html, "fene/expand (o)"_bond_fene_expand.html, "gromos (o)"_bond_gromos.html, "harmonic (ko)"_bond_harmonic.html, "morse (o)"_bond_morse.html, "nonlinear (o)"_bond_nonlinear.html, "quartic (o)"_bond_quartic.html, "table (o)"_bond_table.html :tb(c=4,ea=c) These are additional bond styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "harmonic/shift (o)"_bond_harmonic_shift.html, "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html, "oxdna/fene"_bond_oxdna.html, "oxdna2/fene"_bond_oxdna.html :tb(c=4,ea=c) :line Angle_style potentials :h4 See the "angle_style"_angle_style.html command for an overview of angle potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "none"_angle_none.html, "zero"_angle_zero.html, "hybrid"_angle_hybrid.html, "charmm (ko)"_angle_charmm.html, "class2 (ko)"_angle_class2.html, "cosine (o)"_angle_cosine.html, "cosine/delta (o)"_angle_cosine_delta.html, "cosine/periodic (o)"_angle_cosine_periodic.html, "cosine/squared (o)"_angle_cosine_squared.html, "harmonic (iko)"_angle_harmonic.html, "table (o)"_angle_table.html :tb(c=4,ea=c) These are additional angle styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "cosine/shift (o)"_angle_cosine_shift.html, "cosine/shift/exp (o)"_angle_cosine_shift_exp.html, "dipole (o)"_angle_dipole.html, "fourier (o)"_angle_fourier.html, "fourier/simple (o)"_angle_fourier_simple.html, "quartic (o)"_angle_quartic.html, "sdk"_angle_sdk.html :tb(c=4,ea=c) :line Dihedral_style potentials :h4 See the "dihedral_style"_dihedral_style.html command for an overview of dihedral potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "none"_dihedral_none.html, "zero"_dihedral_zero.html, "hybrid"_dihedral_hybrid.html, "charmm (iko)"_dihedral_charmm.html, "charmmfsw"_dihedral_charmm.html, "class2 (ko)"_dihedral_class2.html, "harmonic (io)"_dihedral_harmonic.html, "helix (o)"_dihedral_helix.html, "multi/harmonic (o)"_dihedral_multi_harmonic.html, "opls (iko)"_dihedral_opls.html :tb(c=4,ea=c) These are additional dihedral styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html, "fourier (io)"_dihedral_fourier.html, "nharmonic (o)"_dihedral_nharmonic.html, "quadratic (o)"_dihedral_quadratic.html, "spherical (o)"_dihedral_spherical.html, "table (o)"_dihedral_table.html :tb(c=4,ea=c) :line Improper_style potentials :h4 See the "improper_style"_improper_style.html command for an overview of improper potentials. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "none"_improper_none.html, "zero"_improper_zero.html, "hybrid"_improper_hybrid.html, "class2 (ko)"_improper_class2.html, "cvff (io)"_improper_cvff.html, "harmonic (iko)"_improper_harmonic.html, "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c) These are additional improper styles in USER packages, which can be used if "LAMMPS is built with the appropriate package"_Section_start.html#start_3. "cossq (o)"_improper_cossq.html, "distance"_improper_distance.html, "fourier (o)"_improper_fourier.html, "ring (o)"_improper_ring.html :tb(c=4,ea=c) :line Kspace solvers :h4 See the "kspace_style"_kspace_style.html command for an overview of Kspace solvers. Click on the style itself for a full description. Some of the styles have accelerated versions, which can be used if LAMMPS is built with the "appropriate accelerated package"_Section_accelerate.html. This is indicated by additional letters in parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "ewald (o)"_kspace_style.html, "ewald/disp"_kspace_style.html, "msm (o)"_kspace_style.html, "msm/cg (o)"_kspace_style.html, "pppm (go)"_kspace_style.html, "pppm/cg (o)"_kspace_style.html, "pppm/disp (i)"_kspace_style.html, "pppm/disp/tip4p"_kspace_style.html, "pppm/stagger"_kspace_style.html, "pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/fix_rhok.txt b/doc/src/fix_rhok.txt new file mode 100644 index 000000000..504630332 --- /dev/null +++ b/doc/src/fix_rhok.txt @@ -0,0 +1,57 @@ +"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 + +fix rhok command :h3 + +fix ID group-ID rhok nx ny nz K a :pre + +ID, group-ID are documented in "fix"_fix.html command +nx, ny, nz = k-vektor of collective density field +K = spring constant of bias potential +a = anchor point of bias potential :ul + +[Examples:] + +fix bias all rhok 16 0 0 4.0 16.0 +fix 1 all npt temp 0.8 0.8 4.0 z 2.2 2.2 8.0 +# output U_bias rho_k_RE rho_k_IM |rho_k| +thermo_style custom step temp pzz lz f_bias f_bias\[1\] f_bias\[2\] f_bias\[3\] :pre + +[Description:] + +The fix applies an force to atoms given by the potential + +:c,image(Eqs/fix_rhok.jpg) + +as described in "(Pedersen)"_#Pedersen. + +This field, that bias configurations with long-range order, +can be used to study crystal-liquid interfaces +and determine melting temperatures "(Pedersen)"_#Pedersen. + +An example of using the interface pinning method +is located in the folder +{examples/USER/pinning} of the source code to LAMMPS. + +[Restrictions:] + +This fix is part of the MISC 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:] + +"thermo_style"_thermo_style.html + +[Default:] none + +:line + +:link(Pedersen) +[(Pedersen)] Pedersen, J. Chem. Phys., 139, 104102 (2013). + diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt index e363273a7..6d51151f3 100644 --- a/doc/src/fixes.txt +++ b/doc/src/fixes.txt @@ -1,170 +1,171 @@ Fixes :h1 diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 5ebf7466c..9d1e92017 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -1,655 +1,656 @@ #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 Section_perf.html Section_tools.html Section_modify.html Section_python.html Section_errors.html Section_history.html tutorial_bash_on_windows.html tutorial_drude.html tutorial_github.html tutorial_pylammps.html body.html manifolds.html angle_coeff.html angle_style.html atom_modify.html atom_style.html balance.html bond_coeff.html bond_style.html bond_write.html boundary.html box.html change_box.html clear.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_h5md.html dump_image.html dump_modify.html dump_molfile.html dump_netcdf.html dump_vtk.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 min_modify.html min_style.html minimize.html molecule.html neb.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 temper_grem.html temper_npt.html thermo.html thermo_modify.html thermo_style.html timer.html timestep.html uncompute.html undump.html unfix.html units.html variable.html velocity.html write_coeff.html write_data.html write_dump.html write_restart.html fix_adapt.html fix_adapt_fep.html fix_addforce.html fix_addtorque.html fix_append_atoms.html fix_atc.html fix_atom_swap.html fix_ave_atom.html fix_ave_chunk.html fix_ave_correlate.html fix_ave_correlate_long.html fix_ave_histo.html fix_ave_time.html fix_aveforce.html fix_balance.html fix_bond_break.html fix_bond_create.html fix_bond_swap.html fix_box_relax.html fix_cmap.html fix_colvars.html fix_controller.html fix_deform.html fix_deposit.html fix_dpd_energy.html fix_dpd_source.html fix_drag.html fix_drude.html fix_drude_transform.html fix_dt_reset.html fix_efield.html fix_ehex.html fix_enforce2d.html fix_eos_cv.html fix_eos_table.html fix_eos_table_rx.html fix_evaporate.html fix_external.html fix_filter_corotate.html fix_flow_gauss.html fix_freeze.html fix_gcmc.html fix_gld.html fix_gle.html fix_gravity.html fix_grem.html fix_halt.html fix_heat.html fix_imd.html fix_indent.html fix_ipi.html fix_langevin.html fix_langevin_drude.html fix_langevin_eff.html fix_latte.html fix_lb_fluid.html fix_lb_momentum.html fix_lb_pc.html fix_lb_rigid_pc_sphere.html fix_lb_viscous.html fix_lineforce.html fix_manifoldforce.html fix_meso.html fix_meso_stationary.html fix_momentum.html fix_move.html fix_mscg.html fix_msst.html fix_mvv_dpd.html fix_neb.html fix_nh.html fix_nh_eff.html fix_nph_asphere.html fix_nph_body.html fix_nph_sphere.html fix_nphug.html fix_npt_asphere.html fix_npt_body.html fix_npt_sphere.html fix_nve.html fix_nve_asphere.html fix_nve_asphere_noforce.html fix_nve_body.html fix_nve_dot.html fix_nve_dotc_langevin.html fix_nve_eff.html fix_nve_limit.html fix_nve_line.html fix_nve_manifold_rattle.html fix_nve_noforce.html fix_nve_sphere.html fix_nve_tri.html fix_nvk.html fix_nvt_asphere.html fix_nvt_body.html fix_nvt_manifold_rattle.html fix_nvt_sllod.html fix_nvt_sllod_eff.html fix_nvt_sphere.html fix_oneway.html fix_orient.html fix_phonon.html fix_pimd.html fix_planeforce.html fix_poems.html fix_pour.html fix_press_berendsen.html fix_print.html fix_property_atom.html fix_python.html fix_qbmsst.html fix_qeq.html fix_qeq_comb.html fix_qeq_reax.html fix_qmmm.html fix_qtb.html fix_reax_bonds.html fix_reaxc_species.html fix_recenter.html fix_restrain.html fix_rigid.html +fix_rhok.html fix_rx.html fix_saed_vtk.html fix_setforce.html fix_shake.html fix_shardlow.html fix_smd.html fix_smd_adjust_dt.html fix_smd_integrate_tlsph.html fix_smd_integrate_ulsph.html fix_smd_move_triangulated_surface.html fix_smd_setvel.html fix_smd_wall_surface.html fix_spring.html fix_spring_chunk.html fix_spring_rg.html fix_spring_self.html fix_srd.html fix_store_force.html fix_store_state.html fix_temp_berendsen.html fix_temp_csvr.html fix_temp_rescale.html fix_temp_rescale_eff.html fix_tfmc.html fix_thermal_conductivity.html fix_ti_spring.html fix_tmd.html fix_ttm.html fix_tune_kspace.html fix_vector.html fix_viscosity.html fix_viscous.html fix_wall.html fix_wall_ees.html fix_wall_gran.html fix_wall_gran_region.html fix_wall_piston.html fix_wall_reflect.html fix_wall_region.html fix_wall_srd.html compute_ackland_atom.html compute_angle.html compute_angle_local.html compute_angmom_chunk.html compute_basal_atom.html compute_body_local.html compute_bond.html compute_bond_local.html compute_centro_atom.html compute_chunk_atom.html compute_cluster_atom.html compute_cna_atom.html compute_cnp_atom.html compute_com.html compute_com_chunk.html compute_contact_atom.html compute_coord_atom.html compute_damage_atom.html compute_dihedral.html compute_dihedral_local.html compute_dilatation_atom.html compute_dipole_chunk.html compute_displace_atom.html compute_dpd.html compute_dpd_atom.html compute_edpd_temp_atom.html compute_erotate_asphere.html compute_erotate_rigid.html compute_erotate_sphere.html compute_erotate_sphere_atom.html 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improper_cossq.html improper_cvff.html improper_distance.html improper_fourier.html improper_harmonic.html improper_hybrid.html improper_none.html improper_ring.html improper_umbrella.html improper_zero.html USER/atc/man_add_molecule.html USER/atc/man_add_species.html USER/atc/man_atom_element_map.html USER/atc/man_atom_weight.html USER/atc/man_atomic_charge.html USER/atc/man_boundary.html USER/atc/man_boundary_dynamics.html USER/atc/man_boundary_faceset.html USER/atc/man_boundary_integral.html USER/atc/man_consistent_fe_initialization.html USER/atc/man_contour_integral.html USER/atc/man_control.html USER/atc/man_control_momentum.html USER/atc/man_control_thermal.html USER/atc/man_control_thermal_correction_max_iterations.html USER/atc/man_decomposition.html USER/atc/man_electron_integration.html USER/atc/man_equilibrium_start.html USER/atc/man_extrinsic_exchange.html USER/atc/man_fe_md_boundary.html USER/atc/man_fem_mesh.html USER/atc/man_filter_scale.html USER/atc/man_filter_type.html USER/atc/man_fix_atc.html USER/atc/man_fix_flux.html USER/atc/man_fix_nodes.html USER/atc/man_hardy_computes.html USER/atc/man_hardy_fields.html USER/atc/man_hardy_gradients.html USER/atc/man_hardy_kernel.html USER/atc/man_hardy_on_the_fly.html USER/atc/man_hardy_rates.html USER/atc/man_initial.html USER/atc/man_internal_atom_integrate.html USER/atc/man_internal_element_set.html USER/atc/man_internal_quadrature.html USER/atc/man_kernel_function.html USER/atc/man_localized_lambda.html USER/atc/man_lumped_lambda_solve.html USER/atc/man_mask_direction.html USER/atc/man_mass_matrix.html USER/atc/man_material.html USER/atc/man_mesh_add_to_nodeset.html USER/atc/man_mesh_create.html USER/atc/man_mesh_create_elementset.html USER/atc/man_mesh_create_faceset_box.html USER/atc/man_mesh_create_faceset_plane.html USER/atc/man_mesh_create_nodeset.html USER/atc/man_mesh_delete_elements.html USER/atc/man_mesh_nodeset_to_elementset.html USER/atc/man_mesh_output.html USER/atc/man_mesh_quadrature.html USER/atc/man_mesh_read.html USER/atc/man_mesh_write.html USER/atc/man_momentum_time_integration.html USER/atc/man_output.html USER/atc/man_output_elementset.html USER/atc/man_output_nodeset.html USER/atc/man_pair_interactions.html USER/atc/man_poisson_solver.html USER/atc/man_read_restart.html USER/atc/man_remove_molecule.html USER/atc/man_remove_source.html USER/atc/man_remove_species.html USER/atc/man_reset_atomic_reference_positions.html USER/atc/man_reset_time.html USER/atc/man_sample_frequency.html USER/atc/man_set.html USER/atc/man_source.html USER/atc/man_source_integration.html USER/atc/man_temperature_definition.html USER/atc/man_thermal_time_integration.html USER/atc/man_time_filter.html USER/atc/man_track_displacement.html USER/atc/man_unfix_flux.html USER/atc/man_unfix_nodes.html USER/atc/man_write_atom_weights.html USER/atc/man_write_restart.html diff --git a/examples/USER/misc/pinning/README.md b/examples/USER/misc/pinning/README.md new file mode 100644 index 000000000..4e011255f --- /dev/null +++ b/examples/USER/misc/pinning/README.md @@ -0,0 +1,74 @@ +# The Interface Pinning method for studying solid-liquid transitions + +In this example we will use the interface pinnig method to study a solid-liquid transition. +This is done by adding a harmonic potential to the Hamiltonian +that bias the system towards two-phase configurations: + + U_bias = 0.5*K*(Q-a)^2 + +The bias field couple to an order-parameter of crystallinity Q. The implementation use long-range order: + + Q=|rho_k|, + +where rho_k is the collective density field of the wave-vector k. +For future reference we note that the structure factor S(k) is given by the variance of the collective density field: + + S(k)=|rho_k|^2. + +### About the method + +It is recommended to get familiar with the interface pinning method by reading: + + [Ulf R. Pedersen, JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) + +A detailed bibliography is provided at + + + +and a brief introduction can be found at YouTube: + + [![Interface Pinning](http://img.youtube.com/vi/F_79JZNdyoQ/0.jpg)](http://www.youtube.com/watch?v=F_79JZNdyoQ) + +### Implimentation in LAMMPS + +For this example we will be using the rhok fix. + + fix [name] [groupID] rhok [nx] [ny] [nz] [K] [a] + +This fix include a harmonic bias potential U_bias=0.5*K*(|rho_k|-a)^2 to the force calculation. +The elements of the wave-vector k is given by the nx, ny and nz input: + + k_x = (2 pi / L_x) * n_x, k_y = (2 pi / L_y) * n_y and k_z = (2 pi / L_z) * n_z. + +We will use a k vector that correspond to a Bragg peak. + +## Example: the Lennard-Jones (LJ) model + +We will use the interface pinning method to study melting of the LJ model +at temperature 0.8 and pressure 2.185. This is a coexistence state-point, and the method +can be used to show this. The present directory contains the input files that we will use: + + in.crystal + in.setup + in.pinning + +1. First we will determine the density of the crystal with the LAMMPS input file in.crystal. + From the output we get that the average density after equilibration is 0.9731. + We need this density to ensure hydrostatic pressure when in a two-phase simulation. + +2. Next, we setup a two-phase configuration using in.setup. + +3. Finally, we run a two-phase simulation with the bias-field applied using in.pinning. + The last column in the output show |rho_k|. We note that after a equilibration period + the value fluctuates around the anchor point (a) -- showing that this is indeed a coexistence + state point. + +The reference [JCP 139, 104102 (2013)](http://dx.doi.org/10.1063/1.4818747) gives details on using the method to find coexistence state points, +and the reference [JCP 142, 044104 (2015)](http://dx.doi.org/10.1063/1.4818747) show how the crystal growth rate can be computed from fluctuations. +That method have been experienced to be most effective in the slightly super-heated regime above the melting temperature. + +## Contact + + Ulf R. Pedersen; + ; + ulf AT urp.dk diff --git a/examples/USER/misc/pinning/in.crystal b/examples/USER/misc/pinning/in.crystal new file mode 100644 index 000000000..55e9e59a0 --- /dev/null +++ b/examples/USER/misc/pinning/in.crystal @@ -0,0 +1,36 @@ +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes +lattice fcc 0.9731 +region my_box block 0 8.0 0 8.0 0 20.0 +create_box 1 my_box +region particles block 0 8.0 0 8.0 0 20.0 +create_atoms 1 region particles +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify tail no +pair_modify shift yes +mass 1 1.0 +velocity all create 1.6 1 mom yes rot yes + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet +fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32 + +# computing long-range order (no bias is added since k=0) +fix bias all rhok 16 0 0 0.0 0.0 + +# output +thermo 50 +thermo_style custom step temp press density f_bias[3] +# dump dumpXYZ all xyz 2000 traj.xyz + +# NOTE: this is cut short to 5000 steps for demonstration purposes +# run 100000 +run 5000 diff --git a/examples/USER/misc/pinning/in.pinning b/examples/USER/misc/pinning/in.pinning new file mode 100644 index 000000000..0c220f480 --- /dev/null +++ b/examples/USER/misc/pinning/in.pinning @@ -0,0 +1,33 @@ +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes +read_data data.halfhalf +pair_coeff 1 1 1.0 1.0 2.5 +mass 1 1.0 + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet + +velocity all create 0.8 1 mom yes rot yes +fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0 +fix 100 all momentum 100 linear 1 1 1 + +# harmonic rho_k bias-field +# nx ny nz K a +fix bias all rhok 16 0 0 4.0 26.00 + +# output U_bias rho_k_RE rho_k_IM |rho_k| +thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3] +thermo 50 +# dump dumpXYZ all xyz 500 traj.xyz + +# NOTE: run reduced for demonstration purposes +# run 50000 +run 5000 diff --git a/examples/USER/misc/pinning/in.setup b/examples/USER/misc/pinning/in.setup new file mode 100644 index 000000000..649b0f534 --- /dev/null +++ b/examples/USER/misc/pinning/in.setup @@ -0,0 +1,41 @@ +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes + +# fcc lattice +lattice fcc 0.9731 +region my_box block 0 8.0 0 8.0 0 20.0 +create_box 1 my_box +region particles block 0 8.0 0 8.0 0 20.0 +create_atoms 1 region particles +pair_coeff 1 1 1.0 1.0 2.5 +mass 1 1.0 +change_box all z final 0.0 34 remap units box + +# select particles in one side of the elongated box +region left plane 0 0 10 0 0 1 +group left region left + +velocity left create 6.0 1 mom yes rot yes + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet +fix ensemble left nve # Note: only move particle in left-hand side +fix langevin left langevin 3.0 0.8 100.0 2017 + +# outout +thermo_style custom step temp pzz pe lz +thermo 100 +# dump dumpXYZ all xyz 100 traj.xyz + +# run reduced for demonstration purposes +# run 10000 +run 5000 +write_data data.halfhalf diff --git a/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1 b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1 new file mode 100644 index 000000000..05fadb5c0 --- /dev/null +++ b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.1 @@ -0,0 +1,187 @@ +LAMMPS (22 Sep 2017) + using 1 OpenMP thread(s) per MPI task +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes +lattice fcc 0.9731 +Lattice spacing in x,y,z = 1.6019 1.6019 1.6019 +region my_box block 0 8.0 0 8.0 0 20.0 +create_box 1 my_box +Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379) + 1 by 1 by 1 MPI processor grid +region particles block 0 8.0 0 8.0 0 20.0 +create_atoms 1 region particles +Created 5120 atoms +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify tail no +pair_modify shift yes +mass 1 1.0 +velocity all create 1.6 1 mom yes rot yes + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet +fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32 + +# computing long-range order (no bias is added since k=0) +fix bias all rhok 16 0 0 0.0 0.0 + +# output +thermo 50 +thermo_style custom step temp press density f_bias[3] +# dump dumpXYZ all xyz 2000 traj.xyz + +# NOTE: this is cut short to 5000 steps for demonstration purposes +# run 100000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.523 | 4.523 | 4.523 Mbytes +Step Temp Press Density f_bias[3] + 0 1.6 -2.7568106 0.9731 71.554175 + 50 0.78457786 3.1029192 0.97362639 54.327705 + 100 0.85528971 2.4670259 0.97213457 55.189308 + 150 0.85241818 2.3210306 0.9698027 56.138125 + 200 0.82301385 2.3448692 0.96708227 55.735326 + 250 0.83076383 2.0890816 0.96425763 55.320625 + 300 0.81602823 2.0118796 0.96173925 54.095736 + 350 0.81084006 1.9122192 0.95979392 54.526429 + 400 0.80776593 1.8502174 0.95869117 54.434901 + 450 0.80694697 1.8435873 0.95851085 53.20809 + 500 0.81384248 1.8111331 0.95917305 53.419395 + 550 0.81027072 1.9222272 0.96056019 54.36723 + 600 0.81199582 2.0291945 0.96248486 54.888582 + 650 0.82507964 2.0706462 0.96467227 55.807137 + 700 0.832562 2.1471442 0.9668913 56.721267 + 750 0.83358138 2.2674672 0.968984 56.723838 + 800 0.83477542 2.3658275 0.97072603 56.234689 + 850 0.84722921 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55.891368 + 1900 0.82298992 2.3059289 0.97181084 55.680563 + 1950 0.82098556 2.2801003 0.97138609 55.754406 + 2000 0.8181203 2.2480175 0.97078591 55.801363 + 2050 0.82822293 2.1208884 0.97004107 55.687 + 2100 0.7976818 2.2711199 0.96930169 55.459844 + 2150 0.81817848 2.0680351 0.96860201 56.514731 + 2200 0.80707457 2.1112141 0.96810519 55.504308 + 2250 0.81651111 2.0077603 0.96781161 55.635702 + 2300 0.80634534 2.0662241 0.96777177 56.051086 + 2350 0.80892831 2.0619333 0.96799037 56.548711 + 2400 0.82454203 1.9585394 0.9684672 56.695235 + 2450 0.81517178 2.075283 0.96921622 56.613082 + 2500 0.80969595 2.1624581 0.97010528 56.57516 + 2550 0.80862964 2.2088622 0.97100774 57.072594 + 2600 0.81468816 2.2293973 0.97192868 56.879212 + 2650 0.82063107 2.2244887 0.97269715 55.454502 + 2700 0.81691618 2.2789954 0.97319841 54.421943 + 2750 0.8141787 2.2981247 0.97340453 54.469921 + 2800 0.81973871 2.2422136 0.9733278 55.959235 + 2850 0.82037399 2.201016 0.97302727 56.685826 + 2900 0.80650164 2.2672955 0.9726128 56.574395 + 2950 0.81752783 2.1317541 0.97207545 56.809412 + 3000 0.80836945 2.1461483 0.97151192 57.205206 + 3050 0.80785109 2.1189056 0.97103049 57.418763 + 3100 0.79835058 2.146416 0.97069705 57.329383 + 3150 0.79792089 2.1388267 0.97051679 57.279852 + 3200 0.79934603 2.1049562 0.97046851 56.351494 + 3250 0.79523232 2.1549779 0.97063956 56.00356 + 3300 0.8004458 2.1145975 0.97096375 55.725509 + 3350 0.79772742 2.166292 0.97143785 55.558075 + 3400 0.80621087 2.1309217 0.97198456 55.816704 + 3450 0.80540626 2.1727557 0.97263267 55.671283 + 3500 0.80867606 2.1905129 0.97321538 55.390086 + 3550 0.80917896 2.2144872 0.97370472 55.742085 + 3600 0.80930722 2.2288938 0.974093 56.23064 + 3650 0.80390523 2.2777327 0.97431886 56.084731 + 3700 0.79620093 2.3143541 0.97435103 55.942797 + 3750 0.80252393 2.2564638 0.9741875 56.042055 + 3800 0.78981264 2.3156481 0.9739121 55.971352 + 3850 0.80391951 2.1804938 0.97351088 55.855858 + 3900 0.81268129 2.0855818 0.97308521 56.288315 + 3950 0.7958182 2.175259 0.97273088 56.140141 + 4000 0.80054484 2.1163279 0.97243129 56.366818 + 4050 0.79760187 2.105362 0.97225308 56.684619 + 4100 0.79283424 2.1357603 0.972206 56.203341 + 4150 0.79543088 2.1036951 0.97227608 56.606315 + 4200 0.79410999 2.1402049 0.97253758 56.277478 + 4250 0.7985469 2.1285154 0.97293622 56.356076 + 4300 0.79700387 2.1470614 0.97337091 56.722298 + 4350 0.80479321 2.1403244 0.97384674 57.212574 + 4400 0.79505512 2.224463 0.97434415 56.561877 + 4450 0.78346648 2.3347865 0.97478611 56.681362 + 4500 0.79811284 2.259123 0.97510069 57.365929 + 4550 0.80015561 2.2345254 0.97523653 57.34799 + 4600 0.79648318 2.2651869 0.97525975 57.502318 + 4650 0.80524865 2.1943025 0.97507638 57.702488 + 4700 0.80397778 2.1758629 0.97478268 57.162107 + 4750 0.78914913 2.2470191 0.9744625 56.849565 + 4800 0.79324889 2.2028993 0.97408817 57.572344 + 4850 0.78993209 2.181763 0.97373372 57.683552 + 4900 0.79041263 2.1604768 0.97348692 56.922312 + 4950 0.79741332 2.1105901 0.97332545 57.488932 + 5000 0.7891178 2.163416 0.97328963 57.365252 +Loop time of 33.6467 on 1 procs for 5000 steps with 5120 atoms + +Performance: 51357.258 tau/day, 148.603 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 24.699 | 24.699 | 24.699 | 0.0 | 73.41 +Neigh | 2.8894 | 2.8894 | 2.8894 | 0.0 | 8.59 +Comm | 0.34907 | 0.34907 | 0.34907 | 0.0 | 1.04 +Output | 0.0056 | 0.0056 | 0.0056 | 0.0 | 0.02 +Modify | 5.5718 | 5.5718 | 5.5718 | 0.0 | 16.56 +Other | | 0.1319 | | | 0.39 + +Nlocal: 5120 ave 5120 max 5120 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7594 ave 7594 max 7594 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 323081 ave 323081 max 323081 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 323081 +Ave neighs/atom = 63.1018 +Neighbor list builds = 248 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:33 diff --git a/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.4 b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.4 new file mode 100644 index 000000000..cec9c69af --- /dev/null +++ b/examples/USER/misc/pinning/log.22Sep2017.crystal.g++.4 @@ -0,0 +1,187 @@ +LAMMPS (22 Sep 2017) + using 1 OpenMP thread(s) per MPI task +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes +lattice fcc 0.9731 +Lattice spacing in x,y,z = 1.6019 1.6019 1.6019 +region my_box block 0 8.0 0 8.0 0 20.0 +create_box 1 my_box +Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379) + 1 by 1 by 4 MPI processor grid +region particles block 0 8.0 0 8.0 0 20.0 +create_atoms 1 region particles +Created 5120 atoms +pair_coeff 1 1 1.0 1.0 2.5 +pair_modify tail no +pair_modify shift yes +mass 1 1.0 +velocity all create 1.6 1 mom yes rot yes + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet +fix ensemble all npt temp 0.8 0.8 4.0 aniso 2.185 2.185 8.0 pchain 32 + +# computing long-range order (no bias is added since k=0) +fix bias all rhok 16 0 0 0.0 0.0 + +# output +thermo 50 +thermo_style custom step temp press density f_bias[3] +# dump dumpXYZ all xyz 2000 traj.xyz + +# NOTE: this is cut short to 5000 steps for demonstration purposes +# run 100000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 21 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.23 | 3.23 | 3.23 Mbytes +Step Temp Press Density f_bias[3] + 0 1.6 -2.7568106 0.9731 71.554175 + 50 0.78457786 3.1029192 0.97362639 54.327705 + 100 0.85528971 2.4670259 0.97213457 55.189308 + 150 0.85241818 2.3210306 0.9698027 56.138125 + 200 0.82301385 2.3448692 0.96708227 55.735326 + 250 0.83076383 2.0890816 0.96425763 55.320625 + 300 0.81602823 2.0118796 0.96173925 54.095736 + 350 0.81084006 1.9122192 0.95979392 54.526429 + 400 0.80776593 1.8502174 0.95869117 54.434901 + 450 0.80694697 1.8435873 0.95851085 53.20809 + 500 0.81384248 1.8111331 0.95917305 53.419395 + 550 0.81027072 1.9222272 0.96056019 54.36723 + 600 0.81199582 2.0291945 0.96248486 54.888582 + 650 0.82507964 2.0706462 0.96467227 55.807137 + 700 0.832562 2.1471442 0.9668913 56.721267 + 750 0.83358138 2.2674672 0.968984 56.723838 + 800 0.83477542 2.3658275 0.97072603 56.234689 + 850 0.84722921 2.3506233 0.97189674 56.262424 + 900 0.83526965 2.4532068 0.97248856 56.219103 + 950 0.83174583 2.4763958 0.97249527 56.409813 + 1000 0.83022557 2.4334341 0.97194093 55.890858 + 1050 0.83208978 2.3478416 0.97092452 54.934691 + 1100 0.82789545 2.272404 0.9696152 54.90894 + 1150 0.82678617 2.1798046 0.96819776 54.927782 + 1200 0.8088841 2.1960256 0.96687735 54.914327 + 1250 0.81512784 2.0736261 0.96579008 53.927291 + 1300 0.81271067 2.0297138 0.96504188 54.289698 + 1350 0.8201767 1.9493976 0.96464115 55.342131 + 1400 0.80880489 2.0016987 0.96468463 55.757758 + 1450 0.8114196 2.0282699 0.96514115 55.865676 + 1500 0.81085664 2.0838361 0.96591869 56.553425 + 1550 0.81257075 2.1283157 0.96694549 56.921544 + 1600 0.82617645 2.1017986 0.96817075 56.858808 + 1650 0.82616141 2.1885582 0.96941073 56.717917 + 1700 0.81634174 2.2996967 0.97047447 56.453745 + 1750 0.82447573 2.2924266 0.97128663 56.916813 + 1800 0.83610432 2.236456 0.97178453 56.400752 + 1850 0.824792 2.3103491 0.97197318 55.891368 + 1900 0.82298989 2.3059287 0.97181084 55.680562 + 1950 0.82098545 2.2801009 0.97138609 55.754404 + 2000 0.81812031 2.2480166 0.97078591 55.801371 + 2050 0.82822262 2.1208887 0.97004108 55.687001 + 2100 0.79768162 2.2711186 0.9693017 55.459852 + 2150 0.81817874 2.0680317 0.96860202 56.514744 + 2200 0.80707412 2.1112032 0.96810521 55.504308 + 2250 0.81650921 2.0077757 0.96781164 55.635717 + 2300 0.80634656 2.066186 0.96777181 56.051088 + 2350 0.80893174 2.0619084 0.96799042 56.548711 + 2400 0.82453783 1.9585503 0.96846727 56.695111 + 2450 0.81517275 2.0752617 0.96921631 56.614046 + 2500 0.80969622 2.1624476 0.9701054 56.574846 + 2550 0.80861922 2.2089505 0.97100787 57.072334 + 2600 0.81468888 2.2293754 0.97192875 56.879416 + 2650 0.82061239 2.2245462 0.97269723 55.442015 + 2700 0.81687473 2.2792015 0.97319852 54.420301 + 2750 0.81416567 2.2982988 0.97340467 54.469427 + 2800 0.81978563 2.2418723 0.97332803 55.965451 + 2850 0.82069759 2.1988948 0.97302752 56.686807 + 2900 0.80631184 2.2684466 0.97261407 56.585682 + 2950 0.81759744 2.1312328 0.97207888 56.812431 + 3000 0.80748056 2.152676 0.97151807 57.178849 + 3050 0.80789237 2.118162 0.97103728 57.433724 + 3100 0.79882523 2.1414744 0.97070338 57.34686 + 3150 0.79803949 2.1359043 0.97052875 57.382544 + 3200 0.79170386 2.1548392 0.97049349 56.465806 + 3250 0.78848813 2.1990144 0.97067557 55.929088 + 3300 0.79820555 2.1304609 0.97101444 55.624487 + 3350 0.79250565 2.1971235 0.97149233 55.933615 + 3400 0.80584844 2.1417239 0.97206083 55.85922 + 3450 0.80685744 2.1640501 0.97266047 55.135963 + 3500 0.80751888 2.1858277 0.97318703 55.407581 + 3550 0.79882754 2.2796452 0.97363149 55.392366 + 3600 0.80219171 2.2715765 0.97392571 55.867887 + 3650 0.79061794 2.3492866 0.97410985 56.0192 + 3700 0.8058483 2.2327904 0.97411924 56.491303 + 3750 0.79460746 2.2941868 0.97397764 55.929912 + 3800 0.80447478 2.2018009 0.97367627 55.663208 + 3850 0.80355335 2.17638 0.97333164 55.637261 + 3900 0.80388417 2.1531434 0.9729647 56.03794 + 3950 0.79557409 2.1853318 0.9726503 56.132348 + 4000 0.79547396 2.1457051 0.97235244 55.552675 + 4050 0.8058384 2.0637678 0.97213346 56.185416 + 4100 0.7976931 2.1028246 0.97208255 56.050347 + 4150 0.79555522 2.115473 0.97216375 56.868136 + 4200 0.79324134 2.1510383 0.97246129 56.462635 + 4250 0.80788167 2.0534887 0.97287821 55.650788 + 4300 0.79389865 2.2019815 0.97337765 55.596846 + 4350 0.79786309 2.1851119 0.97389825 57.000921 + 4400 0.79986518 2.1997541 0.97443778 57.551564 + 4450 0.8063901 2.1893874 0.97493151 57.236138 + 4500 0.80005802 2.250364 0.97533075 57.341358 + 4550 0.79707443 2.2995576 0.97557554 57.338713 + 4600 0.79869949 2.2807889 0.97563277 57.084504 + 4650 0.79694427 2.2673215 0.97544638 57.025663 + 4700 0.79023986 2.2884131 0.97511483 57.131188 + 4750 0.79566823 2.2215519 0.97464304 57.045676 + 4800 0.78936986 2.2268037 0.97410626 57.384178 + 4850 0.79025913 2.1836718 0.973616 57.78438 + 4900 0.80138424 2.0657609 0.9732124 57.888266 + 4950 0.77853735 2.207944 0.97296347 57.312213 + 5000 0.79115984 2.1035893 0.97285578 57.109472 +Loop time of 9.53489 on 4 procs for 5000 steps with 5120 atoms + +Performance: 181229.223 tau/day, 524.390 timesteps/s +99.1% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.312 | 6.4238 | 6.5139 | 3.1 | 67.37 +Neigh | 0.72062 | 0.73538 | 0.74531 | 1.1 | 7.71 +Comm | 0.52697 | 0.64152 | 0.78688 | 14.1 | 6.73 +Output | 0.0028393 | 0.0029888 | 0.0033851 | 0.4 | 0.03 +Modify | 1.6249 | 1.669 | 1.7253 | 2.9 | 17.50 +Other | | 0.06221 | | | 0.65 + +Nlocal: 1280 ave 1289 max 1266 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Nghost: 3346.25 ave 3379 max 3331 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Neighs: 80701.8 ave 81534 max 79755 min +Histogram: 1 0 1 0 0 0 0 0 1 1 + +Total # of neighbors = 322807 +Ave neighs/atom = 63.0482 +Neighbor list builds = 248 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:09 diff --git a/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.1 b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.1 new file mode 100644 index 000000000..c2aaa9a58 --- /dev/null +++ b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.1 @@ -0,0 +1,186 @@ +LAMMPS (22 Sep 2017) + using 1 OpenMP thread(s) per MPI task +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes +read_data data.halfhalf + orthogonal box = (0 0 0) to (12.8152 12.8152 34) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 5120 atoms + reading velocities ... + 5120 velocities +pair_coeff 1 1 1.0 1.0 2.5 +mass 1 1.0 + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet + +velocity all create 0.8 1 mom yes rot yes +fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0 +fix 100 all momentum 100 linear 1 1 1 + +# harmonic rho_k bias-field +# nx ny nz k a +fix bias all rhok 16 0 0 4.0 26.00 + +# output U_bias rho_k_RE rho_k_IM |rho_k| +thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3] +thermo 50 +dump dumpXYZ all xyz 500 traj.xyz + +# NOTE: run reduced for demonstration purposes +# run 50000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.723 | 5.723 | 5.723 Mbytes +Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3] + 0 0.8 5.1566801 -4.8556711 34 179.52419 35.473155 -0.2832763 35.474286 + 50 1.072533 3.8158392 -5.2704532 34.024206 0.010596224 25.927135 -0.063106738 25.927212 + 100 1.1093231 3.6703116 -5.3380965 34.094814 1.8552612 26.958236 -0.51403326 26.963136 + 150 1.1080721 3.8202601 -5.3568368 34.207473 0.39188605 26.420755 -1.0759575 26.442655 + 200 1.1435287 3.3445987 -5.4365298 34.354119 3.0758718 27.239465 -0.19115251 27.240135 + 250 1.1203046 3.4669456 -5.4293867 34.511473 0.8543814 26.652785 -0.20818214 26.653598 + 300 1.1012709 3.4583154 -5.4281803 34.664509 2.4837156 27.097674 0.9518628 27.114387 + 350 1.0439632 3.8953869 -5.368619 34.810399 0.55385719 26.518391 0.64525272 26.52624 + 400 1.0083878 4.0523864 -5.3418278 34.957669 0.34806057 26.404011 0.83368604 26.417169 + 450 0.9675244 4.310087 -5.3089468 35.114208 0.7921285 26.607512 1.077889 26.629336 + 500 0.94605476 4.1050097 -5.3062273 35.284018 0.87757754 26.639125 1.1140858 26.662411 + 550 0.92662323 3.9299063 -5.3062927 35.458565 1.3746441 26.773494 1.7256603 26.829049 + 600 0.89723165 3.7683555 -5.289725 35.629881 0.46692943 26.372973 2.4135502 26.483182 + 650 0.90612566 3.1098837 -5.3267851 35.788537 0.032662126 25.918784 3.2982102 26.127793 + 700 0.9152508 2.6527976 -5.3597799 35.923343 0.014621588 25.834591 3.6093492 26.085503 + 750 0.90156356 2.3474851 -5.3545938 36.031813 0.75225637 26.307204 4.0247215 26.613293 + 800 0.89748513 1.9825103 -5.3610202 36.113888 0.33402511 26.261326 2.7858039 26.408672 + 850 0.89496343 1.8906342 -5.3673514 36.169424 0.85431557 26.534648 2.5150347 26.653573 + 900 0.89463983 1.5654217 -5.3753283 36.20181 1.5689239 26.764737 2.5474794 26.885699 + 950 0.88663832 1.4399476 -5.3703322 36.209971 0.044436903 25.818418 1.2963356 25.850941 + 1000 0.87407208 1.485718 -5.3572665 36.195386 1.4405611 26.828072 1.0520795 26.848693 + 1050 0.87580489 1.163155 -5.3647269 36.160279 0.15319559 26.234791 1.4845964 26.276763 + 1100 0.86978111 1.3743181 -5.3594907 36.104958 1.1313537 25.19895 1.5711793 25.247885 + 1150 0.86987861 1.3212927 -5.3628503 36.035486 0.039865678 25.841762 0.93898962 25.858816 + 1200 0.87142486 1.3293818 -5.3676854 35.954411 0.16827389 25.70952 -0.14639427 25.709936 + 1250 0.87582265 1.3203803 -5.3764058 35.86575 0.25946652 25.639682 0.082696867 25.639815 + 1300 0.87371627 1.4680294 -5.375151 35.772824 0.17697069 25.701417 0.2397926 25.702535 + 1350 0.88617453 1.5923057 -5.3954912 35.681046 0.00049155526 25.973634 -0.74521794 25.984323 + 1400 0.87809636 1.5821707 -5.3850722 35.594706 0.024050814 26.107395 -0.34393685 26.10966 + 1450 0.87912192 1.7820174 -5.3885842 35.514722 0.20999914 25.667238 -0.66933655 25.675964 + 1500 0.88293618 2.0295275 -5.3963602 35.443445 0.60232374 25.376395 -1.9501461 25.451218 + 1550 0.90012542 1.9476472 -5.4249456 35.382791 0.4488038 26.448928 -1.1452474 26.473711 + 1600 0.89155063 2.2462603 -5.4153432 35.332095 0.039621687 26.138157 -0.36825239 26.140751 + 1650 0.8942624 2.343747 -5.4233433 35.294954 0.0089980332 26.064277 0.38189192 26.067075 + 1700 0.90047841 2.451289 -5.4376312 35.27234 0.86985171 26.646438 0.83408084 26.659489 + 1750 0.87586052 2.6381221 -5.4067182 35.264564 6.346204 27.652722 2.6699692 27.78132 + 1800 0.87392582 2.6338176 -5.4109056 35.270073 0.046414129 26.016188 2.6651053 26.152339 + 1850 0.86540415 2.5434301 -5.4058587 35.285902 0.054615472 26.074279 2.1799787 26.165251 + 1900 0.87043082 2.5776772 -5.4216997 35.309062 0.68978148 26.38648 3.2614091 26.587274 + 1950 0.86281992 2.3107762 -5.4188978 35.338501 0.0072672577 25.736893 3.2375012 25.93972 + 2000 0.85905576 2.2894047 -5.4215995 35.36787 0.095633435 26.072085 2.7685848 26.21867 + 2050 0.85793751 2.2382039 -5.4279351 35.395213 0.13602344 25.598457 2.6881027 25.739209 + 2100 0.85585253 2.0765811 -5.4324511 35.418877 0.0059888115 25.754128 3.1436222 25.945279 + 2150 0.86701057 1.8449875 -5.4562208 35.436124 0.097328618 25.413697 4.3268293 25.7794 + 2200 0.85168154 1.9024923 -5.4395776 35.44246 0.20764576 25.094788 5.4406104 25.677784 + 2250 0.8429719 1.870335 -5.4320586 35.438363 0.34419961 24.998478 5.4475709 25.585151 + 2300 0.84176891 1.7100228 -5.4351472 35.422863 0.76036958 24.697018 5.8629967 25.383409 + 2350 0.84601588 1.8539039 -5.4456629 35.395979 0.38437531 25.647986 6.4163366 26.438392 + 2400 0.84637647 1.6299091 -5.4498948 35.36125 0.074236719 24.995872 7.8269968 26.192661 + 2450 0.85650449 1.6828907 -5.4683101 35.316669 0.3671827 25.280669 7.7040329 26.428476 + 2500 0.84963707 1.7305222 -5.4605394 35.265508 0.1406965 25.236741 7.2780025 26.265232 + 2550 0.84084365 1.8758368 -5.4497083 35.208725 0.33937687 24.544376 7.2334512 25.588067 + 2600 0.85317342 1.7781674 -5.4702734 35.149747 0.60378248 24.046307 8.3370138 25.450554 + 2650 0.85487644 2.0065374 -5.4747643 35.090431 0.22483651 24.937101 8.4669004 26.335288 + 2700 0.84550083 1.9363031 -5.4628401 35.034349 0.43442577 24.250196 7.9943738 25.533939 + 2750 0.85843419 2.0473138 -5.484528 34.980671 0.45959294 24.17438 8.179356 25.520629 + 2800 0.86047607 2.0754522 -5.4899966 34.932466 0.00038123477 24.619856 8.3153434 25.986194 + 2850 0.86375793 2.2751324 -5.4977459 34.892337 0.0016455263 24.927259 7.289789 25.971316 + 2900 0.84438986 2.3790377 -5.4721407 34.863512 1.2372354 25.819445 7.132603 26.786523 + 2950 0.8551438 2.2721926 -5.4925958 34.84473 1.5405388 25.956466 6.976385 26.87765 + 3000 0.83737707 2.4009609 -5.4707188 34.834171 0.28507766 25.643879 6.1778846 26.377543 + 3050 0.84923235 2.4187994 -5.4938573 34.830836 0.036512025 25.139252 7.1457857 26.135115 + 3100 0.83872396 2.3811576 -5.4838787 34.833673 0.246984 24.21358 8.4588719 25.648586 + 3150 0.83957817 2.3901421 -5.4913118 34.84163 0.20477984 24.309852 10.088243 26.319984 + 3200 0.84283033 2.17292 -5.5025459 34.853975 1.3367154 24.581685 10.72011 26.817531 + 3250 0.84002379 2.1247709 -5.5044955 34.866106 0.11434509 24.463842 9.4874246 26.239108 + 3300 0.83311101 2.1492058 -5.5000847 34.875625 0.0053284993 23.815298 10.560222 26.051616 + 3350 0.83216701 1.9587594 -5.5043446 34.881623 0.58985562 23.934253 11.475462 26.543073 + 3400 0.82396039 2.1914951 -5.4971506 34.881199 0.098206955 23.393402 10.82936 25.778407 + 3450 0.83483253 1.9783612 -5.5182844 34.877327 7.6571212e-05 23.675355 10.761012 26.006188 + 3500 0.82712062 1.9718522 -5.5111818 34.869214 0.014836125 23.314122 11.312845 25.913872 + 3550 0.8342927 1.9114357 -5.5259968 34.855179 1.4050442 22.442758 11.377192 25.161834 + 3600 0.82631637 1.9836457 -5.5176244 34.835738 0.084637609 23.413286 10.824194 25.794285 + 3650 0.82425697 1.9218541 -5.5178548 34.811901 0.11000071 22.788707 12.022258 25.765478 + 3700 0.82491437 1.9624493 -5.521738 34.782417 0.034984027 23.011433 12.384217 26.132257 + 3750 0.82758167 2.0856442 -5.5283493 34.748872 0.001362163 23.030662 12.122144 26.026098 + 3800 0.81891108 1.9858824 -5.5177774 34.714618 0.17075993 23.21344 12.345683 26.292199 + 3850 0.83392227 2.1631514 -5.5426333 34.681146 0.82106473 22.510204 11.678329 25.359272 + 3900 0.82230654 2.0017132 -5.5276756 34.650221 0.48735732 23.444809 12.339117 26.493638 + 3950 0.81929288 2.1749936 -5.5256673 34.61976 0.089219805 23.540062 11.527925 26.211211 + 4000 0.83415169 2.0446791 -5.5506187 34.591266 0.15593937 23.742282 11.26508 26.279231 + 4050 0.82362522 2.1998083 -5.5375157 34.563164 0.25405351 23.913834 11.081011 26.356408 + 4100 0.82589505 2.3074345 -5.543718 34.537763 0.080213125 24.03253 10.435108 26.200266 + 4150 0.83855297 2.2424199 -5.5658171 34.517758 0.62913338 23.974257 8.5079223 25.439138 + 4200 0.82522111 2.2622619 -5.5493275 34.502472 1.8756517 25.754617 7.9996898 26.968414 + 4250 0.82083124 2.4135193 -5.5464932 34.4919 1.1217436 25.8944 6.7070444 26.748914 + 4300 0.83059704 2.1375109 -5.5653245 34.487366 0.53623038 26.05979 4.9072346 26.517798 + 4350 0.82755047 2.1159821 -5.5650889 34.484506 0.10017723 25.405936 4.3532342 25.776195 + 4400 0.83192877 2.180851 -5.5759565 34.480909 0.053664012 25.993034 2.9844338 26.163805 + 4450 0.81860572 2.2333381 -5.5602138 34.477183 0.037864077 25.792233 1.9038859 25.862406 + 4500 0.82821762 2.1142023 -5.5788682 34.474784 0.088221344 26.20329 0.59417897 26.210025 + 4550 0.8205154 2.0896984 -5.5715531 34.472405 0.016076192 26.083166 -0.58187024 26.089655 + 4600 0.81294948 2.2274108 -5.5642678 34.469014 0.033774986 25.869616 0.14951307 25.870048 + 4650 0.80890532 2.1556346 -5.5622407 34.465277 0.67402048 25.413229 -0.56341819 25.419474 + 4700 0.82070227 1.9852605 -5.583747 34.460206 0.052623237 26.158394 -0.44673492 26.162209 + 4750 0.81451857 2.1097726 -5.5779782 34.451438 0.12221733 25.733718 -0.9911436 25.752798 + 4800 0.81300453 2.0211325 -5.5790076 34.439504 0.34536082 26.358606 -1.7335167 26.415548 + 4850 0.82035497 1.9489595 -5.5929886 34.424097 0.70899626 26.575865 -1.0191012 26.595397 + 4900 0.8127066 2.1312269 -5.584271 34.405998 0.087959314 26.185217 -1.1329105 26.209713 + 4950 0.81252621 2.1094866 -5.5866296 34.387869 0.79067667 26.564722 -1.8456354 26.628759 + 5000 0.80575936 2.1875995 -5.579054 34.370679 0.031787364 26.027557 -2.2666774 26.12607 +Loop time of 32.2397 on 1 procs for 5000 steps with 5120 atoms + +Performance: 53598.557 tau/day, 155.088 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 22.967 | 22.967 | 22.967 | 0.0 | 71.24 +Neigh | 2.9914 | 2.9914 | 2.9914 | 0.0 | 9.28 +Comm | 0.37485 | 0.37485 | 0.37485 | 0.0 | 1.16 +Output | 0.064337 | 0.064337 | 0.064337 | 0.0 | 0.20 +Modify | 5.7143 | 5.7143 | 5.7143 | 0.0 | 17.72 +Other | | 0.1281 | | | 0.40 + +Nlocal: 5120 ave 5120 max 5120 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7962 ave 7962 max 7962 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 296101 ave 296101 max 296101 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 296101 +Ave neighs/atom = 57.8322 +Neighbor list builds = 283 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:32 diff --git a/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.4 b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.4 new file mode 100644 index 000000000..c7a77fb9c --- /dev/null +++ b/examples/USER/misc/pinning/log.22Sep2017.pinning.g++.4 @@ -0,0 +1,186 @@ +LAMMPS (22 Sep 2017) + using 1 OpenMP thread(s) per MPI task +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes +read_data data.halfhalf + orthogonal box = (0 0 0) to (12.8152 12.8152 34) + 1 by 1 by 4 MPI processor grid + reading atoms ... + 5120 atoms + reading velocities ... + 5120 velocities +pair_coeff 1 1 1.0 1.0 2.5 +mass 1 1.0 + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet + +velocity all create 0.8 1 mom yes rot yes +fix ensemble all npt temp 0.8 0.8 4.0 z 2.185 2.185 8.0 +fix 100 all momentum 100 linear 1 1 1 + +# harmonic rho_k bias-field +# nx ny nz k a +fix bias all rhok 16 0 0 4.0 26.00 + +# output U_bias rho_k_RE rho_k_IM |rho_k| +thermo_style custom step temp pzz pe lz f_bias f_bias[1] f_bias[2] f_bias[3] +thermo 50 +dump dumpXYZ all xyz 500 traj.xyz + +# NOTE: run reduced for demonstration purposes +# run 50000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.023 | 4.027 | 4.03 Mbytes +Step Temp Pzz PotEng Lz f_bias f_bias[1] f_bias[2] f_bias[3] + 0 0.8 5.1872229 -4.8361269 34 152.02869 34.711006 -0.72709593 34.71862 + 50 1.0819371 3.9250728 -5.2655842 34.02563 0.51385908 26.505979 0.2187864 26.506882 + 100 1.1182271 3.5397251 -5.3331401 34.100753 2.1059904 27.025883 -0.12127124 27.026156 + 150 1.1121434 3.7845571 -5.3440494 34.213993 1.7206575 26.894862 -1.3261751 26.927539 + 200 1.1446439 3.4114364 -5.4199119 34.358914 2.383615 27.054401 -1.4211151 27.091699 + 250 1.1115073 3.5603047 -5.3988013 34.517397 0.60819391 26.51404 -1.4089688 26.55145 + 300 1.0828478 3.7411116 -5.3842818 34.673948 0.73987465 26.528178 -2.062382 26.608225 + 350 1.0342597 3.9206217 -5.3384367 34.825105 0.99965014 26.657737 -1.6211152 26.706983 + 400 1.0064356 3.9929044 -5.324003 34.97579 0.41927007 26.402623 -1.7087432 26.457859 + 450 0.96799277 4.2764255 -5.2947175 35.133839 0.77739461 26.503753 -2.5217998 26.623456 + 500 0.94691076 4.1007962 -5.2922124 35.301893 0.17015805 26.212252 -2.0421698 26.291683 + 550 0.93675297 3.7404088 -5.3056917 35.474301 0.56247039 26.335926 -3.205722 26.530316 + 600 0.92707577 3.5439822 -5.3176094 35.641282 0.04054693 25.679461 -3.0301039 25.857615 + 650 0.91828226 3.1833648 -5.3278237 35.794766 0.8427054 26.4003 -3.6331211 26.649117 + 700 0.9084826 2.8374306 -5.3327944 35.928138 1.5635222 26.605971 -3.8575939 26.884173 + 750 0.91219559 2.46172 -5.3548299 36.039156 6.3772911 27.350725 -4.8971146 27.785678 + 800 0.90000337 2.2187716 -5.3499181 36.126451 4.9080838 27.085156 -5.1291678 27.566538 + 850 0.9003432 1.8634244 -5.3614648 36.189019 0.0081092188 25.497333 -5.4038153 26.063676 + 900 0.89741573 1.5697398 -5.3660799 36.226074 0.011155479 25.312724 -6.2574069 26.074684 + 950 0.88871454 1.4427205 -5.3604669 36.237407 0.3287078 25.659237 -6.232896 26.405406 + 1000 0.88606353 1.3088636 -5.3626576 36.226015 0.30068168 24.554896 -7.2832017 25.612262 + 1050 0.88527541 1.3194263 -5.3666773 36.19311 0.10646314 24.514921 -7.9419424 25.76928 + 1100 0.87522001 1.2852124 -5.3556811 36.143056 0.13675329 24.865981 -8.446822 26.261489 + 1150 0.8805978 1.246973 -5.3671716 36.0781 0.00043275463 24.187039 -9.4985495 25.98529 + 1200 0.85711495 1.376588 -5.3346243 36.002427 0.47623639 23.691349 -9.4648541 25.512026 + 1250 0.88116805 1.3562001 -5.3731036 35.919289 0.32797055 23.322103 -10.54448 25.595049 + 1300 0.87178482 1.5046564 -5.3610798 35.831278 0.17704849 24.190231 -10.314689 26.29753 + 1350 0.87022621 1.6830825 -5.3603618 35.743318 0.0052854997 23.731157 -10.747465 26.051408 + 1400 0.89019669 1.6144812 -5.3921986 35.659687 1.4152796 22.8393 -10.551347 25.158787 + 1450 0.88852819 1.7587964 -5.3918592 35.580319 0.63560961 23.599033 -12.195 26.563742 + 1500 0.89029085 1.8772498 -5.3966098 35.509232 0.20895386 23.055083 -12.703366 26.323229 + 1550 0.88639722 2.2284824 -5.3933288 35.449043 0.44413965 22.448774 -12.156068 25.528757 + 1600 0.88816451 2.2167704 -5.3994757 35.401661 0.12210235 23.108351 -12.44643 26.247085 + 1650 0.89154791 2.3397824 -5.4086923 35.365815 0.4820208 23.090699 -12.984179 26.490928 + 1700 0.88518032 2.5351236 -5.4041601 35.343757 0.080806002 22.749825 -12.99762 26.201005 + 1750 0.86848721 2.5527491 -5.3851928 35.336433 0.045102165 22.357111 -13.564328 26.15017 + 1800 0.88501061 2.5215825 -5.4169341 35.340849 0.27488483 22.086584 -14.408273 26.370732 + 1850 0.8716061 2.5809558 -5.4045854 35.355038 0.042909785 21.270956 -14.695278 25.853525 + 1900 0.85672517 2.4836326 -5.3902797 35.375469 0.72877764 21.639909 -15.474764 26.603646 + 1950 0.85133731 2.3141629 -5.3902573 35.398523 0.0016908803 21.106617 -15.132733 25.970924 + 2000 0.86152109 2.1562002 -5.4132601 35.419851 0.371016 21.325237 -15.614625 26.430706 + 2050 0.86243551 2.019931 -5.4220349 35.436069 0.017935421 20.4131 -16.255418 26.094698 + 2100 0.87417672 1.8083823 -5.4464117 35.445091 0.18429432 19.75625 -17.365705 26.303558 + 2150 0.85872128 1.7608768 -5.4293103 35.44341 0.91209166 20.149648 -17.480387 26.675312 + 2200 0.86615373 1.8372778 -5.4458315 35.430616 0.10151993 18.559234 -17.885469 25.7747 + 2250 0.85053605 1.7198437 -5.4272104 35.408688 0.96154548 17.200861 -18.562206 25.306622 + 2300 0.85400281 1.7939644 -5.4364682 35.377708 0.12283263 18.759325 -18.358539 26.247823 + 2350 0.85495278 1.5856029 -5.4417321 35.337987 0.20564329 18.967923 -18.248149 26.320658 + 2400 0.84606771 1.7782708 -5.4315646 35.287411 0.10063977 19.185527 -17.878215 26.224321 + 2450 0.85210051 1.8190391 -5.4432116 35.232321 0.69988647 19.268861 -18.325448 26.59156 + 2500 0.85304715 1.7466204 -5.4470889 35.175245 0.0048314937 18.09176 -18.74157 26.04915 + 2550 0.85401123 1.8601945 -5.4509309 35.115748 0.99467901 17.170045 -18.574587 25.294777 + 2600 0.85778606 1.974012 -5.4586742 35.058013 0.0026599702 17.438966 -19.333395 26.036469 + 2650 0.8521239 2.0606329 -5.4526006 35.003616 0.091056354 17.16363 -19.244738 25.786627 + 2700 0.85918482 2.0766792 -5.4658947 34.954171 0.89590606 15.77108 -19.822153 25.330707 + 2750 0.85786577 2.225549 -5.4667773 34.911468 0.26577575 15.769018 -21.128817 26.364538 + 2800 0.86764664 2.2325018 -5.4849414 34.877604 0.47167555 14.950515 -20.675229 25.514369 + 2850 0.85209564 2.3434319 -5.465734 34.852715 2.7350296 13.51553 -20.829996 24.830592 + 2900 0.85757283 2.3512971 -5.4786051 34.836138 0.14816492 14.06033 -21.545946 25.727819 + 2950 0.86098926 2.3480431 -5.4890615 34.826408 0.26401534 13.381395 -22.714827 26.363329 + 3000 0.85413421 2.3243973 -5.4844129 34.823242 0.024244334 12.739486 -22.538687 25.889899 + 3050 0.85015323 2.5479266 -5.4844303 34.825228 0.4463147 12.990582 -21.975063 25.527605 + 3100 0.8530523 2.3643505 -5.495343 34.834883 0.12144265 12.844293 -22.321989 25.753583 + 3150 0.85098478 2.2521299 -5.4990526 34.848419 0.33194916 12.747856 -23.126671 26.4074 + 3200 0.84391449 2.2650057 -5.495222 34.862626 0.031888328 12.788845 -22.782174 26.12627 + 3250 0.84807155 2.1715388 -5.5080873 34.877548 0.082426694 13.316219 -22.09441 25.796989 + 3300 0.83028242 2.242889 -5.4878846 34.89175 1.1334975 14.326678 -22.593363 26.752827 + 3350 0.82924001 2.0324002 -5.4924558 34.903232 0.35473989 14.354166 -22.181868 26.421153 + 3400 0.83032841 2.0003371 -5.4997142 34.908733 0.041677437 14.528378 -21.735998 26.144356 + 3450 0.82908891 1.8683902 -5.5029185 34.907936 0.02365857 15.069507 -21.053887 25.891237 + 3500 0.82842914 1.9165344 -5.5064218 34.898681 0.17663531 15.27043 -20.674834 25.702817 + 3550 0.82735822 1.98221 -5.5088197 34.88272 1.5607134 14.915228 -20.208431 25.116622 + 3600 0.82642915 1.8422766 -5.5110752 34.8611 1.1861112 15.312314 -20.051953 25.229899 + 3650 0.82556781 1.9351408 -5.5130349 34.833406 1.018872 16.152478 -19.454871 25.286252 + 3700 0.82360651 1.9791184 -5.5128431 34.802021 0.14080727 16.907104 -19.401616 25.734663 + 3750 0.83017793 1.9855734 -5.5253254 34.768644 0.15311334 16.969506 -19.331958 25.723311 + 3800 0.82362926 2.1029656 -5.5179624 34.734178 0.10807487 17.892584 -18.542426 25.76754 + 3850 0.82313508 2.0781681 -5.5196175 34.70093 0.13343085 19.072706 -17.28778 25.741707 + 3900 0.83643385 2.0570262 -5.5421224 34.669761 0.00022792038 19.551677 -17.1548 26.010675 + 3950 0.82346174 2.0842322 -5.5252757 34.640849 0.0093759386 20.892792 -15.590263 26.068469 + 4000 0.83485868 2.1196669 -5.5451736 34.612396 0.31198053 21.630258 -15.126984 26.394956 + 4050 0.82729429 2.2033274 -5.5365945 34.585721 0.53752252 21.283533 -14.011497 25.481578 + 4100 0.82040242 2.1757309 -5.5292269 34.562271 0.36031984 22.047609 -12.961927 25.575548 + 4150 0.81932521 2.285666 -5.5307807 34.542102 0.84343149 22.486289 -11.70555 25.350604 + 4200 0.83819319 2.231174 -5.5625532 34.526447 0.47190752 23.311855 -12.57189 26.485751 + 4250 0.82542274 2.1874789 -5.5472057 34.513795 0.70518398 23.411553 -12.614639 26.593795 + 4300 0.81971158 2.241167 -5.5424504 34.503969 0.26707612 23.089805 -12.727793 26.365429 + 4350 0.83255377 2.1295532 -5.5657895 34.496326 0.072548591 23.003138 -12.52181 26.190458 + 4400 0.8128474 2.3327845 -5.5402264 34.490126 0.0013023434 23.020811 -12.029795 25.974482 + 4450 0.82013491 2.3069915 -5.5554953 34.488039 0.041123896 23.632908 -11.178674 26.143394 + 4500 0.81411544 2.2247193 -5.5509183 34.488014 0.54440601 23.010678 -10.938506 25.478269 + 4550 0.82814624 2.1142779 -5.5763482 34.487885 0.1518945 23.696817 -11.351972 26.275585 + 4600 0.82929492 2.090881 -5.5823492 34.486698 0.0045520899 23.538527 -10.929741 25.952292 + 4650 0.81061417 1.9818043 -5.5584018 34.484038 0.012526806 23.993543 -10.219174 26.079142 + 4700 0.81816105 1.9605811 -5.5735005 34.476764 1.2079835 25.151166 -9.1888856 26.777169 + 4750 0.81657042 2.0064313 -5.5744795 34.465784 1.2045017 25.487486 -8.2063886 26.776048 + 4800 0.81789335 2.0838696 -5.5796632 34.451996 0.27642542 24.647157 -7.023095 25.62823 + 4850 0.80649339 1.9892413 -5.5654796 34.436067 0.024697945 25.09823 -6.3492244 25.888874 + 4900 0.81673441 2.0125635 -5.5835037 34.416236 0.0011188576 25.446818 -5.2182483 25.976348 + 4950 0.82250033 1.9770391 -5.5946082 34.394723 0.72696707 26.37002 -3.5122842 26.602896 + 5000 0.80762758 2.075517 -5.5746076 34.371696 0.12796344 26.102184 -2.8094827 26.252946 +Loop time of 10.3394 on 4 procs for 5000 steps with 5120 atoms + +Performance: 167127.370 tau/day, 483.586 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.029 | 6.0128 | 7.1918 | 35.0 | 58.15 +Neigh | 0.65673 | 0.75825 | 0.88597 | 10.3 | 7.33 +Comm | 0.43982 | 1.5284 | 2.4112 | 60.5 | 14.78 +Output | 0.022835 | 0.023039 | 0.023453 | 0.2 | 0.22 +Modify | 1.7294 | 1.9472 | 2.5687 | 25.7 | 18.83 +Other | | 0.06978 | | | 0.67 + +Nlocal: 1280 ave 1404 max 1214 min +Histogram: 2 0 0 1 0 0 0 0 0 1 +Nghost: 3521.25 ave 3581 max 3426 min +Histogram: 1 0 0 0 0 0 1 1 0 1 +Neighs: 73872.2 ave 87973 max 64161 min +Histogram: 1 1 0 0 1 0 0 0 0 1 + +Total # of neighbors = 295489 +Ave neighs/atom = 57.7127 +Neighbor list builds = 278 +Dangerous builds = 0 + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:10 diff --git a/examples/USER/misc/pinning/log.22Sep2017.setup.g++.1 b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.1 new file mode 100644 index 000000000..8606d4ed9 --- /dev/null +++ b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.1 @@ -0,0 +1,141 @@ +LAMMPS (22 Sep 2017) + using 1 OpenMP thread(s) per MPI task +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes + +# fcc lattice +lattice fcc 0.9731 +Lattice spacing in x,y,z = 1.6019 1.6019 1.6019 +region my_box block 0 8.0 0 8.0 0 20.0 +create_box 1 my_box +Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379) + 1 by 1 by 1 MPI processor grid +region particles block 0 8.0 0 8.0 0 20.0 +create_atoms 1 region particles +Created 5120 atoms +pair_coeff 1 1 1.0 1.0 2.5 +mass 1 1.0 +change_box all z final 0.0 34 remap units box + orthogonal box = (0 0 0) to (12.8152 12.8152 34) + +# select particles in one side of the elongated box +region left plane 0 0 10 0 0 1 +group left region left +2688 atoms in group left + +velocity left create 6.0 1 mom yes rot yes + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet +fix ensemble left nve # Note: only move particle in left-hand side +fix langevin left langevin 3.0 0.8 100.0 2017 + +# outout +thermo_style custom step temp pzz pe lz +thermo 100 +# dump dumpXYZ all xyz 100 traj.xyz + +# run reduced for demonstration purposes +# run 10000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes +Step Temp Pzz PotEng Lz + 0 3.1494433 -3.4735106 -6.8707307 34 + 100 1.7727555 6.5330255 -4.8035477 34 + 200 1.7462368 7.0070325 -4.7646426 34 + 300 1.7564888 6.6190123 -4.7894637 34 + 400 1.7641186 6.609684 -4.8064772 34 + 500 1.7383511 6.7304936 -4.7708095 34 + 600 1.731708 6.8574656 -4.7612918 34 + 700 1.7332167 6.6530919 -4.7670014 34 + 800 1.7487537 6.5644963 -4.7907458 34 + 900 1.7353648 6.7115188 -4.7772149 34 + 1000 1.728878 6.4175719 -4.7797216 34 + 1100 1.7471488 6.5346083 -4.813376 34 + 1200 1.7188149 6.2502104 -4.7822235 34 + 1300 1.7151194 6.792534 -4.7781701 34 + 1400 1.7406603 6.6639592 -4.8170174 34 + 1500 1.7090537 6.4677579 -4.770701 34 + 1600 1.7014954 6.2853535 -4.7679742 34 + 1700 1.7064354 6.4352857 -4.7812978 34 + 1800 1.7169971 6.5808758 -4.799426 34 + 1900 1.6822712 6.3746758 -4.7522464 34 + 2000 1.7126546 6.534969 -4.8091595 34 + 2100 1.7086108 6.4679932 -4.8146664 34 + 2200 1.6974952 6.3802129 -4.8052505 34 + 2300 1.6868035 6.4009243 -4.7935769 34 + 2400 1.7107125 6.2318869 -4.8358765 34 + 2500 1.660241 6.4891487 -4.7661183 34 + 2600 1.6801816 6.1988356 -4.8024291 34 + 2700 1.6940298 6.1328187 -4.8290053 34 + 2800 1.6755061 6.4150693 -4.8145473 34 + 2900 1.6749928 6.4248792 -4.8213509 34 + 3000 1.6310737 6.6491291 -4.7673027 34 + 3100 1.6559915 6.2726719 -4.8109181 34 + 3200 1.6574579 5.7132029 -4.8189484 34 + 3300 1.6816136 5.7697439 -4.8652811 34 + 3400 1.6489483 6.4463349 -4.8247812 34 + 3500 1.6557974 5.9763333 -4.8383712 34 + 3600 1.6215459 6.2806534 -4.7954657 34 + 3700 1.6484987 6.0671609 -4.8470777 34 + 3800 1.6473922 5.8688108 -4.8555351 34 + 3900 1.6435957 5.930425 -4.8562076 34 + 4000 1.6514434 6.1962122 -4.872998 34 + 4100 1.6138337 6.4808124 -4.8219373 34 + 4200 1.6215239 5.9467966 -4.8412146 34 + 4300 1.6129295 5.9377323 -4.8414596 34 + 4400 1.6020549 6.1104301 -4.8395939 34 + 4500 1.6047738 6.0816222 -4.8538151 34 + 4600 1.6053565 6.183466 -4.8686817 34 + 4700 1.6088152 5.7416542 -4.894114 34 + 4800 1.5954309 5.694319 -4.8840198 34 + 4900 1.5582564 6.1199614 -4.8429998 34 + 5000 1.5786672 5.8813574 -4.8907344 34 +Loop time of 28.3867 on 1 procs for 5000 steps with 5120 atoms + +Performance: 60873.483 tau/day, 176.139 timesteps/s +99.4% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 22.269 | 22.269 | 22.269 | 0.0 | 78.45 +Neigh | 4.7222 | 4.7222 | 4.7222 | 0.0 | 16.64 +Comm | 0.40821 | 0.40821 | 0.40821 | 0.0 | 1.44 +Output | 0.0042329 | 0.0042329 | 0.0042329 | 0.0 | 0.01 +Modify | 0.88231 | 0.88231 | 0.88231 | 0.0 | 3.11 +Other | | 0.1005 | | | 0.35 + +Nlocal: 5120 ave 5120 max 5120 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 7768 ave 7768 max 7768 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 297167 ave 297167 max 297167 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 297167 +Ave neighs/atom = 58.0404 +Neighbor list builds = 474 +Dangerous builds = 246 +write_data data.halfhalf +Total wall time: 0:00:28 diff --git a/examples/USER/misc/pinning/log.22Sep2017.setup.g++.4 b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.4 new file mode 100644 index 000000000..14088f7c9 --- /dev/null +++ b/examples/USER/misc/pinning/log.22Sep2017.setup.g++.4 @@ -0,0 +1,141 @@ +LAMMPS (22 Sep 2017) + using 1 OpenMP thread(s) per MPI task +units lj +dimension 3 +boundary p p p +atom_style atomic + +# truncated and shifted LJ potential +pair_style lj/cut 2.5 +pair_modify shift yes + +# fcc lattice +lattice fcc 0.9731 +Lattice spacing in x,y,z = 1.6019 1.6019 1.6019 +region my_box block 0 8.0 0 8.0 0 20.0 +create_box 1 my_box +Created orthogonal box = (0 0 0) to (12.8152 12.8152 32.0379) + 1 by 1 by 4 MPI processor grid +region particles block 0 8.0 0 8.0 0 20.0 +create_atoms 1 region particles +Created 5120 atoms +pair_coeff 1 1 1.0 1.0 2.5 +mass 1 1.0 +change_box all z final 0.0 34 remap units box + orthogonal box = (0 0 0) to (12.8152 12.8152 34) + +# select particles in one side of the elongated box +region left plane 0 0 10 0 0 1 +group left region left +2688 atoms in group left + +velocity left create 6.0 1 mom yes rot yes + +# simulation parameters +neighbor 0.6 bin +timestep 0.004 +run_style verlet +fix ensemble left nve # Note: only move particle in left-hand side +fix langevin left langevin 3.0 0.8 100.0 2017 + +# outout +thermo_style custom step temp pzz pe lz +thermo 100 +# dump dumpXYZ all xyz 100 traj.xyz + +# run reduced for demonstration purposes +# run 10000 +run 5000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.1 + ghost atom cutoff = 3.1 + binsize = 1.55, bins = 9 9 22 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.23 | 3.23 | 3.23 Mbytes +Step Temp Pzz PotEng Lz + 0 3.1494433 -3.4735106 -6.8707307 34 + 100 1.7914373 6.4805818 -4.8420353 34 + 200 1.740256 6.6108149 -4.7672571 34 + 300 1.7663827 6.5188941 -4.8103672 34 + 400 1.7440644 6.5156543 -4.7769467 34 + 500 1.7471724 6.5208992 -4.7843928 34 + 600 1.7320106 6.6557835 -4.7654637 34 + 700 1.6839043 6.7689759 -4.7045352 34 + 800 1.7216746 6.66436 -4.7601673 34 + 900 1.7342542 6.3242367 -4.7790803 34 + 1000 1.7338566 6.5803438 -4.7854529 34 + 1100 1.7328856 6.3846366 -4.7902625 34 + 1200 1.7546906 6.5048137 -4.8213443 34 + 1300 1.7163891 6.3903221 -4.7665145 34 + 1400 1.7011627 6.5782672 -4.7517875 34 + 1500 1.7105234 6.5811813 -4.7677748 34 + 1600 1.7334403 6.5032837 -4.8067749 34 + 1700 1.7252102 6.5443871 -4.8058994 34 + 1800 1.721958 6.3378188 -4.8150073 34 + 1900 1.6797892 6.6780506 -4.7538618 34 + 2000 1.7001774 6.3578192 -4.7894018 34 + 2100 1.7127784 6.3219105 -4.8161059 34 + 2200 1.696825 6.536793 -4.7946902 34 + 2300 1.6704578 6.7186933 -4.7609628 34 + 2400 1.6772498 6.3432817 -4.7778471 34 + 2500 1.7073862 6.2153226 -4.8299181 34 + 2600 1.6951557 6.4397257 -4.8156787 34 + 2700 1.6845984 6.0123544 -4.8136864 34 + 2800 1.6550565 6.2489392 -4.7829639 34 + 2900 1.6892315 6.158499 -4.8423004 34 + 3000 1.6814436 6.07976 -4.8400696 34 + 3100 1.6387025 6.330166 -4.7878978 34 + 3200 1.6747855 6.0767043 -4.8481995 34 + 3300 1.6508768 6.2749233 -4.8181888 34 + 3400 1.6426364 6.3934935 -4.8223824 34 + 3500 1.6576512 6.0638185 -4.8559078 34 + 3600 1.6444173 6.1376573 -4.8463113 34 + 3700 1.6480039 5.9943705 -4.8601776 34 + 3800 1.6467212 6.0556591 -4.8722719 34 + 3900 1.6271804 6.116738 -4.8547278 34 + 4000 1.6158134 5.9089534 -4.8477829 34 + 4100 1.6388157 5.9890465 -4.8920284 34 + 4200 1.6182368 6.0639887 -4.8724963 34 + 4300 1.647633 5.6333906 -4.9267536 34 + 4400 1.5856411 6.2675475 -4.8471239 34 + 4500 1.5773417 6.1789163 -4.8469057 34 + 4600 1.6181445 5.7988068 -4.922419 34 + 4700 1.5876712 5.7398111 -4.8853849 34 + 4800 1.5708353 6.2204997 -4.8718872 34 + 4900 1.5514708 5.9782256 -4.8523812 34 + 5000 1.553347 5.9286523 -4.86582 34 +Loop time of 8.10259 on 4 procs for 5000 steps with 5120 atoms + +Performance: 213265.164 tau/day, 617.087 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.2964 | 5.6236 | 5.8982 | 9.0 | 69.40 +Neigh | 1.0562 | 1.1907 | 1.3257 | 8.7 | 14.70 +Comm | 0.43963 | 0.98786 | 1.5968 | 42.5 | 12.19 +Output | 0.0023124 | 0.004741 | 0.0090873 | 4.0 | 0.06 +Modify | 0.018652 | 0.22213 | 0.39884 | 36.4 | 2.74 +Other | | 0.07357 | | | 0.91 + +Nlocal: 1280 ave 1337 max 1211 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Nghost: 3416.25 ave 3549 max 3297 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 74269.8 ave 77932 max 69612 min +Histogram: 1 0 0 0 0 1 0 1 0 1 + +Total # of neighbors = 297079 +Ave neighs/atom = 58.0232 +Neighbor list builds = 474 +Dangerous builds = 247 +write_data data.halfhalf +Total wall time: 0:00:08 diff --git a/src/.gitignore b/src/.gitignore index af973a3aa..0d85b637e 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1,1121 +1,1123 @@ /Makefile.package /Makefile.package.settings /MAKE/MINE /Make.py.last /lmp_* /style_*.h /*_gpu.h /*_gpu.cpp /*_intel.h /*_intel.cpp /*_kokkos.h /*_kokkos.cpp /*_omp.h /*_omp.cpp /*_tally.h /*_tally.cpp /*_rx.h /*_rx.cpp /*_ssa.h /*_ssa.cpp /kokkos.cpp /kokkos.h /kokkos_type.h /kokkos_few.h /manifold*.cpp /manifold*.h /fix_*manifold*.cpp /fix_*manifold*.h /meam*.h /meam*.cpp /pair_meamc.cpp /pair_meamc.h /fix_qeq*.cpp /fix_qeq*.h /compute_test_nbl.cpp /compute_test_nbl.h /pair_multi_lucy.cpp /pair_multi_lucy.h /colvarproxy_lammps.cpp /colvarproxy_lammps.h /colvarproxy_lammps_version.h /fix_colvars.cpp /fix_colvars.h /dump_molfile.cpp /dump_molfile.h /molfile_interface.cpp /molfile_interface.h /type_detector.h /intel_buffers.cpp /intel_buffers.h /intel_intrinsics.h /intel_intrinsics_airebo.h /intel_preprocess.h /intel_simd.h /atom_vec_edpd.cpp /atom_vec_edpd.h /atom_vec_mdpd.cpp /atom_vec_mdpd.h /atom_vec_tdpd.cpp /atom_vec_tdpd.h /compute_edpd_temp_atom.cpp /compute_edpd_temp_atom.h /compute_tdpd_cc_atom.cpp /compute_tdpd_cc_atom.h /fix_edpd_source.cpp /fix_edpd_source.h /fix_mvv_dpd.cpp /fix_mvv_dpd.h /fix_mvv_edpd.cpp /fix_mvv_edpd.h /fix_mvv_tdpd.cpp /fix_mvv_tdpd.h /fix_tdpd_source.cpp /fix_tdpd_source.h /pair_edpd.cpp /pair_edpd.h /pair_mdpd.cpp /pair_mdpd.h /pair_mdpd_rhosum.cpp /pair_mdpd_rhosum.h /pair_tdpd.cpp /pair_tdpd.h /compute_sna_atom.cpp /compute_sna_atom.h /compute_snad_atom.cpp /compute_snad_atom.h /compute_snav_atom.cpp /compute_snav_atom.h /openmp_snap.h /pair_snap.cpp /pair_snap.h /sna.cpp /sna.h /atom_vec_wavepacket.cpp /atom_vec_wavepacket.h /fix_nve_awpmd.cpp /fix_nve_awpmd.h /pair_awpmd_cut.cpp /pair_awpmd_cut.h /dihedral_charmmfsw.cpp /dihedral_charmmfsw.h /pair_lj_charmmfsw_coul_charmmfsh.cpp /pair_lj_charmmfsw_coul_charmmfsh.h /pair_lj_charmmfsw_coul_long.cpp /pair_lj_charmmfsw_coul_long.h /angle_cg_cmm.cpp /angle_cg_cmm.h /angle_charmm.cpp /angle_charmm.h /angle_class2.cpp /angle_class2.h /angle_cosine.cpp /angle_cosine.h /angle_cosine_delta.cpp /angle_cosine_delta.h /angle_cosine_periodic.cpp /angle_cosine_periodic.h /angle_cosine_shift.cpp /angle_cosine_shift.h /angle_cosine_shift_exp.cpp /angle_cosine_shift_exp.h /angle_cosine_squared.cpp /angle_cosine_squared.h /angle_dipole.cpp /angle_dipole.h /angle_fourier.cpp /angle_fourier.h /angle_fourier_simple.cpp /angle_fourier_simple.h /angle_harmonic.cpp /angle_harmonic.h /angle_quartic.cpp /angle_quartic.h /angle_sdk.cpp /angle_sdk.h /angle_table.cpp /angle_table.h /atom_vec_angle.cpp /atom_vec_angle.h /atom_vec_bond.cpp /atom_vec_bond.h /atom_vec_colloid.cpp /atom_vec_colloid.h /atom_vec_dipole.cpp /atom_vec_dipole.h /atom_vec_dpd.cpp /atom_vec_dpd.h /atom_vec_electron.cpp /atom_vec_electron.h /atom_vec_ellipsoid.cpp /atom_vec_ellipsoid.h /atom_vec_full.cpp /atom_vec_full.h /atom_vec_full_hars.cpp /atom_vec_full_hars.h /atom_vec_granular.cpp /atom_vec_granular.h /atom_vec_meso.cpp /atom_vec_meso.h /atom_vec_molecular.cpp /atom_vec_molecular.h /atom_vec_peri.cpp /atom_vec_peri.h /atom_vec_template.cpp /atom_vec_template.h /body_nparticle.cpp /body_nparticle.h /bond_class2.cpp /bond_class2.h /bond_fene.cpp /bond_fene.h /bond_fene_expand.cpp /bond_fene_expand.h /bond_gromos.cpp /bond_gromos.h /bond_harmonic.cpp /bond_harmonic.h /bond_harmonic_shift.cpp /bond_harmonic_shift.h /bond_harmonic_shift_cut.cpp /bond_harmonic_shift_cut.h /bond_morse.cpp /bond_morse.h /bond_nonlinear.cpp /bond_nonlinear.h /bond_oxdna_fene.cpp /bond_oxdna_fene.h /bond_oxdna2_fene.cpp /bond_oxdna2_fene.h /bond_quartic.cpp /bond_quartic.h /bond_table.cpp /bond_table.h /cg_cmm_parms.cpp /cg_cmm_parms.h /commgrid.cpp /commgrid.h /compute_ackland_atom.cpp /compute_ackland_atom.h /compute_basal_atom.cpp /compute_basal_atom.h /compute_body_local.cpp /compute_body_local.h /compute_cnp_atom.cpp /compute_cnp_atom.h /compute_damage_atom.cpp /compute_damage_atom.h /compute_dilatation_atom.cpp /compute_dilatation_atom.h /compute_dpd.cpp /compute_dpd.h /compute_dpd_atom.cpp /compute_dpd_atom.h /compute_erotate_asphere.cpp /compute_erotate_asphere.h /compute_erotate_rigid.cpp /compute_erotate_rigid.h /compute_event_displace.cpp /compute_event_displace.h /compute_fep.cpp /compute_fep.h /compute_force_tally.cpp /compute_force_tally.h /compute_heat_flux_tally.cpp /compute_heat_flux_tally.h /compute_ke_atom_eff.cpp /compute_ke_atom_eff.h /compute_ke_eff.cpp /compute_ke_eff.h /compute_ke_rigid.cpp /compute_ke_rigid.h /compute_meso_e_atom.cpp /compute_meso_e_atom.h /compute_meso_rho_atom.cpp /compute_meso_rho_atom.h /compute_meso_t_atom.cpp /compute_meso_t_atom.h /compute_msd_nongauss.cpp /compute_msd_nongauss.h /compute_pe_tally.cpp /compute_pe_tally.h /compute_plasticity_atom.cpp /compute_plasticity_atom.h /compute_pressure_grem.cpp /compute_pressure_grem.h /compute_rigid_local.cpp /compute_rigid_local.h /compute_spec_atom.cpp /compute_spec_atom.h /compute_stress_tally.cpp /compute_stress_tally.h /compute_temp_asphere.cpp /compute_temp_asphere.h /compute_temp_body.cpp /compute_temp_body.h /compute_temp_deform_eff.cpp /compute_temp_deform_eff.h /compute_temp_eff.cpp /compute_temp_eff.h /compute_temp_region_eff.cpp /compute_temp_region_eff.h /compute_temp_rotate.cpp /compute_temp_rotate.h /compute_ti.cpp /compute_ti.h /compute_voronoi_atom.cpp /compute_voronoi_atom.h /dihedral_charmm.cpp /dihedral_charmm.h /dihedral_class2.cpp /dihedral_class2.h /dihedral_cosine_shift_exp.cpp /dihedral_cosine_shift_exp.h /dihedral_fourier.cpp /dihedral_fourier.h /dihedral_harmonic.cpp /dihedral_harmonic.h /dihedral_helix.cpp /dihedral_helix.h /dihedral_hybrid.cpp /dihedral_hybrid.h /dihedral_multi_harmonic.cpp /dihedral_multi_harmonic.h /dihedral_nharmonic.cpp /dihedral_nharmonic.h /dihedral_opls.cpp /dihedral_opls.h /dihedral_quadratic.cpp /dihedral_quadratic.h /dihedral_spherical.cpp /dihedral_spherical.h /dihedral_table.cpp /dihedral_table.h /dump_atom_gz.cpp /dump_atom_gz.h /dump_xyz_gz.cpp /dump_xyz_gz.h /dump_atom_mpiio.cpp /dump_atom_mpiio.h /dump_cfg_gz.cpp /dump_cfg_gz.h /dump_cfg_mpiio.cpp /dump_cfg_mpiio.h /dump_custom_gz.cpp /dump_custom_gz.h /dump_custom_mpiio.cpp /dump_custom_mpiio.h /dump_h5md.cpp /dump_h5md.h /dump_netcdf.cpp /dump_netcdf.h /dump_netcdf_mpiio.cpp /dump_netcdf_mpiio.h /dump_vtk.cpp /dump_vtk.h /dump_xtc.cpp /dump_xtc.h /dump_xyz_mpiio.cpp /dump_xyz_mpiio.h /ewald.cpp /ewald.h /ewald_cg.cpp /ewald_cg.h /ewald_disp.cpp /ewald_disp.h /ewald_n.cpp /ewald_n.h /fft3d.cpp /fft3d.h /fft3d_wrap.cpp /fft3d_wrap.h /fix_adapt_fep.cpp /fix_adapt_fep.h /fix_addtorque.cpp /fix_addtorque.h /fix_append_atoms.cpp /fix_append_atoms.h /fix_atc.cpp /fix_atc.h /fix_ave_correlate_long.cpp /fix_ave_correlate_long.h /fix_bond_break.cpp /fix_bond_break.h /fix_bond_create.cpp /fix_bond_create.h /fix_bond_swap.cpp /fix_bond_swap.h /fix_cmap.cpp /fix_cmap.h /fix_deposit.cpp /fix_deposit.h /fix_dpd_energy.cpp /fix_dpd_energy.h /fix_efield.cpp /fix_efield.h /fix_eos_cv.cpp /fix_eos_cv.h /fix_eos_table.cpp /fix_eos_table.h /fix_evaporate.cpp /fix_evaporate.h /fix_filter_corotate.cpp /fix_filter_corotate.h /fix_viscosity.cpp /fix_viscosity.h /fix_ehex.cpp /fix_ehex.h /fix_event.cpp /fix_event.h /fix_event_prd.cpp /fix_event_prd.h /fix_event_tad.cpp /fix_event_tad.h /fix_flow_gauss.cpp /fix_flow_gauss.h /fix_freeze.cpp /fix_freeze.h /fix_gcmc.cpp /fix_gcmc.h /fix_gld.cpp /fix_gld.h /fix_gle.cpp /fix_gle.h /fix_gpu.cpp /fix_gpu.h /fix_grem.cpp /fix_grem.h /fix_imd.cpp /fix_imd.h /fix_ipi.cpp /fix_ipi.h /fix_lambdah_calc.cpp /fix_lambdah_calc.h /fix_langevin_eff.cpp /fix_langevin_eff.h /fix_latte.cpp /fix_latte.h /fix_lb_fluid.cpp /fix_lb_fluid.h /fix_lb_momentum.cpp /fix_lb_momentum.h /fix_lb_pc.cpp /fix_lb_pc.h /fix_lb_rigid_pc_sphere.cpp /fix_lb_rigid_pc_sphere.h /fix_lb_viscous.cpp /fix_lb_viscous.h /fix_load_report.cpp /fix_load_report.h /fix_meso.cpp /fix_meso.h /fix_meso_stationary.cpp /fix_meso_stationary.h /fix_mscg.cpp /fix_mscg.h /fix_msst.cpp /fix_msst.h /fix_neb.cpp /fix_neb.h /fix_nh_asphere.cpp /fix_nh_asphere.h /fix_nph_asphere.cpp /fix_nph_asphere.h /fix_npt_asphere.cpp /fix_npt_asphere.h /fix_nve_asphere.cpp /fix_nve_asphere.h /fix_nve_asphere_noforce.cpp /fix_nve_asphere_noforce.h /fix_nve_dot.cpp /fix_nve_dot.h /fix_nve_dotc_langevin.cpp /fix_nve_dotc_langevin.h /fix_nh_body.cpp /fix_nh_body.h /fix_nph_body.cpp /fix_nph_body.h /fix_npt_body.cpp /fix_npt_body.h /fix_nvk.cpp /fix_nvk.h /fix_nvt_body.cpp /fix_nvt_body.h /fix_nve_body.cpp /fix_nve_body.h /fix_nvt_asphere.cpp /fix_nvt_asphere.h /fix_nh_eff.cpp /fix_nh_eff.h /fix_nph_eff.cpp /fix_nph_eff.h /fix_nphug.cpp /fix_nphug.h /fix_npt_eff.cpp /fix_npt_eff.h /fix_nve_eff.cpp /fix_nve_eff.h /fix_nve_line.cpp /fix_nve_line.h /fix_nvt_eff.cpp /fix_nvt_eff.h /fix_nvt_sllod_eff.cpp /fix_nvt_sllod_eff.h /fix_nve_tri.cpp /fix_nve_tri.h /fix_oneway.cpp /fix_oneway.h /fix_orient_bcc.cpp /fix_orient_bcc.h /fix_orient_fcc.cpp /fix_orient_fcc.h /fix_peri_neigh.cpp /fix_peri_neigh.h /fix_phonon.cpp /fix_phonon.h /fix_poems.cpp /fix_poems.h /fix_pour.cpp /fix_pour.h /fix_qeq_comb.cpp /fix_qeq_comb.h /fix_qeq_reax.cpp /fix_qeq_fire.cpp /fix_qeq_fire.h /fix_qeq_reax.h /fix_qmmm.cpp /fix_qmmm.h /fix_reax_bonds.cpp /fix_reax_bonds.h /fix_reaxc.cpp /fix_reaxc.h /fix_reaxc_bonds.cpp /fix_reaxc_bonds.h /fix_reaxc_species.cpp /fix_reaxc_species.h +/fix_rhok.cpp +/fix_rhok.h /fix_rigid.cpp /fix_rigid.h /fix_rigid_nh.cpp /fix_rigid_nh.h /fix_rigid_nph.cpp /fix_rigid_nph.h /fix_rigid_npt.cpp /fix_rigid_npt.h /fix_rigid_nve.cpp /fix_rigid_nve.h /fix_rigid_nvt.cpp /fix_rigid_nvt.h /fix_rigid_nh_small.cpp /fix_rigid_nh_small.h /fix_rigid_nph_small.cpp /fix_rigid_nph_small.h /fix_rigid_npt_small.cpp /fix_rigid_npt_small.h /fix_rigid_nve_small.cpp /fix_rigid_nve_small.h /fix_rigid_nvt_small.cpp /fix_rigid_nvt_small.h /fix_rigid_small.cpp /fix_rigid_small.h /fix_shake.cpp /fix_shake.h /fix_shardlow.cpp /fix_shardlow.h /fix_smd.cpp /fix_smd.h /fix_species.cpp /fix_species.h /fix_spring_pull.cpp /fix_spring_pull.h /fix_srd.cpp /fix_srd.h /fix_temp_rescale_eff.cpp /fix_temp_rescale_eff.h /fix_thermal_conductivity.cpp /fix_thermal_conductivity.h /fix_ti_rs.cpp /fix_ti_rs.h /fix_ti_spring.cpp /fix_ti_spring.h /fix_ttm.cpp /fix_ttm.h /fix_tune_kspace.cpp /fix_tune_kspace.h /fix_wall_colloid.cpp /fix_wall_colloid.h /fix_wall_ees.cpp /fix_wall_ees.h /fix_wall_region_ees.cpp /fix_wall_region_ees.h /fix_wall_gran.cpp /fix_wall_gran.h /fix_wall_gran_region.cpp /fix_wall_gran_region.h /fix_wall_piston.cpp /fix_wall_piston.h /fix_wall_srd.cpp /fix_wall_srd.h /gpu_extra.h /gridcomm.cpp /gridcomm.h /group_ndx.cpp /group_ndx.h /ndx_group.cpp /ndx_group.h /improper_class2.cpp /improper_class2.h /improper_cossq.cpp /improper_cossq.h /improper_cvff.cpp /improper_cvff.h /improper_distance.cpp /improper_distance.h /improper_fourier.cpp /improper_fourier.h /improper_harmonic.cpp /improper_harmonic.h /improper_hybrid.cpp /improper_hybrid.h /improper_ring.cpp /improper_ring.h /improper_umbrella.cpp /improper_umbrella.h /kissfft.h /lj_sdk_common.h /math_complex.h /math_vector.h /mgpt_*.cpp /mgpt_*.h /msm.cpp /msm.h /msm_cg.cpp /msm_cg.h /neb.cpp /neb.h /pair_adp.cpp /pair_adp.h /pair_agni.cpp /pair_agni.h /pair_airebo.cpp /pair_airebo.h /pair_airebo_morse.cpp /pair_airebo_morse.h /pair_body.cpp /pair_body.h /pair_bop.cpp /pair_bop.h /pair_born_coul_long.cpp /pair_born_coul_long.h /pair_born_coul_msm.cpp /pair_born_coul_msm.h /pair_brownian.cpp /pair_brownian.h /pair_brownian_poly.cpp /pair_brownian_poly.h /pair_buck_coul_long.cpp /pair_buck_coul_long.h /pair_buck_coul_msm.cpp /pair_buck_coul_msm.h /pair_buck_coul.cpp /pair_buck_coul.h /pair_buck_long_coul_long.cpp /pair_buck_long_coul_long.h /pair_cdeam.cpp /pair_cdeam.h /pair_cg_cmm.cpp /pair_cg_cmm.h /pair_cg_cmm_coul_cut.cpp /pair_cg_cmm_coul_cut.h /pair_cg_cmm_coul_long.cpp /pair_cg_cmm_coul_long.h /pair_cmm_common.cpp /pair_cmm_common.h /pair_cg_cmm_coul_msm.cpp /pair_cg_cmm_coul_msm.h /pair_comb.cpp /pair_comb.h /pair_comb3.cpp /pair_comb3.h /pair_colloid.cpp /pair_colloid.h /pair_coul_diel.cpp /pair_coul_diel.h /pair_coul_long.cpp /pair_coul_long.h /pair_coul_msm.cpp /pair_coul_msm.h /pair_dipole_cut.cpp /pair_dipole_cut.h /pair_dipole_sf.cpp /pair_dipole_sf.h /pair_dpd_mt.cpp /pair_dpd_mt.h /pair_dsmc.cpp /pair_dsmc.h /pair_eam.cpp /pair_eam.h /pair_eam_opt.cpp /pair_eam_opt.h /pair_eam_alloy.cpp /pair_eam_alloy.h /pair_eam_alloy_opt.cpp /pair_eam_alloy_opt.h /pair_eam_fs.cpp /pair_eam_fs.h /pair_eam_fs_opt.cpp /pair_eam_fs_opt.h /pair_edip.cpp /pair_edip.h /pair_edip_multi.cpp /pair_edip_multi.h /pair_eff_cut.cpp /pair_eff_cut.h /pair_eff_inline.h /pair_eim.cpp /pair_eim.h /pair_gauss_cut.cpp /pair_gauss_cut.h /pair_gayberne.cpp /pair_gayberne.h /pair_gran_easy.cpp /pair_gran_easy.h /pair_gran_hertz_history.cpp /pair_gran_hertz_history.h /pair_gran_hooke.cpp /pair_gran_hooke.h /pair_gran_hooke_history.cpp /pair_gran_hooke_history.h /pair_gw.cpp /pair_gw.h /pair_gw_zbl.cpp /pair_gw_zbl.h /pair_hbond_dreiding_lj.cpp /pair_hbond_dreiding_lj.h /pair_hbond_dreiding_morse.cpp /pair_hbond_dreiding_morse.h /pair_kolmogorov_crespi_z.cpp /pair_kolmogorov_crespi_z.h /pair_lcbop.cpp /pair_lcbop.h /pair_line_lj.cpp /pair_line_lj.h /pair_list.cpp /pair_list.h /pair_lj_charmm_coul_charmm.cpp /pair_lj_charmm_coul_charmm.h /pair_lj_charmm_coul_charmm_implicit.cpp /pair_lj_charmm_coul_charmm_implicit.h /pair_lj_charmm_coul_long.cpp /pair_lj_charmm_coul_long.h /pair_lj_charmm_coul_long_opt.cpp /pair_lj_charmm_coul_long_opt.h /pair_lj_charmm_coul_long_soft.cpp /pair_lj_charmm_coul_long_soft.h /pair_lj_charmm_coul_msm.cpp /pair_lj_charmm_coul_msm.h /pair_lj_class2.cpp /pair_lj_class2.h /pair_lj_class2_coul_cut.cpp /pair_lj_class2_coul_cut.h /pair_lj_class2_coul_long.cpp /pair_lj_class2_coul_long.h /pair_lj_coul.cpp /pair_lj_coul.h /pair_coul_cut_soft.cpp /pair_coul_cut_soft.h /pair_coul_long_soft.cpp /pair_coul_long_soft.h /pair_lj_cut_coul_cut_soft.cpp /pair_lj_cut_coul_cut_soft.h /pair_lj_cut_tip4p_cut.cpp /pair_lj_cut_tip4p_cut.h /pair_lj_cut_coul_long.cpp /pair_lj_cut_coul_long.h /pair_lj_cut_coul_long_opt.cpp /pair_lj_cut_coul_long_opt.h /pair_lj_cut_coul_long_soft.cpp /pair_lj_cut_coul_long_soft.h /pair_lj_cut_coul_msm.cpp /pair_lj_cut_coul_msm.h /pair_lj_cut_dipole_cut.cpp /pair_lj_cut_dipole_cut.h /pair_lj_cut_dipole_long.cpp /pair_lj_cut_dipole_long.h /pair_lj_cut_*hars_*.cpp /pair_lj_cut_*hars_*.h /pair_lj_cut_soft.cpp /pair_lj_cut_soft.h /pair_lj_cut_tip4p_long.cpp /pair_lj_cut_tip4p_long.h /pair_lj_cut_tip4p_long_opt.cpp /pair_lj_cut_tip4p_long_opt.h /pair_lj_cut_tip4p_long_soft.cpp /pair_lj_cut_tip4p_long_soft.h /pair_lj_long_coul_long.cpp /pair_lj_long_coul_long.h /pair_lj_long_coul_long_opt.cpp /pair_lj_long_coul_long_opt.h /pair_lj_long_dipole_long.cpp /pair_lj_long_dipole_long.h /pair_lj_long_tip4p_long.cpp /pair_lj_long_tip4p_long.h /pair_lj_cut_opt.cpp /pair_lj_cut_opt.h /pair_lj_cut_tgpu.cpp /pair_lj_cut_tgpu.h /pair_lj_sdk.cpp /pair_lj_sdk.h /pair_lj_sdk_coul_long.cpp /pair_lj_sdk_coul_long.h /pair_lj_sdk_coul_msm.cpp /pair_lj_sdk_coul_msm.h /pair_lj_sf_dipole_sf.cpp /pair_lj_sf_dipole_sf.h /pair_lubricateU.cpp /pair_lubricateU.h /pair_lubricateU_poly.cpp /pair_lubricateU_poly.h /pair_lubricate_poly.cpp /pair_lubricate_poly.h /pair_lubricate.cpp /pair_lubricate.h /pair_meam.cpp /pair_meam.h /pair_meam_spline.cpp /pair_meam_spline.h /pair_meam_sw_spline.cpp /pair_meam_sw_spline.h /pair_morse_opt.cpp /pair_morse_opt.h /pair_morse_soft.cpp /pair_morse_soft.h /pair_nb3b_harmonic.cpp /pair_nb3b_harmonic.h /pair_nm_cut.cpp /pair_nm_cut.h /pair_nm_cut_coul_cut.cpp /pair_nm_cut_coul_cut.h /pair_nm_cut_coul_long.cpp /pair_nm_cut_coul_long.h /pair_oxdna_*.cpp /pair_oxdna_*.h /pair_oxdna2_*.cpp /pair_oxdna2_*.h /mf_oxdna.h /pair_peri_eps.cpp /pair_peri_eps.h /pair_peri_lps.cpp /pair_peri_lps.h /pair_peri_pmb.cpp /pair_peri_pmb.h /pair_peri_ves.cpp /pair_peri_ves.h /pair_quip.cpp /pair_quip.h /pair_reax.cpp /pair_reax.h /pair_reax_fortran.h /pair_reaxc.cpp /pair_reaxc.h /pair_rebo.cpp /pair_rebo.h /pair_resquared.cpp /pair_resquared.h /pair_sph_heatconduction.cpp /pair_sph_heatconduction.h /pair_sph_idealgas.cpp /pair_sph_idealgas.h /pair_sph_lj.cpp /pair_sph_lj.h /pair_sph_rhosum.cpp /pair_sph_rhosum.h /pair_sph_taitwater.cpp /pair_sph_taitwater.h /pair_sph_taitwater_morris.cpp /pair_sph_taitwater_morris.h /pair_sw.cpp /pair_sw.h /pair_tersoff.cpp /pair_tersoff.h /pair_tersoff_mod.cpp /pair_tersoff_mod.h /pair_tersoff_mod_c.cpp /pair_tersoff_mod_c.h /pair_tersoff_table.cpp /pair_tersoff_table.h /pair_tersoff_zbl.cpp /pair_tersoff_zbl.h /pair_tip4p_cut.cpp /pair_tip4p_cut.h /pair_tip4p_long.cpp /pair_tip4p_long.h /pair_tip4p_long_soft.cpp /pair_tip4p_long_soft.h /pair_tri_lj.cpp /pair_tri_lj.h /pair_yukawa_colloid.cpp /pair_yukawa_colloid.h /pair_momb.cpp /pair_momb.h /pppm.cpp /pppm.h /pppm_cg.cpp /pppm_cg.h /pppm_disp.cpp /pppm_disp.h /pppm_disp_tip4p.cpp /pppm_disp_tip4p.h /pppm_old.cpp /pppm_old.h /pppm_proxy.cpp /pppm_proxy.h /pppm_stagger.cpp /pppm_stagger.h /pppm_tip4p.cpp /pppm_tip4p.h /pppm_tip4p_proxy.cpp /pppm_tip4p_proxy.h /pppm_tip4p_cg.cpp /pppm_tip4p_cg.h /prd.cpp /prd.h /python_impl.cpp /python_impl.h /python_compat.h /fix_python.cpp /fix_python.h /pair_python.cpp /pair_python.h /reader_molfile.cpp /reader_molfile.h /reaxc_allocate.cpp /reaxc_allocate.h /reaxc_basic_comm.cpp /reaxc_basic_comm.h /reaxc_bond_orders.cpp /reaxc_bond_orders.h /reaxc_bonds.cpp /reaxc_bonds.h /reaxc_control.cpp /reaxc_control.h /reaxc_defs.h /reaxc_ffield.cpp /reaxc_ffield.h /reaxc_forces.cpp /reaxc_forces.h /reaxc_hydrogen_bonds.cpp /reaxc_hydrogen_bonds.h /reaxc_init_md.cpp /reaxc_init_md.h /reaxc_io_tools.cpp /reaxc_io_tools.h /reaxc_list.cpp /reaxc_list.h /reaxc_lookup.cpp /reaxc_lookup.h /reaxc_multi_body.cpp /reaxc_multi_body.h /reaxc_nonbonded.cpp /reaxc_nonbonded.h /reaxc_reset_tools.cpp /reaxc_reset_tools.h /reaxc_system_props.cpp /reaxc_system_props.h /reaxc_tool_box.cpp /reaxc_tool_box.h /reaxc_torsion_angles.cpp /reaxc_torsion_angles.h /reaxc_traj.cpp /reaxc_traj.h /reaxc_types.h /reaxc_valence_angles.cpp /reaxc_valence_angles.h /reaxc_vector.cpp /reaxc_vector.h /remap.cpp /remap.h /remap_wrap.cpp /remap_wrap.h /restart_mpiio.cpp /restart_mpiio.h /smd_kernels.h /smd_material_models.cpp /smd_material_models.h /smd_math.h /tad.cpp /tad.h /temper.cpp /temper.h /temper_grem.cpp /temper_grem.h /temper_npt.cpp /temper_npt.h /thr_data.cpp /thr_data.h /verlet_split.cpp /verlet_split.h /write_dump.cpp /write_dump.h /xdr_compat.cpp /xdr_compat.h /atom_vec_smd.cpp /atom_vec_smd.h /compute_saed.cpp /compute_saed.h /compute_saed_consts.h /compute_smd_contact_radius.cpp /compute_smd_contact_radius.h /compute_smd_damage.cpp /compute_smd_damage.h /compute_smd_hourglass_error.cpp /compute_smd_hourglass_error.h /compute_smd_internal_energy.cpp /compute_smd_internal_energy.h /compute_smd_plastic_strain.cpp /compute_smd_plastic_strain.h /compute_smd_plastic_strain_rate.cpp /compute_smd_plastic_strain_rate.h /compute_smd_rho.cpp /compute_smd_rho.h /compute_smd_tlsph_defgrad.cpp /compute_smd_tlsph_defgrad.h /compute_smd_tlsph_dt.cpp /compute_smd_tlsph_dt.h /compute_smd_tlsph_num_neighs.cpp /compute_smd_tlsph_num_neighs.h /compute_smd_tlsph_shape.cpp /compute_smd_tlsph_shape.h /compute_smd_tlsph_strain.cpp /compute_smd_tlsph_strain.h /compute_smd_tlsph_strain_rate.cpp /compute_smd_tlsph_strain_rate.h /compute_smd_tlsph_stress.cpp /compute_smd_tlsph_stress.h /compute_smd_triangle_mesh_vertices.cpp /compute_smd_triangle_mesh_vertices.h /compute_smd_ulsph_effm.cpp /compute_smd_ulsph_effm.h /compute_smd_ulsph_num_neighs.cpp /compute_smd_ulsph_num_neighs.h /compute_smd_ulsph_strain.cpp /compute_smd_ulsph_strain.h /compute_smd_ulsph_strain_rate.cpp /compute_smd_ulsph_strain_rate.h /compute_smd_ulsph_stress.cpp /compute_smd_ulsph_stress.h /compute_smd_vol.cpp /compute_smd_vol.h /compute_temp_cs.cpp /compute_temp_cs.h /compute_temp_drude.cpp /compute_temp_drude.h /compute_xrd.cpp /compute_xrd.h /compute_xrd_consts.h /fix_atom_swap.cpp /fix_atom_swap.h /fix_ave_spatial_sphere.cpp /fix_ave_spatial_sphere.h /fix_drude.cpp /fix_drude.h /fix_drude_transform.cpp /fix_drude_transform.h /fix_langevin_drude.cpp /fix_langevin_drude.h /fix_pimd.cpp /fix_pimd.h /fix_qbmsst.cpp /fix_qbmsst.h /fix_qtb.cpp /fix_qtb.h /fix_rattle.cpp /fix_rattle.h /fix_saed_vtk.cpp /fix_saed_vtk.h /fix_smd_adjust_dt.cpp /fix_smd_adjust_dt.h /fix_smd_integrate_tlsph.cpp /fix_smd_integrate_tlsph.h /fix_smd_integrate_ulsph.cpp /fix_smd_integrate_ulsph.h /fix_smd_move_triangulated_surface.cpp /fix_smd_move_triangulated_surface.h /fix_smd_setvel.cpp /fix_smd_setvel.h /fix_smd_tlsph_reference_configuration.cpp /fix_smd_tlsph_reference_configuration.h /fix_smd_wall_surface.cpp /fix_smd_wall_surface.h /fix_srp.cpp /fix_srp.h /fix_tfmc.cpp /fix_tfmc.h /fix_ttm_mod.cpp /fix_ttm_mod.h /pair_born_coul_long_cs.cpp /pair_born_coul_long_cs.h /pair_born_coul_dsf_cs.cpp /pair_born_coul_dsf_cs.h /pair_buck_coul_long_cs.cpp /pair_buck_coul_long_cs.h /pair_coul_long_cs.cpp /pair_coul_long_cs.h /pair_lj_cut_thole_long.cpp /pair_lj_cut_thole_long.h /pair_plum_hb.cpp /pair_plum_hb.h /pair_plum_hp.cpp /pair_plum_hp.h /pair_polymorphic.cpp /pair_polymorphic.h /pair_smd_hertz.cpp /pair_smd_hertz.h /pair_smd_tlsph.cpp /pair_smd_tlsph.h /pair_smd_triangulated_surface.cpp /pair_smd_triangulated_surface.h /pair_smd_ulsph.cpp /pair_smd_ulsph.h /pair_srp.cpp /pair_srp.h /pair_thole.cpp /pair_thole.h /pair_buck_mdf.cpp /pair_buck_mdf.h /pair_dpd_conservative.cpp /pair_dpd_conservative.h /pair_dpd_fdt.cpp /pair_dpd_fdt.h /pair_dpd_fdt_energy.cpp /pair_dpd_fdt_energy.h /pair_lennard_mdf.cpp /pair_lennard_mdf.h /pair_lj_cut_coul_long_cs.cpp /pair_lj_cut_coul_long_cs.h /pair_lj_mdf.cpp /pair_lj_mdf.h /pair_mgpt.cpp /pair_mgpt.h /pair_morse_smooth_linear.cpp /pair_morse_smooth_linear.h /pair_smtbq.cpp /pair_smtbq.h /pair_vashishta*.cpp /pair_vashishta*.h diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 65146abd5..8f3782586 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -1,77 +1,78 @@ The files in this package are a potpourri of (mostly) unrelated features contributed to LAMMPS by users. Each feature is a single pair of files (*.cpp and *.h). More information about each feature can be found by reading its doc page in the LAMMPS doc directory. The doc page which lists all LAMMPS input script commands is as follows: doc/Section_commands.html, subsection 3.5 User-contributed features are listed at the bottom of the fix, compute, pair, etc sections. The list of features and author of each is given below. You should contact the author directly if you have specific questions about the feature or its coding. ------------------------------------------------------------ angle_style cosine/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 angle_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 angle_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 angle_style fourier/simple, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 angle_style dipole, Mario Orsi, orsimario at gmail.com, 10 Jan 12 angle_style quartic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 bond_style harmonic/shift, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 bond_style harmonic/shift/cut, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 compute ackland/atom, Gerolf Ziegenhain, gerolf at ziegenhain.com, 4 Oct 2007 compute basal/atom, Christopher Barrett, cdb333 at cavs.msstate.edu, 3 Mar 2013 compute cnp/atom, Paulo Branicio (USC), branicio at usc.edu, 31 May 2017 compute temp/rotate, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 compute PRESSURE/GREM, David Stelter, dstelter@bu.edu, 22 Nov 16 dihedral_style cosine/shift/exp, Carsten Svaneborg, science at zqex.dk, 8 Aug 11 dihedral_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 dihedral_style nharmonic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 dihedral_style quadratic, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 dihedral_style spherical, Andrew Jewett, jewett.aij@gmail.com, 15 Jul 16 dihedral_style table, Andrew Jewett, jewett.aij@gmail.com, 10 Jan 12 fix addtorque, Laurent Joly (U Lyon), ljoly.ulyon at gmail.com, 8 Aug 11 fix ave/correlate/long, Jorge Ramirez (UPM Madrid), jorge.ramirez at upm.es, 21 Oct 2015 fix filter/corotate, Lukas Fath (KIT), lukas.fath at kit.edu, 15 Mar 2017 fix flow/gauss, Joel Eaves (CU Boulder), Joel.Eaves@Colorado.edu, 23 Aug 2016 fix gle, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 fix grem, David Stelter, dstelter@bu.edu, 22 Nov 16 fix imd, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 2009 fix ipi, Michele Ceriotti (EPFL Lausanne), michele.ceriotti at gmail.com, 24 Nov 2014 fix nvk, Efrem Braun (UC Berkeley), efrem.braun at gmail.com, https://github.com/lammps/lammps/pull/310 fix pimd, Yuxing Peng (U Chicago), yuxing at uchicago.edu, 24 Nov 2014 +fix rhok, Ulf Pedersen (Roskilde U), ulf AT urp.dk, 25 Sep 2017 fix smd, Axel Kohlmeyer, akohlmey at gmail.com, 19 May 2008 fix ti/spring, Rodrigo Freitas (Unicamp/Brazil), rodrigohb at gmail.com, 7 Nov 2013 fix ttm/mod, Sergey Starikov and Vasily Pisarev (JIHT), pisarevvv at gmail.com, 2 Feb 2015 fix wall/ees, Abdoreza Ershadinia, a.ershadinia at gmail.com, Jul 2017 fix wall/region/ees, Abdoreza Ershadinia, a.ershadinia at gmail.com, Jul 2017 improper_style cossq, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12 improper_style fourier, Loukas Peristeras, loukas.peristeras at scienomics.com, 27 Oct 12 improper_style ring, Georgios Vogiatzis, gvog at chemeng.ntua.gr, 25 May 12 improper_style distance, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style agni, Axel Kohlmeyer, akohlmey at gmail.com, 9 Nov 16 pair_style buck/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style coul/diel, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style dipole/sf, Mario Orsi, orsimario at gmail.com, 8 Aug 11 pair_style edip, Luca Ferraro, luca.ferraro at caspur.it, 15 Sep 11 pair_style eam/cd, Alexander Stukowski, stukowski at mm.tu-darmstadt.de, 7 Nov 09 pair_style gauss/cut, Axel Kohlmeyer, akohlmey at gmail.com, 1 Dec 11 pair_style lennard/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style list, Axel Kohlmeyer (Temple U), akohlmey at gmail.com, 1 Jun 13 pair_style lj/mdf, Paolo Raiteri, p.raiteri at curtin.edu.au, 2 Dec 15 pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17 pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12 pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12 pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16 pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14 pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11 pair_style momb, Kristen Fichthorn, Tonnam Balankura, Ya Zhou, fichthorn@psu.edu, 18 Mar 17 temper/grem, David Stelter, dstelter@bu.edu, 22 Nov 16 temper/npt, Amulya K. Pervaje, Cody K. Addington, amulyapervaje@gmail.com , 31 Aug 17 diff --git a/src/USER-MISC/fix_rhok.cpp b/src/USER-MISC/fix_rhok.cpp new file mode 100644 index 000000000..58b0e95a9 --- /dev/null +++ b/src/USER-MISC/fix_rhok.cpp @@ -0,0 +1,245 @@ +/* ---------------------------------------------------------------------- + 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: Ulf R. Pedersen, ulf@urp.dk +------------------------------------------------------------------------- */ + +#include +#include +#include +#include + +#include "fix_rhok.h" +#include "atom.h" +#include "domain.h" +#include "error.h" +#include "force.h" +#include "respa.h" +#include "update.h" +#include "citeme.h" + +using namespace LAMMPS_NS; +using namespace FixConst; + +static const char cite_fix_rhok[] = + "Bias on the collective density field (fix rhok):\n\n" + "@Article{pedersen_jcp139_104102_2013,\n" + "title = {Direct calculation of the solid-liquid Gibbs free energy difference in a single equilibrium simulation},\n" + "volume = {139},\n" + "number = {10},\n" + "url = {http://aip.scitation.org/doi/10.1063/1.4818747},\n" + "doi = {10.1063/1.4818747},\n" + "urldate = {2017-10-03},\n" + "journal = {J. Chem. Phys.},\n" + "author = {Pedersen, Ulf R.},\n" + "year = {2013},\n" + "pages = {104102}\n" + "}\n\n"; + +FixRhok::FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv ) + : Fix( inLMP, inArgc, inArgv ) +{ + + if (lmp->citeme) lmp->citeme->add(cite_fix_rhok); + + // Check arguments + if( inArgc != 8 ) + error->all(FLERR,"Illegal fix rhoKUmbrella command" ); + + // Set up fix flags + scalar_flag = 1; // have compute_scalar + vector_flag = 1; // have compute_vector... + size_vector = 3; // ...with this many components + global_freq = 1; // whose value can be computed at every timestep + thermo_energy = 1; // this fix changes system's potential energy + extscalar = 0; // but the deltaPE might not scale with # of atoms + extvector = 0; // neither do the components of the vector + + // Parse fix options + int n[3]; + + n[0] = force->inumeric(FLERR,inArgv[3]); + n[1] = force->inumeric(FLERR,inArgv[4]); + n[2] = force->inumeric(FLERR,inArgv[5]); + + mK[0] = n[0]*(2*M_PI / (domain->boxhi[0] - domain->boxlo[0])); + mK[1] = n[1]*(2*M_PI / (domain->boxhi[1] - domain->boxlo[1])); + mK[2] = n[2]*(2*M_PI / (domain->boxhi[2] - domain->boxlo[2])); + + mKappa = force->numeric(FLERR,inArgv[6]); + mRhoK0 = force->numeric(FLERR,inArgv[7]); +} + +// Methods that this fix implements +// -------------------------------- + +// Tells LAMMPS where this fix should act +int +FixRhok::setmask() +{ + int mask = 0; + + // This fix modifies forces... + mask |= POST_FORCE; + mask |= POST_FORCE_RESPA; + mask |= MIN_POST_FORCE; + + // ...and potential energies + mask |= THERMO_ENERGY; + + return mask; +} + +// Initializes the fix at the beginning of a run +void +FixRhok::init() +{ + // RESPA boilerplate + if( strcmp( update->integrate_style, "respa" ) == 0 ) + mNLevelsRESPA = ((Respa *) update->integrate)->nlevels; + + // Count the number of affected particles + int nThisLocal = 0; + int *mask = atom->mask; + int nlocal = atom->nlocal; + for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU + if( mask[i] & groupbit ) { // ...only those affected by this fix + nThisLocal++; + } + } + MPI_Allreduce( &nThisLocal, &mNThis, + 1, MPI_INT, MPI_SUM, world ); + mSqrtNThis = sqrt( mNThis ); +} + +// Initial application of the fix to a system (when doing MD) +void +FixRhok::setup( int inVFlag ) +{ + if( strcmp( update->integrate_style, "verlet" ) == 0 ) + post_force( inVFlag ); + else + { + ((Respa *) update->integrate)->copy_flevel_f( mNLevelsRESPA - 1 ); + post_force_respa( inVFlag, mNLevelsRESPA - 1,0 ); + ((Respa *) update->integrate)->copy_f_flevel( mNLevelsRESPA - 1 ); + } +} + +// Initial application of the fix to a system (when doing minimization) +void +FixRhok::min_setup( int inVFlag ) +{ + post_force( inVFlag ); +} + +// Modify the forces calculated in the main force loop of ordinary MD +void +FixRhok::post_force( int inVFlag ) +{ + double **x = atom->x; + double **f = atom->f; + int *mask = atom->mask; + int nlocal = atom->nlocal; + + // Loop over locally-owned atoms affected by this fix and calculate the + // partial rhoK's + mRhoKLocal[0] = 0.0; + mRhoKLocal[1] = 0.0; + + for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU + if( mask[i] & groupbit ) { // ...only those affected by this fix + + // rho_k = sum_i exp( - i k.r_i ) + mRhoKLocal[0] += cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] ); + mRhoKLocal[1] -= sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] ); + } + } + + // Now calculate mRhoKGlobal + MPI_Allreduce( mRhoKLocal, mRhoKGlobal, + 2, MPI_DOUBLE, MPI_SUM, world ); + + // Info: < \sum_{i,j} e^{-ik.(r_i - r_j)} > ~ N, so + // we define rho_k as (1 / sqrt(N)) \sum_i e^{-i k.r_i}, so that + // is intensive. + mRhoKGlobal[0] /= mSqrtNThis; + mRhoKGlobal[1] /= mSqrtNThis; + + // We'll need magnitude of rho_k + double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0] + + mRhoKGlobal[1]*mRhoKGlobal[1] ); + + for( int i = 0; i < nlocal; i++ ) { // Iterate through all atoms on this CPU + if( mask[i] & groupbit ) { // ...only those affected by this fix + + // Calculate forces + // U = kappa/2 ( |rho_k| - rho_k^0 )^2 + // f_i = -grad_i U = -kappa ( |rho_k| - rho_k^0 ) grad_i |rho_k| + // grad_i |rho_k| = Re( rho_k* (-i k e^{-i k . r_i} / sqrt(N)) ) / |rho_k| + // + // In terms of real and imag parts of rho_k, + // + // Re( rho_k* (-i k e^{-i k . r_i}) ) = + // (- Re[rho_k] * sin( k . r_i ) - Im[rho_k] * cos( k . r_i )) * k + + double sinKRi = sin( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] ); + double cosKRi = cos( mK[0]*x[i][0] + mK[1]*x[i][1] + mK[2]*x[i][2] ); + + double prefactor = mKappa * ( rhoK - mRhoK0 ) / rhoK + * (-mRhoKGlobal[0]*sinKRi - mRhoKGlobal[1]*cosKRi) / mSqrtNThis; + f[i][0] -= prefactor * mK[0]; + f[i][1] -= prefactor * mK[1]; + f[i][2] -= prefactor * mK[2]; + } + } +} + +// Forces in RESPA loop +void +FixRhok::post_force_respa( int inVFlag, int inILevel, int inILoop ) +{ + if( inILevel == mNLevelsRESPA - 1 ) + post_force( inVFlag ); +} + +// Forces in minimization loop +void +FixRhok::min_post_force( int inVFlag ) +{ + post_force( inVFlag ); +} + +// Compute the change in the potential energy induced by this fix +double +FixRhok::compute_scalar() +{ + double rhoK = sqrt( mRhoKGlobal[0]*mRhoKGlobal[0] + + mRhoKGlobal[1]*mRhoKGlobal[1] ); + + return 0.5 * mKappa * (rhoK - mRhoK0) * (rhoK - mRhoK0); +} + +// Compute the ith component of the vector +double +FixRhok::compute_vector( int inI ) +{ + if( inI == 0 ) + return mRhoKGlobal[0]; // Real part + else if( inI == 1 ) + return mRhoKGlobal[1]; // Imagniary part + else if( inI == 2 ) + return sqrt( mRhoKGlobal[0]*mRhoKGlobal[0] + + mRhoKGlobal[1]*mRhoKGlobal[1] ); + else + return 12345.0; +} diff --git a/src/USER-MISC/fix_rhok.h b/src/USER-MISC/fix_rhok.h new file mode 100644 index 000000000..c950c08b1 --- /dev/null +++ b/src/USER-MISC/fix_rhok.h @@ -0,0 +1,77 @@ +/* -*- c++ -*- ---------------------------------------------------------- + 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. +------------------------------------------------------------------------- */ + +#ifdef FIX_CLASS + +FixStyle(rhok,FixRhok) + +#else + +#ifndef LMP_FIX_RHOK_H +#define LMP_FIX_RHOK_H + +#include "fix.h" + +namespace LAMMPS_NS { + +class FixRhok : public Fix +{ +public: + // Constructor: all the parameters to this fix specified in + // the LAMMPS input get passed in + FixRhok( LAMMPS* inLMP, int inArgc, char** inArgv ); + virtual ~FixRhok() {}; + + // Methods that this fix implements + // -------------------------------- + + // Tells LAMMPS where this fix should act + int setmask(); + + // Initializes the fix at the beginning of a run + void init(); + + // Initial application of the fix to a system (when doing MD / minimization) + void setup( int inVFlag ); + void min_setup( int inVFlag ); + + // Modify the forces calculated in the main force loop, either when + // doing usual MD, RESPA MD or minimization + void post_force( int inVFlag ); + void post_force_respa( int inVFlag, int inILevel, int inILoop ); + void min_post_force( int inVFlag ); + + // Compute the change in the potential energy induced by this fix + double compute_scalar(); + + // Compute the ith component of the vector associated with this fix + double compute_vector( int inI ); + +private: + // RESPA boilerplate + int mNLevelsRESPA; + + // Defining parameters for this umbrella + double mK[3], mKappa, mRhoK0; + + // Number of particles affected by the fix + int mNThis; + double mSqrtNThis; + + // Real and imaginary parts of rho_k := sum_i exp( - i k . r_i ) + double mRhoKLocal[2], mRhoKGlobal[2]; +}; + +} // namespace LAMMPS_NS + +#endif // __FIX_RHOK__ +#endif // FIX_CLASS +