diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 48f11b3c6..78969bc4a 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -1,1246 +1,1247 @@ "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 :tb(c=3,ea=c) +"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, "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, "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. "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 (gkio)"_pair_buck.html, "buck/coul/cut (gkio)"_pair_buck.html, "buck/coul/long (gkio)"_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 (go)"_pair_dpd.html, "dpd/tstat (go)"_pair_dpd.html, "dsmc"_pair_dsmc.html, "eam (gkiot)"_pair_eam.html, "eam/alloy (gkiot)"_pair_eam.html, "eam/fs (gkiot)"_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 (kio)"_pair_charmm.html, "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html, "lj/charmm/coul/long (gkio)"_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 (gkio)"_pair_sw.html, "table (gko)"_pair_table.html, "tersoff (gkio)"_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, "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 (ko)"_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 (o)"_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 (ko)"_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/commands.txt b/doc/src/commands.txt index 7889ea5e7..06752f696 100644 --- a/doc/src/commands.txt +++ b/doc/src/commands.txt @@ -1,111 +1,112 @@ Commands :h1 diff --git a/doc/src/lammps.book b/doc/src/lammps.book index f4d3566a6..86dfe78af 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -1,652 +1,653 @@ #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_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_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 compute_event_displace.html compute_fep.html compute_global_atom.html compute_group_group.html compute_gyration.html compute_gyration_chunk.html compute_heat_flux.html compute_hexorder_atom.html compute_improper.html compute_improper_local.html compute_inertia_chunk.html compute_ke.html compute_ke_atom.html compute_ke_atom_eff.html compute_ke_eff.html compute_ke_rigid.html compute_meso_e_atom.html compute_meso_rho_atom.html compute_meso_t_atom.html compute_msd.html compute_msd_chunk.html compute_msd_nongauss.html compute_omega_chunk.html compute_orientorder_atom.html compute_pair.html compute_pair_local.html compute_pe.html compute_pe_atom.html compute_plasticity_atom.html compute_pressure.html compute_property_atom.html compute_property_chunk.html compute_property_local.html compute_rdf.html compute_reduce.html compute_rigid_local.html compute_saed.html compute_slice.html compute_smd_contact_radius.html compute_smd_damage.html compute_smd_hourglass_error.html compute_smd_internal_energy.html compute_smd_plastic_strain.html compute_smd_plastic_strain_rate.html compute_smd_rho.html compute_smd_tlsph_defgrad.html compute_smd_tlsph_dt.html compute_smd_tlsph_num_neighs.html compute_smd_tlsph_shape.html compute_smd_tlsph_strain.html compute_smd_tlsph_strain_rate.html compute_smd_tlsph_stress.html compute_smd_triangle_mesh_vertices.html compute_smd_ulsph_num_neighs.html compute_smd_ulsph_strain.html compute_smd_ulsph_strain_rate.html compute_smd_ulsph_stress.html compute_smd_vol.html compute_sna_atom.html compute_stress_atom.html compute_tally.html compute_tdpd_cc_atom.html compute_temp.html compute_temp_asphere.html compute_temp_body.html compute_temp_chunk.html compute_temp_com.html compute_temp_cs.html compute_temp_deform.html compute_temp_deform_eff.html compute_temp_drude.html compute_temp_eff.html compute_temp_partial.html compute_temp_profile.html compute_temp_ramp.html compute_temp_region.html compute_temp_region_eff.html compute_temp_rotate.html compute_temp_sphere.html compute_ti.html compute_torque_chunk.html compute_vacf.html compute_vcm_chunk.html compute_voronoi_atom.html compute_xrd.html pair_adp.html pair_agni.html pair_airebo.html pair_awpmd.html pair_beck.html pair_body.html pair_bop.html pair_born.html pair_brownian.html pair_buck.html pair_buck_long.html pair_charmm.html pair_class2.html pair_colloid.html pair_comb.html pair_coul.html pair_coul_diel.html pair_cs.html pair_dipole.html pair_dpd.html pair_dpd_fdt.html pair_dsmc.html pair_eam.html pair_edip.html pair_eff.html pair_eim.html pair_exp6_rx.html pair_gauss.html pair_gayberne.html pair_gran.html pair_gromacs.html pair_gw.html pair_hbond_dreiding.html pair_hybrid.html pair_kim.html pair_kolmogorov_crespi_z.html pair_lcbop.html pair_line_lj.html pair_list.html pair_lj.html pair_lj96.html pair_lj_cubic.html pair_lj_expand.html pair_lj_long.html pair_lj_smooth.html pair_lj_smooth_linear.html pair_lj_soft.html pair_lubricate.html pair_lubricateU.html pair_mdf.html pair_meam.html pair_meam_spline.html pair_meam_sw_spline.html pair_meso.html pair_mgpt.html pair_mie.html pair_momb.html pair_morse.html pair_multi_lucy.html pair_multi_lucy_rx.html pair_nb3b_harmonic.html pair_nm.html pair_none.html pair_oxdna.html pair_oxdna2.html pair_peri.html pair_polymorphic.html pair_python.html pair_quip.html pair_reax.html pair_reaxc.html pair_resquared.html pair_sdk.html pair_smd_hertz.html pair_smd_tlsph.html pair_smd_triangulated_surface.html pair_smd_ulsph.html pair_smtbq.html pair_snap.html pair_soft.html pair_sph_heatconduction.html pair_sph_idealgas.html pair_sph_lj.html pair_sph_rhosum.html pair_sph_taitwater.html pair_sph_taitwater_morris.html pair_srp.html pair_sw.html pair_table.html pair_table_rx.html pair_tersoff.html pair_tersoff_mod.html pair_tersoff_zbl.html pair_thole.html pair_tri_lj.html pair_vashishta.html pair_yukawa.html pair_yukawa_colloid.html pair_zbl.html pair_zero.html bond_class2.html bond_fene.html bond_fene_expand.html bond_oxdna.html bond_harmonic.html bond_harmonic_shift.html bond_harmonic_shift_cut.html bond_hybrid.html bond_morse.html bond_none.html bond_nonlinear.html bond_quartic.html bond_table.html bond_zero.html angle_charmm.html angle_class2.html angle_cosine.html angle_cosine_delta.html angle_cosine_periodic.html angle_cosine_shift.html angle_cosine_shift_exp.html angle_cosine_squared.html angle_dipole.html angle_fourier.html angle_fourier_simple.html angle_harmonic.html angle_hybrid.html angle_none.html angle_quartic.html angle_sdk.html angle_table.html angle_zero.html dihedral_charmm.html dihedral_class2.html dihedral_cosine_shift_exp.html dihedral_fourier.html dihedral_harmonic.html dihedral_helix.html dihedral_hybrid.html dihedral_multi_harmonic.html dihedral_nharmonic.html dihedral_none.html dihedral_opls.html dihedral_quadratic.html dihedral_spherical.html dihedral_table.html dihedral_zero.html improper_class2.html 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/doc/src/temper_npt.txt b/doc/src/temper_npt.txt new file mode 100644 index 000000000..4ad49f9e3 --- /dev/null +++ b/doc/src/temper_npt.txt @@ -0,0 +1,67 @@ +"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 +temper/npt command :h3 + +[Syntax:] + +temper/npt N M temp fix-ID seed1 seed2 pressure index :pre + +N = total # of timesteps to run +M = attempt a tempering swap every this many steps +temp = initial temperature for this ensemble +fix-ID = ID of the fix that will control temperature and pressure during the run +seed1 = random # seed used to decide on adjacent temperature to partner with +seed2 = random # seed for Boltzmann factor in Metropolis swap +pressure = setpoint pressure for the ensemble +index = which temperature (0 to N-1) I am simulating (optional) :ul + +[Examples:] + +temper/npt 100000 100 $t nptfix 0 58728 1 +temper/npt 2500000 1000 300 nptfix 0 32285 $p +temper/npt 5000000 2000 $t nptfix 0 12523 1 $w :pre + +[Description:] + +Run a parallel tempering or replica exchange simulation using multiple +replicas (ensembles) of a system in the isothermal-isobaric (NPT) +ensemble. The command temper/npt works like "temper"_temper.html but +requires running replicas in the NPT ensemble instead of the canonical +(NVT) ensemble and allows for pressure to be set in the ensembles. +These multiple ensembles can run in parallel at different temperatures +or different pressures. The acceptance criteria for temper/npt is +specific to the NPT ensemble and can be found in references +"(Okabe)"_#Okabe2 and "(Mori)"_#Mori2. + +Apart from the difference in acceptance criteria and the specification +of pressure, this command works much like the "temper"_temper.html +command. See the documentation on "temper"_temper.html for information +on how the parallel tempering is handled in general. + +:line + +[Restrictions:] + +This command can only be used if LAMMPS was built with the USER-MISC +package. See the "Making LAMMPS"_Section_start.html#start_3 section +for more info on packages. + +This command should be used with a fix that maintains the +isothermal-isobaric (NPT) ensemble. + +[Related commands:] + +"temper"_temper.html, "variable"_variable.html, "fix_npt"_fix_nh.html + +[Default:] none + +:link(Okabe2) +[(Okabe)] T. Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001). + +:link(Mori2) +[(Mori)] Y. Mori, Y. Okamoto, J. Phys. Soc. Jpn., 7, 074003 (2010). diff --git a/examples/USER/misc/temper_npt/data.peptide b/examples/USER/misc/temper_npt/data.peptide new file mode 100644 index 000000000..f9dfb6e48 --- /dev/null +++ b/examples/USER/misc/temper_npt/data.peptide @@ -0,0 +1,6531 @@ +LAMMPS Description + + 2004 atoms + 1365 bonds + 786 angles + 207 dihedrals + 12 impropers + + 14 atom types + 18 bond types + 31 angle types + 21 dihedral types + 2 improper types + + 36.840194 64.211560 xlo xhi + 41.013691 68.385058 ylo yhi + 29.768095 57.139462 zlo zhi + +Masses + + 1 12.0110 + 2 12.0110 + 3 15.9990 + 4 1.0080 + 5 14.0070 + 6 12.0110 + 7 12.0110 + 8 12.0110 + 9 15.9990 + 10 1.0080 + 11 1.0080 + 12 32.0660 + 13 16.0000 + 14 1.0100 + +Pair Coeffs + + 1 0.110000 3.563595 0.110000 3.563595 + 2 0.080000 3.670503 0.010000 3.385415 + 3 0.120000 3.029056 0.120000 2.494516 + 4 0.022000 2.351973 0.022000 2.351973 + 5 0.200000 3.296325 0.200000 2.761786 + 6 0.020000 4.053589 0.010000 3.385415 + 7 0.055000 3.875410 0.010000 3.385415 + 8 0.070000 3.550053 0.070000 3.550053 + 9 0.152100 3.153782 0.152100 3.153782 + 10 0.046000 0.400014 0.046000 0.400014 + 11 0.030000 2.420037 0.030000 2.420037 + 12 0.450000 3.563595 0.450000 3.563595 + 13 0.152100 3.150570 0.152100 3.150570 + 14 0.046000 0.400014 0.046000 0.400014 + +Bond Coeffs + + 1 249.999999 1.490000 + 2 620.000001 1.230000 + 3 370.000000 1.345000 + 4 322.000001 1.111000 + 5 319.999999 1.430000 + 6 440.000000 0.997000 + 7 222.500001 1.538000 + 8 330.000001 1.080000 + 9 230.000000 1.490000 + 10 309.000001 1.111000 + 11 305.000000 1.375000 + 12 340.000001 1.080000 + 13 334.300000 1.411000 + 14 545.000001 0.960000 + 15 222.500001 1.530000 + 16 198.000000 1.818000 + 17 239.999999 1.816000 + 18 450.000000 0.957200 + +Angle Coeffs + + 1 33.000000 109.500000 30.000000 2.163000 + 2 50.000000 120.000000 0.000000 0.000000 + 3 34.000000 123.000000 0.000000 0.000000 + 4 80.000000 121.000000 0.000000 0.000000 + 5 80.000000 116.500000 0.000000 0.000000 + 6 80.000000 122.500000 0.000000 0.000000 + 7 35.500000 108.400000 5.400000 1.802000 + 8 50.000000 107.000000 0.000000 0.000000 + 9 70.000000 113.500000 0.000000 0.000000 + 10 48.000000 108.000000 0.000000 0.000000 + 11 35.000000 117.000000 0.000000 0.000000 + 12 51.800000 107.500000 0.000000 0.000000 + 13 33.430000 110.100000 22.530000 2.179000 + 14 52.000000 108.000000 0.000000 0.000000 + 15 50.000000 109.500000 0.000000 0.000000 + 16 35.000000 111.000000 0.000000 0.000000 + 17 45.800000 122.300000 0.000000 0.000000 + 18 49.300000 107.500000 0.000000 0.000000 + 19 40.000000 120.000000 35.000000 2.416200 + 20 30.000000 120.000000 22.000000 2.152500 + 21 45.200000 120.000000 0.000000 0.000000 + 22 65.000000 108.000000 0.000000 0.000000 + 23 35.500000 109.000000 5.400000 1.802000 + 24 36.000000 115.000000 0.000000 0.000000 + 25 58.350000 113.500000 11.160000 2.561000 + 26 58.000000 114.500000 0.000000 0.000000 + 27 26.500000 110.100000 22.530000 2.179000 + 28 34.000000 95.000000 0.000000 0.000000 + 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b/examples/USER/misc/temper_npt/in.temper_npt @@ -0,0 +1,29 @@ +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +run 500 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 +group peptide type <= 12 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8 new file mode 100644 index 000000000..66c290c29 --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8 @@ -0,0 +1,24 @@ +LAMMPS (17 Aug 2017) +Running on 8 partitions of processors +Step T0 T1 T2 T3 T4 T5 T6 T7 +500 0 1 2 3 4 5 6 7 +600 0 1 2 3 5 4 7 6 +700 0 2 1 4 6 3 7 5 +800 0 2 1 4 6 3 7 5 +900 0 2 1 3 6 4 7 5 +1000 0 2 1 3 7 4 6 5 +1100 0 1 2 3 7 4 6 5 +1200 0 1 2 3 7 4 6 5 +1300 0 1 2 4 7 3 5 6 +1400 0 1 2 4 7 3 5 6 +1500 0 2 1 4 7 3 5 6 +1600 1 3 0 4 6 2 5 7 +1700 1 3 0 4 5 2 6 7 +1800 0 3 1 4 5 2 6 7 +1900 0 3 2 4 5 1 6 7 +2000 1 2 3 5 4 0 6 7 +2100 2 1 3 5 4 0 6 7 +2200 2 1 3 4 5 0 7 6 +2300 1 2 4 3 5 0 7 6 +2400 1 2 4 3 5 0 6 7 +2500 2 1 3 4 5 0 6 7 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0 new file mode 100644 index 000000000..15fbef885 --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.0 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 0 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 275 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 275 275 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 221.73889 -7683.7524 1219.961 -5139.8856 -23756.591 0.996067 + 100 253.40719 -6992.3405 479.6715 -4999.6856 12620.614 1.0124851 + 150 273.60252 -6943.8714 474.24744 -4836.0631 6691.4146 1.0213937 + 200 265.37126 -7274.7854 1059.7586 -4630.6111 -17765.088 1.0221471 + 250 263.1769 -6503.9902 470.29014 -4462.3859 21936.742 1.0159924 + 300 274.03852 -7026.6057 1021.3683 -4369.0734 -14847.42 1.0095778 + 350 283.20032 -6715.3608 688.9769 -4335.5187 3430.7111 1.0045615 + 400 282.2987 -6645.6692 598.6786 -4361.5086 6318.9525 1.0001513 + 450 265.89091 -6977.5705 985.58718 -4404.465 -13261.32 0.99833097 + 500 270.30038 -6683.7902 650.5748 -4419.37 10014.277 1.000501 +Loop time of 11.0158 on 2 procs for 500 steps with 2004 atoms + +Performance: 7.843 ns/day, 3.060 hours/ns, 45.389 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.6893 | 7.8012 | 7.9131 | 4.0 | 70.82 +Bond | 0.085948 | 0.089635 | 0.093322 | 1.2 | 0.81 +Kspace | 1.1113 | 1.2333 | 1.3552 | 11.0 | 11.20 +Neigh | 1.2316 | 1.2336 | 1.2356 | 0.2 | 11.20 +Comm | 0.24281 | 0.24305 | 0.2433 | 0.0 | 2.21 +Output | 0.00052857 | 0.00053537 | 0.00054216 | 0.0 | 0.00 +Modify | 0.35968 | 0.38071 | 0.40175 | 3.4 | 3.46 +Other | | 0.03378 | | | 0.31 + +Nlocal: 1002 ave 1012 max 992 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8737.5 ave 8747 max 8728 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 359463 ave 359931 max 358995 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 718926 +Ave neighs/atom = 358.746 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 50 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 275 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.269166 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0224625 + estimated relative force accuracy = 6.76451e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 270.30038 -6683.7883 650.5748 -4419.3682 10014.295 1.000501 + 550 270.02511 -6875.5939 861.97452 -4401.4176 -7136.4285 1.005266 + 600 278.94444 -6786.546 772.05516 -4349.0356 1262.4902 1.0110761 + 650 283.8929 -6763.9691 734.90211 -4334.0667 3664.1311 1.0138933 + 700 276.67406 -6889.5452 847.87041 -4389.775 -4754.9929 1.0145005 + 750 266.09032 -6720.4921 700.27463 -4431.5085 5654.8094 1.013756 + 800 277.69948 -6917.9358 860.12186 -4399.7918 -4729.7009 1.0124281 + 850 278.00722 -6808.1267 798.69768 -4349.5695 1468.5155 1.0139727 + 900 276.49266 -6784.5965 818.01248 -4315.7673 2510.6047 1.0158115 + 950 270.36225 -6847.6403 901.97122 -4331.4544 -3448.3968 1.0175668 + 1000 276.75533 -6809.4075 781.83481 -4375.1877 3379.8584 1.0173101 + 1050 271.67172 -6913.3268 847.97269 -4443.3211 -2045.5605 1.016761 + 1100 265.73149 -6867.7958 840.08439 -4441.1449 -323.23893 1.0170333 + 1150 274.51451 -6834.9841 792.48751 -4403.4906 2604.0644 1.0175885 + 1200 274.22914 -6919.9496 890.14423 -4392.5032 -3454.4418 1.0167016 + 1250 274.13019 -6817.7256 825.11317 -4355.901 2067.3849 1.0181714 + 1300 287.36094 -6906.5403 854.11016 -4336.7237 -438.01206 1.0180794 + 1350 275.51763 -6911.8172 855.25923 -4411.5627 -742.96412 1.0180086 + 1400 269.90457 -6919.4028 855.55485 -4452.3659 311.08918 1.0213368 + 1450 276.99478 -6980.8317 913.69108 -4413.326 -1810.1051 1.0265437 + 1500 282.20313 -6926.698 863.56525 -4378.2213 932.7594 1.0301769 + 1550 276.82056 -6917.141 910.22058 -4354.146 -899.64097 1.0361201 + 1600 278.2946 -6903.7351 893.14524 -4349.0145 1399.9679 1.0421849 + 1650 270.12097 -6863.0844 879.81355 -4370.4967 1132.9864 1.0410741 + 1700 274.02565 -6912.4818 893.37432 -4383.0202 -1359.393 1.0366624 + 1750 276.77322 -6866.3214 899.18224 -4314.6474 887.47588 1.0332821 + 1800 287.02945 -6961.9217 950.89476 -4297.2996 -1298.0904 1.0313542 + 1850 279.37232 -6930.51 898.78906 -4363.711 397.74804 1.0309206 + 1900 277.14727 -6978.8634 915.53145 -4408.6069 636.36898 1.0285813 + 1950 275.14272 -7010.256 927.28727 -4440.212 -2352.6961 1.0241747 + 2000 270.84972 -6967.52 913.42253 -4436.9722 1669.9637 1.0251906 + 2050 276.70108 -6992.4582 993.37473 -4347.0223 -500.38379 1.0325714 + 2100 278.49569 -6922.9266 939.43518 -4320.7155 700.24515 1.0385166 + 2150 279.69822 -6896.5008 923.58805 -4302.9571 702.22759 1.0415681 + 2200 284.136 -6951.6694 974.70903 -4280.5086 352.95043 1.0452009 + 2250 292.01941 -6960.5848 964.01635 -4253.0483 2680.7007 1.0430517 + 2300 277.58812 -6995.5006 1010.8176 -4327.3258 -1508.9961 1.0328658 + 2350 270.61616 -6978.93 966.12478 -4397.0745 -1636.7434 1.0267664 + 2400 279.36012 -6991.4739 957.43125 -4366.1056 432.00482 1.0260429 + 2450 286.38546 -7074.807 1004.3206 -4360.6042 160.9109 1.0251585 + 2500 269.98622 -6932.0456 957.35208 -4362.724 1748.1568 1.0186556 +Loop time of 46.7361 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.395 ns/day, 3.246 hours/ns, 42.793 timesteps/s +99.2% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 32.381 | 32.617 | 32.854 | 4.1 | 69.79 +Bond | 0.3601 | 0.36578 | 0.37147 | 0.9 | 0.78 +Kspace | 4.6658 | 4.933 | 5.2002 | 12.0 | 10.56 +Neigh | 4.9833 | 4.9921 | 5.0009 | 0.4 | 10.68 +Comm | 0.96477 | 0.96532 | 0.96587 | 0.1 | 2.07 +Output | 0.0021896 | 0.0022331 | 0.0022767 | 0.1 | 0.00 +Modify | 1.4424 | 1.5379 | 1.6334 | 7.7 | 3.29 +Other | | 1.322 | | | 2.83 + +Nlocal: 1002 ave 1011 max 993 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8835 ave 8847 max 8823 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 366395 ave 367166 max 365624 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 732790 +Ave neighs/atom = 365.664 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 195 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1 new file mode 100644 index 000000000..ebdb7b7f3 --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.1 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 1 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 280 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 280 280 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 222.19861 -7681.6246 1220.9355 -5134.0385 -23782.584 0.99586813 + 100 254.66243 -6984.8813 480.32613 -4984.0772 12653.925 1.0120499 + 150 275.28565 -6924.9875 473.42216 -4807.9551 6796.8759 1.0208676 + 200 266.52981 -7245.4283 1066.0809 -4588.0144 -17643.106 1.0213699 + 250 265.06051 -6458.7243 468.97999 -4407.1839 22476.585 1.0143215 + 300 276.91573 -6986.8723 1020.9402 -4312.5895 -14559.244 1.005554 + 350 284.26789 -6635.8191 681.27092 -4257.3089 2625.7849 0.99664411 + 400 284.48799 -6543.0099 637.61352 -4206.8431 7901.0269 0.99079237 + 450 271.30029 -6770.4441 1003.5624 -4147.0663 -13046.51 0.9856127 + 500 292.02418 -6514.8219 628.56367 -4142.7096 9871.7492 0.98625432 +Loop time of 11.1841 on 2 procs for 500 steps with 2004 atoms + +Performance: 7.725 ns/day, 3.107 hours/ns, 44.706 timesteps/s +98.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.8072 | 7.9267 | 8.0463 | 4.2 | 70.88 +Bond | 0.08858 | 0.091102 | 0.093624 | 0.8 | 0.81 +Kspace | 1.1403 | 1.2665 | 1.3927 | 11.2 | 11.32 +Neigh | 1.2478 | 1.2496 | 1.2514 | 0.2 | 11.17 +Comm | 0.21574 | 0.23191 | 0.24809 | 3.4 | 2.07 +Output | 0.00054431 | 0.00054872 | 0.00055313 | 0.0 | 0.00 +Modify | 0.36159 | 0.38512 | 0.40864 | 3.8 | 3.44 +Other | | 0.03255 | | | 0.29 + +Nlocal: 1002 ave 1026 max 978 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8640.5 ave 8690 max 8591 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 354518 ave 367457 max 341580 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 709037 +Ave neighs/atom = 353.811 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 49 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 280 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268766 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0227872 + estimated relative force accuracy = 6.8623e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 292.02418 -6514.8215 628.56367 -4142.7092 9871.7534 0.98625432 + 550 282.55729 -6813.6685 882.47773 -4244.1648 -5377.4053 0.98629839 + 600 274.41644 -6737.0424 793.45027 -4305.1716 -306.54594 0.98725369 + 650 274.38967 -6664.1973 722.25014 -4303.6865 4628.1283 0.99175575 + 700 282.07693 -6819.1345 897.72476 -4237.2518 -7210.1942 0.99693402 + 750 281.80476 -6580.3192 776.69527 -4121.091 5466.9616 1.0060075 + 800 288.76507 -6726.7205 885.07773 -4117.5529 -2623.0756 1.0132495 + 850 289.21519 -6755.4289 847.00353 -4181.648 776.75991 1.0160602 + 900 280.679 -6694.3766 777.91069 -4240.6544 2272.2098 1.0170439 + 950 280.93616 -6813.8865 910.52053 -4226.0191 -3872.8603 1.0202606 + 1000 289.91762 -6710.0317 786.39268 -4192.6678 4456.0575 1.0222223 + 1050 292.7318 -6830.313 882.85834 -4199.6812 -2434.3412 1.0214856 + 1100 280.61029 -6789.3828 846.07872 -4267.9028 580.25027 1.0202095 + 1150 277.27283 -6806.9599 852.2013 -4299.2838 18.428929 1.0180062 + 1200 284.68488 -6849.8644 877.54803 -4272.5875 -1041.3591 1.0171686 + 1250 290.47153 -6864.5918 827.15634 -4303.1571 2658.2245 1.0175104 + 1300 279.84219 -6892.8497 884.4759 -4337.5586 -1800.8783 1.0176916 + 1350 275.59818 -6848.0359 848.53171 -4354.028 1599.2311 1.0197901 + 1400 276.67929 -6893.565 900.40614 -4341.2278 295.46659 1.0221449 + 1450 281.18148 -6902.3901 931.40362 -4292.1748 -1585.1315 1.0243322 + 1500 282.82339 -6846.4364 887.9988 -4269.8228 2142.9076 1.0291373 + 1550 291.40537 -6898.3742 920.23257 -4238.2876 -355.99408 1.0308242 + 1600 279.9548 -6863.2068 923.64788 -4268.0713 233.83555 1.0259922 + 1650 282.90611 -6848.3952 903.97971 -4255.3069 369.65523 1.0200083 + 1700 292.24099 -6884.346 965.54265 -4173.9603 -971.39092 1.0155909 + 1750 285.95609 -6805.2486 955.25719 -4142.6727 646.23287 1.012031 + 1800 293.50173 -6823.8152 919.24584 -4152.199 530.19678 1.0078324 + 1850 300.737 -6918.3747 942.10944 -4180.6963 -949.67639 1.0061029 + 1900 284.98969 -6913.5357 956.78373 -4255.2032 -163.02524 1.0095568 + 1950 282.78589 -6905.1978 951.94384 -4264.8631 -891.31043 1.0177223 + 2000 289.82463 -6977.0203 1022.9525 -4223.6518 -540.73403 1.0269481 + 2050 292.13474 -6900.8375 924.54552 -4232.0833 2656.3028 1.0310097 + 2100 284.54116 -6958.82 968.35681 -4291.5924 -286.70605 1.0264636 + 2150 268.14376 -6966.2184 973.69354 -4391.5558 -1446.0052 1.0190957 + 2200 275.09872 -6957.02 982.37472 -4332.1512 -1449.1984 1.0199163 + 2250 285.69237 -7002.4814 1014.3438 -4282.3934 -1530.0347 1.0264012 + 2300 282.59746 -6922.8242 980.57612 -4254.9822 381.8231 1.0332785 + 2350 290.98138 -6993.8628 1022.527 -4234.0132 -559.9386 1.0396092 + 2400 281.29903 -6963.5226 967.13898 -4316.8702 1438.7922 1.0452404 + 2450 278.44605 -6968.5134 945.32295 -4360.7108 1102.9302 1.0498791 + 2500 278.65789 -7034.3651 1032.8711 -4337.7496 -923.32414 1.0527955 +Loop time of 46.7418 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s +98.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 33.141 | 33.146 | 33.152 | 0.1 | 70.91 +Bond | 0.36441 | 0.36647 | 0.36853 | 0.3 | 0.78 +Kspace | 4.9269 | 4.9539 | 4.9808 | 1.2 | 10.60 +Neigh | 5.2154 | 5.223 | 5.2306 | 0.3 | 11.17 +Comm | 0.90923 | 0.97305 | 1.0369 | 6.5 | 2.08 +Output | 0.0021682 | 0.0027286 | 0.003289 | 1.1 | 0.01 +Modify | 1.454 | 1.5534 | 1.6528 | 8.0 | 3.32 +Other | | 0.5229 | | | 1.12 + +Nlocal: 1002 ave 1005 max 999 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 9059.5 ave 9084 max 9035 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 378277 ave 380641 max 375913 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 756554 +Ave neighs/atom = 377.522 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 197 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2 new file mode 100644 index 000000000..42d42381c --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.2 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 2 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 285 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 285 285 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 222.63643 -7679.59 1221.8685 -5128.4568 -23807.78 0.99567623 + 100 255.85049 -6977.7653 480.95894 -4969.235 12685.571 1.0116281 + 150 276.83083 -6906.8603 472.9485 -4781.076 6899.3786 1.0203576 + 200 267.19755 -7210.264 1068.2756 -4546.6687 -17521.505 1.0207097 + 250 263.8837 -6392.2545 463.0506 -4353.6698 22886.964 1.0130132 + 300 280.88953 -6919.81 1005.9833 -4236.7581 -14774.964 1.0024942 + 350 289.59472 -6621.8351 734.60058 -4158.1911 2409.0738 0.99451628 + 400 288.29076 -6495.283 634.61137 -4139.4136 6594.965 0.98796525 + 450 281.92055 -6838.8449 1025.3043 -4130.3164 -12795.112 0.98591519 + 500 298.25519 -6578.7232 652.75467 -4145.2172 10282.835 0.98902709 +Loop time of 11.0965 on 2 procs for 500 steps with 2004 atoms + +Performance: 7.786 ns/day, 3.082 hours/ns, 45.059 timesteps/s +99.1% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.9379 | 7.9449 | 7.952 | 0.2 | 71.60 +Bond | 0.090588 | 0.090927 | 0.091265 | 0.1 | 0.82 +Kspace | 1.1684 | 1.176 | 1.1837 | 0.7 | 10.60 +Neigh | 1.2553 | 1.2556 | 1.256 | 0.0 | 11.32 +Comm | 0.20599 | 0.21536 | 0.22474 | 2.0 | 1.94 +Output | 0.00049877 | 0.00050557 | 0.00051236 | 0.0 | 0.00 +Modify | 0.35224 | 0.37667 | 0.40111 | 4.0 | 3.39 +Other | | 0.03635 | | | 0.33 + +Nlocal: 1002 ave 1007 max 997 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8699.5 ave 8735 max 8664 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 355600 ave 363554 max 347647 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 711201 +Ave neighs/atom = 354.891 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 50 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 285 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268844 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0227233 + estimated relative force accuracy = 6.84305e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 298.25519 -6578.7239 652.75467 -4145.218 10282.81 0.98902709 + 550 280.55812 -6800.9339 904.37474 -4221.4693 -6284.3677 0.99138729 + 600 282.54117 -6736.9067 793.64464 -4256.3323 379.51956 0.99544144 + 650 289.246 -6695.3988 727.43292 -4241.0045 3741.9292 1.0004679 + 700 298.37935 -6898.8951 912.35329 -4205.0492 -5179.2622 1.0029455 + 750 276.21453 -6657.3814 738.83164 -4269.3936 6422.8684 1.003042 + 800 273.34049 -6770.7481 842.34057 -4296.411 -2699.1945 1.0011122 + 850 279.30106 -6766.7842 807.51048 -4291.6893 -583.46522 1.0039015 + 900 286.09076 -6808.4366 807.15205 -4293.1617 1405.0223 1.0062162 + 950 283.04021 -6838.8107 869.45604 -4279.4454 -2826.6403 1.008228 + 1000 278.36762 -6776.1595 827.04427 -4287.104 2510.6216 1.0123638 + 1050 276.46194 -6858.6173 893.69758 -4314.2864 -1818.0617 1.0153108 + 1100 270.91883 -6818.5634 864.2518 -4336.7738 1021.1432 1.0153455 + 1150 274.70844 -6747.0957 849.98378 -4256.948 1453.2165 1.0141005 + 1200 292.66211 -6864.4907 917.17522 -4199.958 -2889.5663 1.0130738 + 1250 288.1024 -6814.0744 887.46443 -4206.4766 2384.4467 1.0139599 + 1300 286.54446 -6864.9998 900.886 -4253.2821 -2397.0043 1.0140796 + 1350 274.86169 -6804.6738 866.75191 -4296.843 1112.3802 1.0143892 + 1400 275.30771 -6837.4182 904.04812 -4289.6282 136.99961 1.0170328 + 1450 296.09129 -6868.8691 910.61078 -4190.4268 -1076.0085 1.0204782 + 1500 292.50596 -6812.8248 889.10378 -4177.2959 1069.9919 1.0198406 + 1550 284.3886 -6876.901 909.58572 -4269.3554 -1153.6899 1.0177539 + 1600 276.41187 -6876.8574 907.69862 -4318.8244 114.8894 1.0158964 + 1650 275.68967 -6919.4356 902.04604 -4371.3672 -1493.2092 1.0141832 + 1700 271.20923 -6893.2373 912.27766 -4361.688 -563.23529 1.0157743 + 1750 279.40649 -6842.0743 892.63677 -4281.2237 944.83039 1.0207184 + 1800 282.84659 -6889.8537 934.73963 -4266.3608 -895.12942 1.0238833 + 1850 279.58052 -6900.6624 951.17313 -4280.2364 648.68857 1.024366 + 1900 276.44092 -6841.9805 881.15423 -4310.3185 1052.7352 1.0229576 + 1950 289.89625 -6960.295 949.2514 -4280.2 -2500.9996 1.0210089 + 2000 283.75058 -6908.6985 930.56698 -4283.9809 1529.221 1.0211902 + 2050 284.00141 -6837.2348 943.57188 -4198.0147 -710.45695 1.0190262 + 2100 294.53504 -6879.4583 983.431 -4137.4874 -496.16699 1.0172736 + 2150 296.46029 -6854.8307 926.58211 -4158.2139 757.20038 1.017548 + 2200 284.26196 -6896.5957 989.5222 -4209.8697 -1953.1733 1.0187998 + 2250 284.51713 -6852.3924 938.51853 -4215.1465 210.72971 1.0208918 + 2300 289.88921 -6867.2253 969.05163 -4167.372 -80.492209 1.0240397 + 2350 296.17997 -6836.2421 954.2497 -4113.6314 -389.76698 1.0272081 + 2400 309.56546 -6833.5714 970.44217 -4014.8493 610.57346 1.0294586 + 2450 300.61402 -6827.9964 1025.4417 -4007.7199 1121.4824 1.0284326 + 2500 298.82336 -6815.7862 945.53298 -4086.1097 -726.1131 1.0224541 +Loop time of 46.7423 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s +99.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 32.492 | 32.625 | 32.758 | 2.3 | 69.80 +Bond | 0.3584 | 0.36552 | 0.37265 | 1.2 | 0.78 +Kspace | 4.7476 | 4.8898 | 5.0319 | 6.4 | 10.46 +Neigh | 5.1461 | 5.1463 | 5.1464 | 0.0 | 11.01 +Comm | 0.86246 | 0.89403 | 0.92559 | 3.3 | 1.91 +Output | 0.0020437 | 0.0020902 | 0.0021367 | 0.1 | 0.00 +Modify | 1.4279 | 1.5187 | 1.6095 | 7.4 | 3.25 +Other | | 1.301 | | | 2.78 + +Nlocal: 1002 ave 1010 max 994 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8922 ave 9009 max 8835 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 367689 ave 371637 max 363741 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 735378 +Ave neighs/atom = 366.955 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 200 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3 new file mode 100644 index 000000000..b97559765 --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.3 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 3 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 290 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 290 290 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 223.053 -7677.6519 1222.7567 -5123.1433 -23832.135 0.99549097 + 100 256.97829 -6970.9352 481.56411 -4955.0662 12716.194 1.0112202 + 150 278.44824 -6890.5623 472.60764 -4755.4621 6994.6533 1.0198648 + 200 271.15638 -7198.8095 1073.0275 -4506.826 -17647.735 1.020128 + 250 271.19291 -6398.4699 477.07511 -4302.2206 23076.406 1.0123626 + 300 295.5039 -6953.4923 1007.5309 -4181.6369 -15039.211 1.0007168 + 350 297.29537 -6594.1646 707.50773 -4111.6362 1990.9893 0.99116796 + 400 294.93533 -6450.921 630.83559 -4059.1555 6431.7427 0.98805162 + 450 295.23265 -6781.3296 1002.9096 -4015.715 -12070.145 0.98722232 + 500 284.70036 -6389.6524 668.83647 -4020.9946 10958.208 0.98502274 +Loop time of 11.0942 on 2 procs for 500 steps with 2004 atoms + +Performance: 7.788 ns/day, 3.082 hours/ns, 45.069 timesteps/s +99.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7626 | 7.8378 | 7.913 | 2.7 | 70.65 +Bond | 0.086271 | 0.08859 | 0.090909 | 0.8 | 0.80 +Kspace | 1.1309 | 1.2146 | 1.2982 | 7.6 | 10.95 +Neigh | 1.2958 | 1.2978 | 1.2999 | 0.2 | 11.70 +Comm | 0.24052 | 0.24249 | 0.24445 | 0.4 | 2.19 +Output | 0.00055242 | 0.00056267 | 0.00057292 | 0.0 | 0.01 +Modify | 0.35597 | 0.3786 | 0.40124 | 3.7 | 3.41 +Other | | 0.03375 | | | 0.30 + +Nlocal: 1002 ave 1015 max 989 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8686.5 ave 8717 max 8656 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 354166 ave 365049 max 343283 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 708332 +Ave neighs/atom = 353.459 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 52 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 290 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268731 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228157 + estimated relative force accuracy = 6.87089e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 284.70036 -6389.6523 668.83647 -4020.9946 10958.208 0.98502274 + 550 290.90514 -6715.0579 911.30009 -4066.8904 -6474.803 0.98383517 + 600 283.07652 -6555.4875 766.62589 -4098.7355 261.44315 0.98334866 + 650 293.39943 -6543.5525 727.38701 -4064.4058 5298.0746 0.98688936 + 700 295.77284 -6702.0803 912.68434 -4023.4658 -6806.6079 0.98957885 + 750 302.19503 -6545.9025 745.53299 -3996.0952 4624.9549 0.9931176 + 800 292.89947 -6664.6734 861.73293 -4054.1658 -1569.2753 0.99667377 + 850 288.96376 -6637.9753 841.33585 -4071.3632 -864.6336 1.0003373 + 900 291.22538 -6602.7272 806.80566 -4057.1422 2231.0477 1.0028411 + 950 290.78982 -6720.7893 893.26995 -4091.3406 -3898.6743 1.0021058 + 1000 285.74827 -6640.6252 810.15614 -4124.3911 558.53066 1.0051325 + 1050 288.3183 -6717.0357 867.9383 -4127.675 355.99916 1.0122228 + 1100 291.39421 -6746.7014 879.64717 -4127.2669 -736.99584 1.011619 + 1150 290.47863 -6710.1637 836.85441 -4138.9885 1105.9666 1.0069336 + 1200 288.94451 -6726.3595 867.56238 -4133.6359 -901.95525 1.0026837 + 1250 290.75557 -6716.8398 867.19843 -4113.6671 1376.8368 1.0000807 + 1300 289.52654 -6715.6758 904.46364 -4082.5758 -1400.2433 0.99935875 + 1350 292.30663 -6661.0526 904.32661 -4011.491 196.73374 0.99704618 + 1400 301.41479 -6661.807 880.88881 -3981.3023 1079.6673 0.99635503 + 1450 301.10415 -6704.7089 950.31941 -3956.6283 -1083.4574 0.99740883 + 1500 303.52341 -6687.1744 886.70817 -3988.2608 901.20455 0.99756877 + 1550 290.70908 -6738.4941 931.37971 -4071.4177 -56.269366 0.99843015 + 1600 289.8778 -6709.348 888.89193 -4089.7225 506.51952 1.0003118 + 1650 288.12183 -6724.4008 896.24971 -4107.9017 -1229.6117 1.004563 + 1700 297.81604 -6743.9356 906.62851 -4059.1778 1032.1913 1.0116813 + 1750 304.22415 -6761.8681 932.14203 -4013.3368 1825.359 1.015764 + 1800 286.62853 -6698.3527 911.17615 -4075.843 -1160.6136 1.0169905 + 1850 292.7719 -6787.8009 918.61838 -4121.1696 1455.4151 1.0203418 + 1900 290.87293 -6806.1448 960.43892 -4109.0309 -829.39096 1.022593 + 1950 304.5232 -6848.8518 954.93165 -4075.7453 915.93096 1.0221703 + 2000 286.15289 -6721.328 941.83273 -4071.0015 194.2717 1.0167052 + 2050 305.2696 -6720.8244 968.69939 -3929.4938 -1154.2389 1.0114409 + 2100 298.14935 -6678.8136 975.17824 -3923.516 794.1643 1.0070072 + 2150 301.51333 -6734.6863 950.33572 -3984.1464 -537.44292 1.0048337 + 2200 298.25074 -6736.277 945.4083 -4010.144 211.60185 1.0060101 + 2250 297.20864 -6820.7924 941.75394 -4104.5356 772.05119 1.0087884 + 2300 286.08552 -6853.0967 990.41746 -4154.5877 -760.47968 1.0110651 + 2350 295.49972 -6888.1433 937.27703 -4186.5667 966.37988 1.0150101 + 2400 289.60528 -6888.0768 967.74071 -4191.2297 1140.8847 1.0176507 + 2450 290.7003 -6906.443 998.89141 -4171.9073 -363.47638 1.0151765 + 2500 291.05855 -6817.2894 972.06896 -4107.4372 415.89846 1.0117849 +Loop time of 46.7412 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.394 ns/day, 3.246 hours/ns, 42.789 timesteps/s +99.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 31.884 | 32.272 | 32.659 | 6.8 | 69.04 +Bond | 0.34239 | 0.35991 | 0.37742 | 2.9 | 0.77 +Kspace | 4.6486 | 5.0781 | 5.5076 | 19.1 | 10.86 +Neigh | 5.1657 | 5.1742 | 5.1828 | 0.4 | 11.07 +Comm | 0.96743 | 0.96831 | 0.96918 | 0.1 | 2.07 +Output | 0.0021966 | 0.0022568 | 0.002317 | 0.1 | 0.00 +Modify | 1.4428 | 1.5251 | 1.6074 | 6.7 | 3.26 +Other | | 1.362 | | | 2.91 + +Nlocal: 1002 ave 1004 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8824 ave 8848 max 8800 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 363564 ave 364653 max 362474 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 727127 +Ave neighs/atom = 362.838 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 201 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4 new file mode 100644 index 000000000..ad7e1fdb5 --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.4 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 4 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 295 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 295 295 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 223.44965 -7675.7636 1223.6082 -5118.0353 -23854.901 0.99531214 + 100 258.05368 -6964.3986 482.14839 -4941.5246 12745.624 1.010825 + 150 279.95689 -6874.6176 472.25664 -4730.8609 7091.9355 1.0193879 + 200 275.57578 -7193.9232 1079.6288 -4468.952 -17877.542 1.0195441 + 250 279.43717 -6402.2754 479.97988 -4253.8984 23273.809 1.0116181 + 300 292.20824 -6863.5426 998.78846 -4120.1066 -14524.477 0.99985013 + 350 297.83477 -6520.8204 705.46814 -4037.1112 1640.5321 0.99100268 + 400 300.71476 -6441.8834 652.50284 -3993.9443 7052.2304 0.98787311 + 450 298.04546 -6757.2898 986.07239 -3991.7184 -11211.612 0.98470906 + 500 290.54704 -6432.0836 676.82263 -4020.5317 9503.0303 0.98022653 +Loop time of 11.0411 on 2 procs for 500 steps with 2004 atoms + +Performance: 7.825 ns/day, 3.067 hours/ns, 45.286 timesteps/s +99.2% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7513 | 7.8142 | 7.8771 | 2.3 | 70.77 +Bond | 0.087844 | 0.089858 | 0.091872 | 0.7 | 0.81 +Kspace | 1.1507 | 1.2078 | 1.2649 | 5.2 | 10.94 +Neigh | 1.2777 | 1.2798 | 1.282 | 0.2 | 11.59 +Comm | 0.21883 | 0.2369 | 0.25497 | 3.7 | 2.15 +Output | 0.00052476 | 0.00053084 | 0.00053692 | 0.0 | 0.00 +Modify | 0.35187 | 0.38007 | 0.40828 | 4.6 | 3.44 +Other | | 0.03188 | | | 0.29 + +Nlocal: 1002 ave 1018 max 986 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8685.5 ave 8713 max 8658 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 352674 ave 363841 max 341507 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 705348 +Ave neighs/atom = 351.97 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 51 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 295 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268595 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0229274 + estimated relative force accuracy = 6.90452e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 290.54704 -6432.0826 676.82263 -4020.5307 9503.0509 0.98022653 + 550 299.80307 -6732.1631 858.08424 -4084.0858 -5804.5234 0.97922483 + 600 282.09517 -6605.4814 819.96587 -4101.2486 -819.40251 0.98081741 + 650 294.53657 -6522.7525 767.04478 -3997.1588 4596.0585 0.98382352 + 700 305.841 -6619.4153 905.5064 -3887.8662 -5973.5686 0.98622017 + 750 307.23206 -6438.653 789.70387 -3814.6009 6681.8219 0.98950206 + 800 307.87505 -6564.5918 887.75178 -3838.6527 -1917.6181 0.98688326 + 850 298.61627 -6528.5749 847.91654 -3897.7513 -3785.6609 0.9806677 + 900 300.37107 -6492.7964 828.13288 -3871.2792 3123.0873 0.97992098 + 950 313.50832 -6648.6955 936.69562 -3840.1788 -3465.5075 0.97832705 + 1000 300.79594 -6452.6853 828.10459 -3828.6598 2639.7489 0.9724972 + 1050 316.04685 -6570.6422 935.04399 -3748.6208 -2434.9525 0.96835974 + 1100 311.0203 -6489.14 897.50532 -3734.6686 -1557.8625 0.97044387 + 1150 311.75575 -6489.2845 888.02191 -3739.9054 1954.7864 0.97411485 + 1200 304.34674 -6521.7138 905.22814 -3799.3644 -1699.1298 0.98025305 + 1250 305.82 -6594.6645 927.05285 -3841.6942 1061.9124 0.98818343 + 1300 300.78043 -6566.1931 942.90743 -3827.4574 -864.10057 0.99107957 + 1350 314.72676 -6545.9508 912.22446 -3754.6305 606.75529 0.9929135 + 1400 315.913 -6551.4197 960.628 -3704.6134 1064.6728 0.99029667 + 1450 309.18966 -6497.0696 918.08358 -3732.9498 -1325.2759 0.98343775 + 1500 312.58526 -6494.4875 891.16465 -3737.013 1380.3782 0.98291945 + 1550 317.55684 -6590.3216 970.14576 -3724.1828 -1866.6608 0.9847875 + 1600 307.38151 -6552.4153 940.826 -3776.3487 -390.22458 0.98596757 + 1650 295.78641 -6508.499 880.69089 -3861.7969 -1368.3717 0.98931642 + 1700 306.06415 -6655.9157 976.17248 -3852.3681 -1599.4137 0.99512042 + 1750 303.02767 -6625.01 920.50823 -3895.2561 2274.9319 1.0015941 + 1800 295.63701 -6674.2337 928.57382 -3980.5406 -290.52041 1.0049878 + 1850 302.04323 -6768.1711 959.29198 -4005.5112 -688.59334 1.0096755 + 1900 299.41653 -6746.3896 940.56717 -4018.1373 1011.075 1.0170047 + 1950 298.83395 -6766.5655 950.11421 -4032.2445 -187.97792 1.0202189 + 2000 299.45823 -6824.2159 958.18625 -4078.0956 -715.67202 1.0223031 + 2050 290.49349 -6835.2073 950.68063 -4150.1172 -345.43177 1.0232367 + 2100 283.23103 -6798.203 936.42547 -4170.729 300.36081 1.0201704 + 2150 295.58133 -6797.5304 933.21906 -4099.5245 -293.26979 1.0191458 + 2200 287.12783 -6693.6112 942.32795 -4036.9686 -1430.1972 1.0191149 + 2250 301.19592 -6762.0204 998.15337 -3965.5579 -956.39215 1.0207659 + 2300 303.62433 -6716.6297 960.83467 -3942.987 77.237938 1.0202529 + 2350 292.95455 -6741.789 993.45295 -3999.2326 1009.5683 1.0189011 + 2400 295.01475 -6781.545 966.72586 -4053.4151 109.26284 1.0174852 + 2450 300.36482 -6827.3015 978.76759 -4055.187 -395.9959 1.0168907 + 2500 303.77029 -6833.9094 987.05071 -4033.1791 259.58796 1.0139892 +Loop time of 46.7422 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s +99.3% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 31.75 | 32.061 | 32.372 | 5.5 | 68.59 +Bond | 0.36191 | 0.36261 | 0.36331 | 0.1 | 0.78 +Kspace | 4.6321 | 4.925 | 5.2179 | 13.2 | 10.54 +Neigh | 5.3267 | 5.3348 | 5.3429 | 0.3 | 11.41 +Comm | 0.88959 | 0.96174 | 1.0339 | 7.4 | 2.06 +Output | 0.0022326 | 0.0022967 | 0.0023608 | 0.1 | 0.00 +Modify | 1.4187 | 1.5349 | 1.6512 | 9.4 | 3.28 +Other | | 1.56 | | | 3.34 + +Nlocal: 1002 ave 1009 max 995 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8864 ave 8880 max 8848 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 364886 ave 365536 max 364236 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 729772 +Ave neighs/atom = 364.158 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 206 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5 new file mode 100644 index 000000000..078ab383b --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.5 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 5 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 300 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 300 300 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 223.82864 -7673.9648 1224.4256 -5113.1564 -23877.062 0.99513919 + 100 259.08234 -6958.1555 482.71038 -4928.5779 12773.331 1.010442 + 150 281.33296 -6859.1832 472.14676 -4707.3204 7185.467 1.0189247 + 200 278.97145 -7183.3765 1085.5768 -4432.1832 -18068.845 1.0189951 + 250 279.03591 -6351.7829 479.41881 -4206.3627 23082.567 1.0112758 + 300 300.6326 -6884.9027 1026.5309 -4063.426 -13809.886 0.99975981 + 350 305.9627 -6542.2739 749.87415 -3965.6303 1365.919 0.98893682 + 400 300.95813 -6356.16 664.78738 -3894.4833 7945.2634 0.98104761 + 450 305.74067 -6698.3004 1016.1128 -3856.7437 -11928.509 0.97692928 + 500 295.19123 -6343.4664 707.06763 -3873.9411 9895.6164 0.97622451 +Loop time of 11.1232 on 2 procs for 500 steps with 2004 atoms + +Performance: 7.768 ns/day, 3.090 hours/ns, 44.951 timesteps/s +99.0% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.8133 | 7.8368 | 7.8603 | 0.8 | 70.45 +Bond | 0.088746 | 0.089125 | 0.089505 | 0.1 | 0.80 +Kspace | 1.2047 | 1.2319 | 1.2591 | 2.5 | 11.07 +Neigh | 1.3081 | 1.31 | 1.3119 | 0.2 | 11.78 +Comm | 0.21978 | 0.23832 | 0.25687 | 3.8 | 2.14 +Output | 0.00053644 | 0.00054514 | 0.00055385 | 0.0 | 0.00 +Modify | 0.35216 | 0.38209 | 0.41202 | 4.8 | 3.44 +Other | | 0.03448 | | | 0.31 + +Nlocal: 1002 ave 1003 max 1001 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8664.5 ave 8679 max 8650 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 350634 ave 352508 max 348761 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 701269 +Ave neighs/atom = 349.935 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 52 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 300 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.26848 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0230214 + estimated relative force accuracy = 6.93284e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 295.19123 -6343.4702 707.06763 -3873.9449 9895.5638 0.97622451 + 550 302.94979 -6642.4394 911.36179 -3922.2969 -5410.8109 0.97461641 + 600 297.33068 -6551.2919 805.26047 -3970.8 -646.78096 0.97348192 + 650 294.80947 -6578.9544 780.59748 -4038.1786 3293.0695 0.97423526 + 700 286.5511 -6718.4475 944.64841 -4062.9279 -5230.2518 0.97771554 + 750 294.49463 -6602.2482 777.88337 -4066.0662 4142.887 0.9831379 + 800 291.06018 -6664.3537 858.09465 -4068.466 -2624.3753 0.98991103 + 850 293.82285 -6689.8325 860.75951 -4074.7853 -435.3378 0.99623629 + 900 287.38111 -6671.9376 837.28605 -4118.8247 2185.0063 0.99906496 + 950 288.54911 -6783.7293 916.92837 -4144.0005 -2644.9104 0.99578685 + 1000 293.00277 -6687.2173 803.00518 -4134.8207 2220.968 0.98936787 + 1050 301.16902 -6760.9066 892.18697 -4070.5711 -2974.6886 0.98583275 + 1100 309.08554 -6738.1202 875.08899 -4017.6166 921.61791 0.98892607 + 1150 298.58252 -6674.1083 871.86516 -4019.5376 944.64401 0.98978942 + 1200 298.47184 -6760.3869 925.22004 -4053.1221 -798.3384 0.98947798 + 1250 291.12935 -6703.3237 856.27457 -4108.8431 544.44438 0.98937896 + 1300 293.02206 -6830.1194 917.90705 -4162.7058 432.93648 0.98837688 + 1350 282.12152 -6775.1505 898.35169 -4192.3746 -968.85129 0.98738197 + 1400 284.13008 -6684.782 848.15892 -4140.2066 -909.72792 0.98855422 + 1450 283.07781 -6640.5698 889.19504 -4061.241 120.67624 0.99460963 + 1500 299.32129 -6744.9956 896.07755 -4061.8016 -500.39827 1.002166 + 1550 290.06547 -6763.7114 921.50981 -4110.3475 1970.1344 1.0045278 + 1600 294.31127 -6824.5224 885.60385 -4181.7147 -1450.5522 1.0021664 + 1650 289.14351 -6837.8321 902.7679 -4208.7148 -36.719886 1.0010127 + 1700 284.10327 -6855.1076 903.75736 -4255.0939 984.04625 1.0006878 + 1750 280.04385 -6904.9119 918.67229 -4314.2203 -1431.4015 1.0004286 + 1800 281.68654 -6818.1122 846.72598 -4289.5591 520.17793 1.0021784 + 1850 286.93593 -6902.5226 934.50057 -4254.8531 -793.77873 1.0057534 + 1900 292.37295 -6876.9829 886.20947 -4245.1425 1563.8149 1.0119959 + 1950 278.61219 -6897.2099 935.36125 -4298.3772 -498.09374 1.0139668 + 2000 278.03754 -6936.4809 912.07762 -4364.3628 -475.0812 1.0140553 + 2050 280.17142 -6999.6889 907.21584 -4419.692 -483.15119 1.0159549 + 2100 275.01317 -7045.1909 966.49463 -4436.7129 516.29126 1.0192102 + 2150 275.36286 -6985.3989 879.47784 -4461.8499 -33.602001 1.0183533 + 2200 276.11062 -7026.4293 936.6898 -4441.2038 -1270.9384 1.0213402 + 2250 283.79417 -7011.4884 977.04948 -4340.0281 -178.52826 1.0266779 + 2300 276.26548 -6911.7259 909.12359 -4353.142 1380.5761 1.0284968 + 2350 279.5692 -7056.2521 960.48747 -4426.5792 202.29669 1.0282733 + 2400 270.18994 -6995.9308 932.57134 -4450.1735 -1921.755 1.0261097 + 2450 273.41894 -6999.2367 955.71826 -4411.0536 -376.50236 1.0265598 + 2500 279.53567 -6995.6096 941.2382 -4385.3862 300.84721 1.0300527 +Loop time of 46.7426 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.394 ns/day, 3.246 hours/ns, 42.788 timesteps/s +98.6% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 32.111 | 32.533 | 32.954 | 7.4 | 69.60 +Bond | 0.36551 | 0.36836 | 0.3712 | 0.5 | 0.79 +Kspace | 4.9203 | 5.3226 | 5.7249 | 17.4 | 11.39 +Neigh | 5.2618 | 5.2695 | 5.2772 | 0.3 | 11.27 +Comm | 0.89292 | 0.96319 | 1.0335 | 7.2 | 2.06 +Output | 0.0021534 | 0.0022 | 0.0022466 | 0.1 | 0.00 +Modify | 1.4108 | 1.5304 | 1.65 | 9.7 | 3.27 +Other | | 0.7537 | | | 1.61 + +Nlocal: 1002 ave 1023 max 981 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8955 ave 9060 max 8850 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 370398 ave 378514 max 362281 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 740795 +Ave neighs/atom = 369.658 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 200 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6 new file mode 100644 index 000000000..7dbd6f612 --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.6 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 6 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 305 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 305 305 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 224.19041 -7672.2342 1225.2069 -5108.4844 -23898.427 0.9949719 + 100 260.06304 -6952.1103 483.25334 -4916.1343 12800.907 1.01007 + 150 282.69922 -6844.8106 472.2939 -4684.6433 7274.1665 1.0184736 + 200 283.07925 -7183.2915 1096.3999 -4396.7493 -18428.465 1.0184431 + 250 283.61722 -6327.2943 475.82271 -4158.1172 23020.286 1.0107938 + 300 301.71789 -6811.4188 1004.2807 -4005.7126 -14017.258 0.99889097 + 350 311.03337 -6506.7477 765.85039 -3883.8531 763.04925 0.98860598 + 400 317.775 -6392.1118 666.55754 -3828.2587 7828.8386 0.98148763 + 450 303.51186 -6657.5211 1017.7742 -3827.6103 -12704.511 0.97662555 + 500 296.45297 -6312.4144 719.53961 -3822.8838 8469.2935 0.97646495 +Loop time of 10.8893 on 2 procs for 500 steps with 2004 atoms + +Performance: 7.934 ns/day, 3.025 hours/ns, 45.917 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.7295 | 7.7574 | 7.7852 | 1.0 | 71.24 +Bond | 0.088436 | 0.089395 | 0.090353 | 0.3 | 0.82 +Kspace | 1.1269 | 1.16 | 1.1931 | 3.1 | 10.65 +Neigh | 1.2353 | 1.2377 | 1.2402 | 0.2 | 11.37 +Comm | 0.21436 | 0.23339 | 0.25242 | 3.9 | 2.14 +Output | 0.00055766 | 0.00056684 | 0.00057602 | 0.0 | 0.01 +Modify | 0.34907 | 0.37832 | 0.40758 | 4.8 | 3.47 +Other | | 0.03245 | | | 0.30 + +Nlocal: 1002 ave 1007 max 997 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8685.5 ave 8750 max 8621 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 350698 ave 351936 max 349459 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 701395 +Ave neighs/atom = 349.998 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 50 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 305 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268487 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0230158 + estimated relative force accuracy = 6.93113e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 296.45297 -6312.4159 719.53961 -3822.8853 8469.2763 0.97646495 + 550 303.89646 -6501.1353 863.14038 -3823.5621 -2928.2904 0.98030197 + 600 309.76597 -6524.1714 843.08835 -3831.606 -871.10399 0.98376234 + 650 299.00298 -6442.6354 805.96883 -3851.4506 3266.5866 0.98567102 + 700 309.92953 -6599.5125 902.18135 -3846.8775 -4895.7743 0.9877618 + 750 310.03453 -6432.9154 800.77648 -3781.0583 4312.9432 0.98939465 + 800 313.79353 -6482.8645 876.10518 -3733.2354 459.73904 0.9883653 + 850 308.0727 -6473.4666 891.51665 -3742.5826 -1645.1499 0.9829221 + 900 312.68166 -6456.773 820.7786 -3769.109 2194.8957 0.97822936 + 950 305.94065 -6546.0017 902.97469 -3816.3892 -2693.7918 0.97584317 + 1000 298.40902 -6464.4155 886.05639 -3796.6893 592.46618 0.9764313 + 1050 308.71394 -6480.6485 854.83864 -3782.6139 843.67793 0.97834087 + 1100 309.34645 -6526.4283 897.66923 -3781.7868 -297.6956 0.98046791 + 1150 303.65216 -6540.534 858.53216 -3869.0276 623.45838 0.98196819 + 1200 298.33689 -6610.5403 897.10898 -3932.1923 -1107.1097 0.98263413 + 1250 302.10596 -6587.4254 875.62056 -3908.0623 1244.7382 0.98273784 + 1300 316.19456 -6618.7414 894.33747 -3836.5445 -1399.1921 0.98252654 + 1350 302.28789 -6625.1555 938.19878 -3882.1279 -57.818071 0.98275084 + 1400 301.42717 -6602.0706 858.72022 -3943.6606 1462.1175 0.97898596 + 1450 299.43442 -6655.6584 893.68574 -3974.1807 383.13882 0.97462948 + 1500 301.76848 -6653.4568 896.33172 -3955.3975 -756.22375 0.96978565 + 1550 310.10887 -6664.8547 953.35222 -3859.9781 -1305.0786 0.96689812 + 1600 297.16621 -6510.7805 907.3012 -3829.2299 992.41943 0.96413868 + 1650 295.71413 -6598.1621 990.18935 -3842.3931 -2049.7934 0.96131396 + 1700 303.88264 -6629.5417 931.13321 -3884.0582 -630.7683 0.96321179 + 1750 300.85941 -6666.8007 941.42895 -3929.0719 357.85887 0.96822524 + 1800 299.34518 -6674.9694 932.15075 -3955.5595 -914.97614 0.97074982 + 1850 298.12166 -6610.2338 910.63353 -3919.6462 1390.5062 0.97402953 + 1900 307.86527 -6647.8711 931.49082 -3878.2514 -1629.6931 0.97542316 + 1950 305.04604 -6616.6069 937.35845 -3857.952 858.37861 0.97770539 + 2000 305.41215 -6597.2293 916.75863 -3856.9883 763.6265 0.98001111 + 2050 294.66502 -6632.9068 1035.729 -3837.8618 -2248.1496 0.98430681 + 2100 300.5948 -6569.1213 956.22884 -3818.1724 291.3677 0.99188971 + 2150 305.73836 -6623.7387 1021.1569 -3777.1519 -603.41468 1.0003649 + 2200 316.63308 -6681.0402 972.23429 -3818.3283 948.97143 1.0073383 + 2250 306.36381 -6653.5361 947.42424 -3876.9476 900.19264 1.010245 + 2300 301.9961 -6699.2583 1022.4799 -3873.6918 -499.39887 1.0119712 + 2350 307.25098 -6642.8345 970.32723 -3838.0461 366.40507 1.0118686 + 2400 311.79941 -6675.2645 1030.8811 -3782.7656 -1083.5459 1.0113601 + 2450 309.31064 -6630.1585 958.35981 -3825.0401 471.39091 1.0099697 + 2500 301.87691 -6689.2603 967.59935 -3919.2859 -854.45149 1.0097679 +Loop time of 46.7431 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.394 ns/day, 3.246 hours/ns, 42.787 timesteps/s +99.4% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 31.029 | 31.472 | 31.916 | 7.9 | 67.33 +Bond | 0.36154 | 0.36249 | 0.36343 | 0.2 | 0.78 +Kspace | 4.7001 | 5.1269 | 5.5536 | 18.8 | 10.97 +Neigh | 5.311 | 5.3205 | 5.33 | 0.4 | 11.38 +Comm | 0.86766 | 0.94238 | 1.0171 | 7.7 | 2.02 +Output | 0.0022194 | 0.0022837 | 0.0023479 | 0.1 | 0.00 +Modify | 1.4059 | 1.5219 | 1.638 | 9.4 | 3.26 +Other | | 1.994 | | | 4.27 + +Nlocal: 1002 ave 1012 max 992 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8807.5 ave 8818 max 8797 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 363096 ave 369482 max 356711 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 726193 +Ave neighs/atom = 362.372 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 207 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7 b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7 new file mode 100644 index 000000000..b6757e1f1 --- /dev/null +++ b/examples/USER/misc/temper_npt/log.temper_npt-17Aug17.g++.8.7 @@ -0,0 +1,211 @@ +LAMMPS (17 Aug 2017) +Processor partition = 7 + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide +# Demonstrating temper/npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 310 ${temper_T} 100.0 iso 1 1 1000 +fix myfix all npt temp 310 310 100.0 iso 1 1 1000 +run 500 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 0 190.0857 -6442.768 70.391457 -5237.4579 20361.998 0.98480122 + 50 224.5362 -7670.5503 1225.9519 -5103.9909 -23918.514 0.99480995 + 100 261.00419 -6946.2961 483.78483 -4904.1694 12827.309 1.0097087 + 150 284.14624 -6832.0094 472.66187 -4662.8346 7354.8252 1.0180355 + 200 284.05862 -7160.8537 1102.3553 -4362.5087 -18524.276 1.0178951 + 250 290.82577 -6319.5357 471.77841 -4111.3638 22989.86 1.0099523 + 300 306.50487 -6809.5465 1015.3715 -3964.1684 -13215.763 0.99625687 + 350 319.20654 -6502.4307 761.98704 -3834.601 -965.94424 0.98284646 + 400 316.81299 -6295.1539 646.79195 -3756.8102 8469.8917 0.97675631 + 450 312.90373 -6639.6427 1048.7063 -3722.7251 -13014.646 0.97486033 + 500 319.55848 -6335.5865 712.00927 -3715.6334 9980.2286 0.97468964 +Loop time of 10.7877 on 2 procs for 500 steps with 2004 atoms + +Performance: 8.009 ns/day, 2.997 hours/ns, 46.349 timesteps/s +99.1% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 7.6698 | 7.7211 | 7.7724 | 1.8 | 71.57 +Bond | 0.085352 | 0.086755 | 0.088159 | 0.5 | 0.80 +Kspace | 1.089 | 1.1417 | 1.1944 | 4.9 | 10.58 +Neigh | 1.2554 | 1.2554 | 1.2554 | 0.0 | 11.64 +Comm | 0.16438 | 0.17539 | 0.1864 | 2.6 | 1.63 +Output | 0.00045967 | 0.0004642 | 0.00046873 | 0.0 | 0.00 +Modify | 0.35006 | 0.37517 | 0.40028 | 4.1 | 3.48 +Other | | 0.0317 | | | 0.29 + +Nlocal: 1002 ave 1004 max 1000 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8709.5 ave 8714 max 8705 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 350398 ave 352725 max 348070 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 700795 +Ave neighs/atom = 349.698 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 51 +Dangerous builds = 0 +temper/npt 2000 100 ${temper_T} myfix 0 58728 1 +temper/npt 2000 100 310 myfix 0 58728 1 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268436 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0230577 + estimated relative force accuracy = 6.94376e-05 + using double precision FFTs + 3d grid and FFT values/proc = 6776 1800 +Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.95 | 15.96 Mbytes +Step Temp E_pair E_mol TotEng Press Density + 500 319.55848 -6335.5878 712.00927 -3715.6347 9980.2224 0.97468964 + 550 312.3068 -6517.9692 882.51888 -3770.8031 -4737.1103 0.97368346 + 600 306.74828 -6500.9408 860.97959 -3808.5014 -1687.6369 0.97333001 + 650 309.25363 -6453.3615 753.23233 -3853.711 4484.0534 0.97330212 + 700 305.22336 -6644.7434 922.38867 -3899.9996 -5823.8028 0.97262421 + 750 297.24363 -6480.4086 771.41874 -3934.2782 5025.8889 0.97337406 + 800 300.89643 -6587.4079 835.06282 -3955.8242 -1517.9426 0.97460241 + 850 305.43206 -6685.1173 846.71999 -4014.7961 -1788.398 0.97836973 + 900 289.95008 -6574.8681 806.12799 -4037.575 2604.847 0.98232784 + 950 299.22424 -6671.7556 898.72395 -3986.4946 -2702.719 0.98919804 + 1000 305.3932 -6576.089 826.21317 -3926.5066 2254.7456 0.99471125 + 1050 304.62574 -6619.698 893.18161 -3907.7293 -1010.7916 0.99551385 + 1100 304.13778 -6603.0961 846.91376 -3940.3087 -211.63132 0.99359493 + 1150 285.80722 -6557.1116 859.12907 -3991.5526 1777.6534 0.99165538 + 1200 295.20871 -6612.8101 855.05738 -3995.1906 -389.55216 0.98957199 + 1250 301.4547 -6623.3355 907.78288 -3915.6984 1193.6428 0.98887879 + 1300 302.29836 -6545.5769 862.86619 -3877.8194 443.76145 0.9853829 + 1350 309.29624 -6539.3158 878.22476 -3814.4185 -769.46378 0.98002173 + 1400 311.28962 -6582.4295 939.53596 -3784.3195 -239.11773 0.97952655 + 1450 307.46833 -6597.7591 922.88062 -3839.1196 453.60414 0.98288752 + 1500 308.8234 -6660.3138 910.39719 -3906.0672 356.0472 0.98507945 + 1550 297.42322 -6596.3955 938.61921 -3881.9924 -883.10576 0.98730686 + 1600 309.492 -6649.4174 963.57197 -3838.0041 470.91335 0.99194955 + 1650 309.46921 -6602.6445 958.19972 -3796.7395 1417.6814 0.99437216 + 1700 308.27043 -6575.0156 941.02926 -3793.4384 -445.78985 0.99171728 + 1750 306.31262 -6515.703 929.60371 -3757.2406 944.20045 0.98661702 + 1800 308.63008 -6484.7465 959.53268 -3682.5186 333.02755 0.98504191 + 1850 316.69569 -6520.4677 975.02618 -3654.5901 -835.64735 0.98329409 + 1900 316.03266 -6531.6456 948.03331 -3696.7196 -745.03047 0.98236945 + 1950 308.97313 -6562.2733 955.48033 -3762.0496 -1147.5825 0.983921 + 2000 305.67836 -6611.4675 991.3364 -3795.0594 -2361.1127 0.98852677 + 2050 312.66709 -6687.3067 980.96042 -3839.5479 -244.80211 0.99714887 + 2100 307.23751 -6664.4853 963.74125 -3866.3633 268.84485 1.0050595 + 2150 296.36081 -6633.5455 966.74219 -3897.3626 -741.15958 1.0135557 + 2200 306.79331 -6709.7668 989.09713 -3888.9411 -108.31295 1.0211476 + 2250 310.62715 -6713.5021 973.14019 -3885.7431 1576.0539 1.0235204 + 2300 304.34901 -6675.1811 1001.4509 -3856.5955 -481.96378 1.0180933 + 2350 300.55584 -6592.7909 993.96783 -3804.3356 114.74351 1.0116595 + 2400 307.16641 -6626.7049 984.70783 -3808.0408 620.2875 1.0087872 + 2450 301.62279 -6643.7063 978.76012 -3864.0884 72.614095 1.0085247 + 2500 307.17634 -6691.4794 975.63125 -3881.8326 495.45555 1.0099428 +Loop time of 46.7465 on 2 procs for 2000 steps with 2004 atoms + +Performance: 7.393 ns/day, 3.246 hours/ns, 42.784 timesteps/s +99.1% CPU use with 2 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 31.19 | 31.703 | 32.216 | 9.1 | 67.82 +Bond | 0.35397 | 0.35463 | 0.35528 | 0.1 | 0.76 +Kspace | 4.3783 | 4.8922 | 5.4062 | 23.2 | 10.47 +Neigh | 5.2885 | 5.2889 | 5.2893 | 0.0 | 11.31 +Comm | 0.67571 | 0.71687 | 0.75803 | 4.9 | 1.53 +Output | 0.0019109 | 0.0019529 | 0.0019948 | 0.1 | 0.00 +Modify | 1.4216 | 1.5185 | 1.6154 | 7.9 | 3.25 +Other | | 2.271 | | | 4.86 + +Nlocal: 1002 ave 1010 max 994 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Nghost: 8811.5 ave 8832 max 8791 min +Histogram: 1 0 0 0 0 0 0 0 0 1 +Neighs: 363080 ave 367967 max 358193 min +Histogram: 1 0 0 0 0 0 0 0 0 1 + +Total # of neighbors = 726160 +Ave neighs/atom = 362.355 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 207 +Dangerous builds = 0 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 + 19 = # of size 2 clusters + 6 = # of size 3 clusters + 3 = # of size 4 clusters + 640 = # of frozen angles +group peptide type <= 12 +84 atoms in group peptide +Total wall time: 0:00:58 diff --git a/src/.gitignore b/src/.gitignore index 5513386b1..a5d6773c5 100644 --- a/src/.gitignore +++ b/src/.gitignore @@ -1,1114 +1,1116 @@ /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 /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_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 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/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_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 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/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 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/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/REPLICA/data.peptide b/src/REPLICA/data.peptide new file mode 100644 index 000000000..f9dfb6e48 --- /dev/null +++ b/src/REPLICA/data.peptide @@ -0,0 +1,6531 @@ +LAMMPS Description + + 2004 atoms + 1365 bonds + 786 angles + 207 dihedrals + 12 impropers + + 14 atom types + 18 bond types + 31 angle types + 21 dihedral types + 2 improper types + + 36.840194 64.211560 xlo xhi + 41.013691 68.385058 ylo yhi + 29.768095 57.139462 zlo zhi + +Masses + + 1 12.0110 + 2 12.0110 + 3 15.9990 + 4 1.0080 + 5 14.0070 + 6 12.0110 + 7 12.0110 + 8 12.0110 + 9 15.9990 + 10 1.0080 + 11 1.0080 + 12 32.0660 + 13 16.0000 + 14 1.0100 + +Pair Coeffs + + 1 0.110000 3.563595 0.110000 3.563595 + 2 0.080000 3.670503 0.010000 3.385415 + 3 0.120000 3.029056 0.120000 2.494516 + 4 0.022000 2.351973 0.022000 2.351973 + 5 0.200000 3.296325 0.200000 2.761786 + 6 0.020000 4.053589 0.010000 3.385415 + 7 0.055000 3.875410 0.010000 3.385415 + 8 0.070000 3.550053 0.070000 3.550053 + 9 0.152100 3.153782 0.152100 3.153782 + 10 0.046000 0.400014 0.046000 0.400014 + 11 0.030000 2.420037 0.030000 2.420037 + 12 0.450000 3.563595 0.450000 3.563595 + 13 0.152100 3.150570 0.152100 3.150570 + 14 0.046000 0.400014 0.046000 0.400014 + +Bond Coeffs + + 1 249.999999 1.490000 + 2 620.000001 1.230000 + 3 370.000000 1.345000 + 4 322.000001 1.111000 + 5 319.999999 1.430000 + 6 440.000000 0.997000 + 7 222.500001 1.538000 + 8 330.000001 1.080000 + 9 230.000000 1.490000 + 10 309.000001 1.111000 + 11 305.000000 1.375000 + 12 340.000001 1.080000 + 13 334.300000 1.411000 + 14 545.000001 0.960000 + 15 222.500001 1.530000 + 16 198.000000 1.818000 + 17 239.999999 1.816000 + 18 450.000000 0.957200 + +Angle Coeffs + + 1 33.000000 109.500000 30.000000 2.163000 + 2 50.000000 120.000000 0.000000 0.000000 + 3 34.000000 123.000000 0.000000 0.000000 + 4 80.000000 121.000000 0.000000 0.000000 + 5 80.000000 116.500000 0.000000 0.000000 + 6 80.000000 122.500000 0.000000 0.000000 + 7 35.500000 108.400000 5.400000 1.802000 + 8 50.000000 107.000000 0.000000 0.000000 + 9 70.000000 113.500000 0.000000 0.000000 + 10 48.000000 108.000000 0.000000 0.000000 + 11 35.000000 117.000000 0.000000 0.000000 + 12 51.800000 107.500000 0.000000 0.000000 + 13 33.430000 110.100000 22.530000 2.179000 + 14 52.000000 108.000000 0.000000 0.000000 + 15 50.000000 109.500000 0.000000 0.000000 + 16 35.000000 111.000000 0.000000 0.000000 + 17 45.800000 122.300000 0.000000 0.000000 + 18 49.300000 107.500000 0.000000 0.000000 + 19 40.000000 120.000000 35.000000 2.416200 + 20 30.000000 120.000000 22.000000 2.152500 + 21 45.200000 120.000000 0.000000 0.000000 + 22 65.000000 108.000000 0.000000 0.000000 + 23 35.500000 109.000000 5.400000 1.802000 + 24 36.000000 115.000000 0.000000 0.000000 + 25 58.350000 113.500000 11.160000 2.561000 + 26 58.000000 114.500000 0.000000 0.000000 + 27 26.500000 110.100000 22.530000 2.179000 + 28 34.000000 95.000000 0.000000 0.000000 + 29 46.100000 111.300000 0.000000 0.000000 + 30 51.500000 109.500000 0.000000 0.000000 + 31 55.000000 104.520000 0.000000 0.000000 + +Dihedral Coeffs + + 1 0.200000 1 180 1.000000 + 2 1.800000 1 0 1.000000 + 3 0.000000 1 0 1.000000 + 4 1.600000 1 0 0.500000 + 5 2.500000 2 180 0.500000 + 6 2.500000 2 180 1.000000 + 7 0.600000 1 0 1.000000 + 8 0.200000 3 0 1.000000 + 9 0.230000 2 180 1.000000 + 10 0.040000 3 0 1.000000 + 11 1.400000 1 0 1.000000 + 12 3.100000 2 180 1.000000 + 13 4.200000 2 180 1.000000 + 14 3.100000 2 180 0.500000 + 15 0.990000 2 180 1.000000 + 16 2.400000 2 180 1.000000 + 17 0.195000 3 0 1.000000 + 18 0.240000 1 180 0.500000 + 19 0.370000 3 0 0.500000 + 20 0.280000 3 0 1.000000 + 21 0.010000 3 0 1.000000 + +Improper Coeffs + + 1 120.000000 0.000000 + 2 20.000000 0.000000 + +Atoms + + 1 1 1 0.510 43.99993 58.52678 36.78550 0 0 0 + 2 1 2 -0.270 45.10395 58.23499 35.86693 0 0 0 + 3 1 3 -0.510 43.81519 59.54928 37.43995 0 0 0 + 4 1 4 0.090 45.71714 57.34797 36.13434 0 0 0 + 5 1 4 0.090 45.72261 59.13657 35.67007 0 0 0 + 6 1 4 0.090 44.66624 58.09539 34.85538 0 0 0 + 7 1 5 -0.470 43.28193 57.47427 36.91953 0 0 0 + 8 1 6 0.070 42.07157 57.45486 37.62418 0 0 0 + 9 1 1 0.510 42.19985 57.57789 39.12163 0 0 0 + 10 1 3 -0.510 41.88641 58.62251 39.70398 0 0 0 + 11 1 7 -0.180 41.25052 56.15304 37.41811 0 0 0 + 12 1 8 0.000 40.88511 55.94638 35.97460 0 0 0 + 13 1 8 -0.115 41.48305 54.96372 35.11223 0 0 0 + 14 1 8 -0.115 39.74003 56.60996 35.46443 0 0 0 + 15 1 8 -0.115 41.02111 54.75715 33.80764 0 0 0 + 16 1 8 -0.115 39.26180 56.39194 34.12024 0 0 0 + 17 1 8 0.110 39.92330 55.46092 33.27135 0 0 0 + 18 1 9 -0.540 39.48164 55.22919 31.91865 0 0 0 + 19 1 10 0.310 43.60633 56.61693 36.52744 0 0 0 + 20 1 4 0.090 41.49619 58.31145 37.30543 0 0 0 + 21 1 4 0.090 41.88498 55.29476 37.72657 0 0 0 + 22 1 4 0.090 40.30899 56.19690 38.00627 0 0 0 + 23 1 11 0.115 42.31528 54.36176 35.44606 0 0 0 + 24 1 11 0.115 39.26330 57.31216 36.13230 0 0 0 + 25 1 11 0.115 41.62695 54.10606 33.19490 0 0 0 + 26 1 11 0.115 38.42147 56.98236 33.78612 0 0 0 + 27 1 10 0.430 38.78233 55.86217 31.74004 0 0 0 + 28 1 5 -0.470 42.79933 56.56370 39.79000 0 0 0 + 29 1 7 -0.020 42.96709 56.75379 41.28116 0 0 0 + 30 1 1 0.510 43.83019 55.68988 41.92255 0 0 0 + 31 1 3 -0.510 44.98521 55.93104 42.21713 0 0 0 + 32 1 10 0.310 43.13466 55.75696 39.30966 0 0 0 + 33 1 4 0.090 42.04692 56.86721 41.83507 0 0 0 + 34 1 4 0.090 43.52938 57.66324 41.43329 0 0 0 + 35 1 5 -0.470 43.26792 54.43342 42.07043 0 0 0 + 36 1 7 -0.020 43.92411 53.28930 42.63327 0 0 0 + 37 1 1 0.510 43.51012 53.02289 44.10510 0 0 0 + 38 1 3 -0.510 42.35086 53.07863 44.50806 0 0 0 + 39 1 10 0.310 42.28859 54.34993 41.90323 0 0 0 + 40 1 4 0.090 44.98464 53.47473 42.54797 0 0 0 + 41 1 4 0.090 43.49715 52.54787 41.97419 0 0 0 + 42 1 5 -0.470 44.51925 52.64535 44.88133 0 0 0 + 43 1 6 0.070 44.47588 52.35054 46.24397 0 0 0 + 44 1 1 0.510 45.40218 53.34579 46.94730 0 0 0 + 45 1 3 -0.510 45.23520 54.55893 46.92038 0 0 0 + 46 1 7 -0.180 44.77960 50.82831 46.50232 0 0 0 + 47 1 8 0.000 43.72184 49.84551 45.98093 0 0 0 + 48 1 8 -0.115 44.14810 49.00477 44.97195 0 0 0 + 49 1 8 -0.115 42.43499 49.66652 46.53541 0 0 0 + 50 1 8 -0.115 43.26154 48.00434 44.46769 0 0 0 + 51 1 8 -0.115 41.54732 48.79670 45.95416 0 0 0 + 52 1 8 -0.115 41.98220 47.90746 44.95574 0 0 0 + 53 1 10 0.310 45.39510 52.50937 44.42482 0 0 0 + 54 1 4 0.090 43.51312 52.58974 46.67092 0 0 0 + 55 1 4 0.090 44.89709 50.54313 47.56965 0 0 0 + 56 1 4 0.090 45.72096 50.49337 46.01654 0 0 0 + 57 1 11 0.115 45.13573 49.07933 44.54134 0 0 0 + 58 1 11 0.115 42.07869 50.34816 47.29358 0 0 0 + 59 1 11 0.115 43.47793 47.29281 43.68456 0 0 0 + 60 1 11 0.115 40.52625 48.76134 46.30425 0 0 0 + 61 1 11 0.115 41.35446 47.13287 44.54059 0 0 0 + 62 1 5 -0.470 46.41448 52.86278 47.68291 0 0 0 + 63 1 6 0.070 47.25136 53.68184 48.51163 0 0 0 + 64 1 1 0.510 48.33905 54.40097 47.73886 0 0 0 + 65 1 3 -0.510 49.27132 53.85220 47.16549 0 0 0 + 66 1 7 -0.180 47.88329 52.75681 49.60227 0 0 0 + 67 1 7 -0.140 48.82515 53.51102 50.61578 0 0 0 + 68 1 12 -0.090 48.12492 55.00373 51.43039 0 0 0 + 69 1 2 -0.220 47.70783 54.12980 53.04072 0 0 0 + 70 1 10 0.310 46.67199 51.90088 47.73231 0 0 0 + 71 1 4 0.090 46.64593 54.43552 48.99310 0 0 0 + 72 1 4 0.090 48.41361 51.90817 49.11968 0 0 0 + 73 1 4 0.090 47.08748 52.35196 50.26341 0 0 0 + 74 1 4 0.090 49.16067 52.81305 51.41238 0 0 0 + 75 1 4 0.090 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79 80 83 + 203 3 81 79 80 84 + 204 3 64 79 80 84 + 205 3 81 79 80 82 + 206 3 64 79 80 83 + 207 3 64 79 80 82 + +Impropers + + 1 2 7 1 8 19 + 2 1 1 2 7 3 + 3 1 9 8 28 10 + 4 2 28 9 29 32 + 5 1 30 29 35 31 + 6 2 35 30 36 39 + 7 1 37 36 42 38 + 8 2 42 37 43 53 + 9 1 44 43 62 45 + 10 2 62 44 63 70 + 11 1 64 63 79 65 + 12 2 79 64 80 81 diff --git a/src/REPLICA/in.temper_npt b/src/REPLICA/in.temper_npt new file mode 100644 index 000000000..40db3c960 --- /dev/null +++ b/src/REPLICA/in.temper_npt @@ -0,0 +1,32 @@ +# Solvated 5-mer peptide +# Demonstrating temper_npt +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + +neighbor 2.0 bin +neigh_modify delay 5 + +timestep 2.0 + +thermo_style custom step temp epair emol etotal press density +thermo 50 + +variable temper_T world 275 280 285 290 295 300 305 310 +variable rep world 0 1 2 3 4 5 6 7 +fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000 +run 500 +temper_npt 2000 100 ${temper_T} myfix 0 58728 1 +fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31 +group peptide type <= 12 + + + diff --git a/src/REPLICA/temper_npt.cpp b/src/REPLICA/temper_npt.cpp new file mode 100644 index 000000000..a043c6140 --- /dev/null +++ b/src/REPLICA/temper_npt.cpp @@ -0,0 +1,381 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing Authors: Amulya K. Pervaje and Cody K. Addington + Contact Email: amulyapervaje@gmail.com + temper_npt is a modification of temper that is applicable to the NPT ensemble + uses the npt acceptance criteria for parallel tempering (replica exchange) as given in + Mori, Y .; Okamoto, Y . Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble. J. Phys. Soc. Japan 2010, 79, 74003. + + temper_npt N M temp fix-ID seed1 seed2 pressure index(optional) + refer to documentation for temper, only difference with temper_npt is that the pressure is specified as the 7th argument, the 8th argument is the same optional index argument used in temper +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "temper_npt.h" +#include "universe.h" +#include "domain.h" +#include "atom.h" +#include "update.h" +#include "integrate.h" +#include "modify.h" +#include "compute.h" +#include "force.h" +#include "output.h" +#include "thermo.h" +#include "fix.h" +#include "random_park.h" +#include "finish.h" +#include "timer.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define TEMPER_DEBUG 0 + +/* ---------------------------------------------------------------------- */ + +TemperNpt::TemperNpt(LAMMPS *lmp) : Pointers(lmp) {} + +/* ---------------------------------------------------------------------- */ + +TemperNpt::~TemperNpt() +{ + MPI_Comm_free(&roots); + if (ranswap) delete ranswap; + delete ranboltz; + delete [] set_temp; + delete [] temp2world; + delete [] world2temp; + delete [] world2root; +} + +/* ---------------------------------------------------------------------- + perform tempering with inter-world swaps +------------------------------------------------------------------------- */ + +void TemperNpt::command(int narg, char **arg) +{ + if (universe->nworlds == 1) + error->all(FLERR,"Must have more than one processor partition to temper"); + if (domain->box_exist == 0) + error->all(FLERR,"temper_npt command before simulation box is defined"); + if (narg != 7 && narg != 8) + error->universe_all(FLERR,"Illegal temper command"); + + int nsteps = force->inumeric(FLERR,arg[0]); + nevery = force->inumeric(FLERR,arg[1]); + double temp = force->numeric(FLERR,arg[2]); + double press_set = force->numeric(FLERR,arg[6]); + + for (whichfix = 0; whichfix < modify->nfix; whichfix++) + if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break; + if (whichfix == modify->nfix) + error->universe_all(FLERR,"Tempering fix ID is not defined"); + + seed_swap = force->inumeric(FLERR,arg[4]); + seed_boltz = force->inumeric(FLERR,arg[5]); + + my_set_temp = universe->iworld; + if (narg == 8) my_set_temp = force->inumeric(FLERR,arg[6]); + + // swap frequency must evenly divide total # of timesteps + + if (nevery <= 0) + error->universe_all(FLERR,"Invalid frequency in temper command"); + nswaps = nsteps/nevery; + if (nswaps*nevery != nsteps) + error->universe_all(FLERR,"Non integer # of swaps in temper command"); + + // fix style must be appropriate for temperature control, i.e. it needs + // to provide a working Fix::reset_target() and must not change the volume. + + if ((strcmp(modify->fix[whichfix]->style,"npt") != 0)) error->universe_all(FLERR,"Tempering temperature fix is not supported"); + + // setup for long tempering run + + update->whichflag = 1; + update->nsteps = nsteps; + update->beginstep = update->firststep = update->ntimestep; + update->endstep = update->laststep = update->firststep + nsteps; + if (update->laststep < 0) + error->all(FLERR,"Too many timesteps"); + + lmp->init(); + + // local storage + + me_universe = universe->me; + MPI_Comm_rank(world,&me); + nworlds = universe->nworlds; + iworld = universe->iworld; + boltz = force->boltz; + nktv2p = force->nktv2p; + + // pe_compute = ptr to thermo_pe compute + // notify compute it will be called at first swap + + int id = modify->find_compute("thermo_pe"); + if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute"); + Compute *pe_compute = modify->compute[id]; + pe_compute->addstep(update->ntimestep + nevery); + + // create MPI communicator for root proc from each world + + int color; + if (me == 0) color = 0; + else color = 1; + MPI_Comm_split(universe->uworld,color,0,&roots); + + // RNGs for swaps and Boltzmann test + // warm up Boltzmann RNG + + if (seed_swap) ranswap = new RanPark(lmp,seed_swap); + else ranswap = NULL; + ranboltz = new RanPark(lmp,seed_boltz + me_universe); + for (int i = 0; i < 100; i++) ranboltz->uniform(); + + // world2root[i] = global proc that is root proc of world i + + world2root = new int[nworlds]; + if (me == 0) + MPI_Allgather(&me_universe,1,MPI_INT,world2root,1,MPI_INT,roots); + MPI_Bcast(world2root,nworlds,MPI_INT,0,world); + + // create static list of set temperatures + // allgather tempering arg "temp" across root procs + // bcast from each root to other procs in world + + set_temp = new double[nworlds]; + if (me == 0) MPI_Allgather(&temp,1,MPI_DOUBLE,set_temp,1,MPI_DOUBLE,roots); + MPI_Bcast(set_temp,nworlds,MPI_DOUBLE,0,world); + + // create world2temp only on root procs from my_set_temp + // create temp2world on root procs from world2temp, + // then bcast to all procs within world + + world2temp = new int[nworlds]; + temp2world = new int[nworlds]; + if (me == 0) { + MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots); + for (int i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i; + } + MPI_Bcast(temp2world,nworlds,MPI_INT,0,world); + + // if restarting tempering, reset temp target of Fix to current my_set_temp + + if (narg == 8) { + double new_temp = set_temp[my_set_temp]; + modify->fix[whichfix]->reset_target(new_temp); + } + + // setup tempering runs + + int i,which,partner,swap,partner_set_temp,partner_world; + double pe,pe_partner, delr,boltz_factor,new_temp, press_units; + + if (me_universe == 0 && universe->uscreen) + fprintf(universe->uscreen,"Setting up tempering ...\n"); + + update->integrate->setup(); + + if (me_universe == 0) { + if (universe->uscreen) { + fprintf(universe->uscreen,"Step"); + for (int i = 0; i < nworlds; i++) + fprintf(universe->uscreen," T%d",i); + fprintf(universe->uscreen,"\n"); + } + if (universe->ulogfile) { + fprintf(universe->ulogfile,"Step"); + for (int i = 0; i < nworlds; i++) + fprintf(universe->ulogfile," T%d",i); + fprintf(universe->ulogfile,"\n"); + } + print_status(); + } + + timer->init(); + timer->barrier_start(); + + for (int iswap = 0; iswap < nswaps; iswap++) { + + // run for nevery timesteps + + update->integrate->run(nevery); + + // compute PE + // notify compute it will be called at next swap + + pe = pe_compute->compute_scalar(); + pe_compute->addstep(update->ntimestep + nevery); + double boxlox=domain->boxlo[0]; + double boxhix=domain->boxhi[0]; + double boxloy=domain->boxlo[1]; + double boxhiy=domain->boxhi[1]; + double boxloz=domain->boxlo[2]; + double boxhiz=domain->boxhi[2]; + double vol = (boxhix - boxlox)*(boxhiy - boxloy)*(boxhiz - boxloz); + double vol_partner = vol; + // which = which of 2 kinds of swaps to do (0,1) + + if (!ranswap) which = iswap % 2; + else if (ranswap->uniform() < 0.5) which = 0; + else which = 1; + + // partner_set_temp = which set temp I am partnering with for this swap + + if (which == 0) { + if (my_set_temp % 2 == 0) partner_set_temp = my_set_temp + 1; + else partner_set_temp = my_set_temp - 1; + } else { + if (my_set_temp % 2 == 1) partner_set_temp = my_set_temp + 1; + else partner_set_temp = my_set_temp - 1; + } + + // partner = proc ID to swap with + // if partner = -1, then I am not a proc that swaps + + partner = -1; + if (me == 0 && partner_set_temp >= 0 && partner_set_temp < nworlds) { + partner_world = temp2world[partner_set_temp]; + partner = world2root[partner_world]; + } + + // swap with a partner, only root procs in each world participate + // hi proc sends PE to low proc + // lo proc make Boltzmann decision on whether to swap + // lo proc communicates decision back to hi proc + + swap = 0; + if (partner != -1) { + if (me_universe > partner) { + MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld); + } + else { + MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE); + } + if (me_universe > partner) { + MPI_Send(&vol,1, MPI_DOUBLE,partner,0,universe->uworld); + } + else { + MPI_Recv(&vol_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE); + } + // Acceptance criteria changed for NPT ensemble + if (me_universe < partner) { + press_units = press_set/nktv2p; + delr = (pe_partner - pe)*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp])) + press_units*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp]))*(vol_partner - vol); + boltz_factor = -delr; + if (boltz_factor >= 0.0) swap = 1; + else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1; + } + + if (me_universe < partner) + MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld); + else + MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE); +#ifdef TEMPER_DEBUG + if (me_universe < partner) + fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g, vol = %g %g\n", + me_universe,partner,swap,my_set_temp,partner_set_temp, + pe,pe_partner,boltz_factor,exp(boltz_factor), vol, vol_partner); +#endif + + } + + // bcast swap result to other procs in my world + + MPI_Bcast(&swap,1,MPI_INT,0,world); + + // rescale kinetic energy via velocities if move is accepted + + if (swap) scale_velocities(partner_set_temp,my_set_temp); + + // if my world swapped, all procs in world reset temp target of Fix + + if (swap) { + new_temp = set_temp[partner_set_temp]; + modify->fix[whichfix]->reset_target(new_temp); + } + + // update my_set_temp and temp2world on every proc + // root procs update their value if swap took place + // allgather across root procs + // bcast within my world + + if (swap) my_set_temp = partner_set_temp; + if (me == 0) { + MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots); + for (i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i; + } + MPI_Bcast(temp2world,nworlds,MPI_INT,0,world); + + // print out current swap status + + if (me_universe == 0) print_status(); + } + + timer->barrier_stop(); + + update->integrate->cleanup(); + + Finish finish(lmp); + finish.end(1); + + update->whichflag = 0; + update->firststep = update->laststep = 0; + update->beginstep = update->endstep = 0; +} + +/* ---------------------------------------------------------------------- + scale kinetic energy via velocities a la Sugita +------------------------------------------------------------------------- */ + +void TemperNpt::scale_velocities(int t_partner, int t_me) +{ + double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]); + + double **v = atom->v; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + v[i][0] = v[i][0]*sfactor; + v[i][1] = v[i][1]*sfactor; + v[i][2] = v[i][2]*sfactor; + } +} + +/* ---------------------------------------------------------------------- + proc 0 prints current tempering status +------------------------------------------------------------------------- */ + +void TemperNpt::print_status() +{ + if (universe->uscreen) { + fprintf(universe->uscreen,BIGINT_FORMAT,update->ntimestep); + for (int i = 0; i < nworlds; i++) + fprintf(universe->uscreen," %d",world2temp[i]); + fprintf(universe->uscreen,"\n"); + } + if (universe->ulogfile) { + fprintf(universe->ulogfile,BIGINT_FORMAT,update->ntimestep); + for (int i = 0; i < nworlds; i++) + fprintf(universe->ulogfile," %d",world2temp[i]); + fprintf(universe->ulogfile,"\n"); + fflush(universe->ulogfile); + } +} diff --git a/src/REPLICA/temper_npt.h b/src/REPLICA/temper_npt.h new file mode 100644 index 000000000..984f2839b --- /dev/null +++ b/src/REPLICA/temper_npt.h @@ -0,0 +1,118 @@ +/* -*- 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. + + Contributing Authors: Amulya K. Pervaje and Cody K. Addington + Contact Email: amulyapervaje@gmail.com + temper_npt is a modification of temper that is applicable to the NPT ensemble + uses the npt acceptance criteria for parallel tempering (replica exchange) as given in + Mori, Y .; Okamoto, Y . Generalized-Ensemble Algorithms for the Isobaric–Isothermal Ensemble. J. Phys. Soc. Japan 2010, 79, 74003. + + temper_npt N M temp fix-ID seed1 seed2 pressure index(optional) + refer to documentation for temper, only difference with temper_npt is that the pressure is s +pecified as the 7th argument, the 8th argument is the same optional index argument used in temp +er +------------------------------------------------------------------------- */ + +#ifdef COMMAND_CLASS + +CommandStyle(temper_npt,TemperNpt) + +#else + +#ifndef LMP_TEMPERNPT_H +#define LMP_TEMPERNPT_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class TemperNpt : protected Pointers { + public: + TemperNpt(class LAMMPS *); + ~TemperNpt(); + void command(int, char **); + + private: + int me,me_universe; // my proc ID in world and universe + int iworld,nworlds; // world info + double boltz; // copy from output->boltz + double nktv2p; + MPI_Comm roots; // MPI comm with 1 root proc from each world + class RanPark *ranswap,*ranboltz; // RNGs for swapping and Boltz factor + int nevery; // # of timesteps between swaps + int nswaps; // # of tempering swaps to perform + int seed_swap; // 0 = toggle swaps, n = RNG for swap direction + int seed_boltz; // seed for Boltz factor comparison + int whichfix; // index of temperature fix to use + int fixstyle; // what kind of temperature fix is used + + int my_set_temp; // which set temp I am simulating + double *set_temp; // static list of replica set temperatures + int *temp2world; // temp2world[i] = world simulating set temp i + int *world2temp; // world2temp[i] = temp simulated by world i + int *world2root; // world2root[i] = root proc of world i + + void scale_velocities(int, int); + void print_status(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Must have more than one processor partition to temper + +Cannot use the temper command with only one processor partition. Use +the -partition command-line option. + +E: TemperNpt command before simulation box is defined + +The temper command cannot be used before a read_data, read_restart, or +create_box command. + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Tempering fix ID is not defined + +The fix ID specified by the temper command does not exist. + +E: Invalid frequency in temper command + +Nevery must be > 0. + +E: Non integer # of swaps in temper command + +Swap frequency in temper command must evenly divide the total # of +timesteps. + +E: Tempering temperature fix is not valid + +The fix specified by the temper command is not one that controls +temperature (nvt or langevin). + +E: Too many timesteps + +The cummulative timesteps must fit in a 64-bit integer. + +E: Tempering could not find thermo_pe compute + +This compute is created by the thermo command. It must have been +explicitly deleted by a uncompute command. + +*/ diff --git a/src/USER-MISC/README b/src/USER-MISC/README index 2fd25df9b..65146abd5 100644 --- a/src/USER-MISC/README +++ b/src/USER-MISC/README @@ -1,76 +1,77 @@ 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 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/temper_npt.cpp b/src/USER-MISC/temper_npt.cpp new file mode 100644 index 000000000..572a52b1a --- /dev/null +++ b/src/USER-MISC/temper_npt.cpp @@ -0,0 +1,380 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, Sandia National Laboratories + Steve Plimpton, sjplimp@sandia.gov + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ---------------------------------------------------------------------- + Contributing Authors: Amulya K. Pervaje and Cody K. Addington, + (North Carolina State University) + Contact Email: amulyapervaje@gmail.com +------------------------------------------------------------------------- */ + +#include +#include +#include +#include "temper_npt.h" +#include "universe.h" +#include "domain.h" +#include "atom.h" +#include "update.h" +#include "integrate.h" +#include "modify.h" +#include "compute.h" +#include "force.h" +#include "output.h" +#include "thermo.h" +#include "fix.h" +#include "random_park.h" +#include "finish.h" +#include "timer.h" +#include "memory.h" +#include "error.h" + +using namespace LAMMPS_NS; + +#define TEMPER_DEBUG 0 + +/* ---------------------------------------------------------------------- */ + +TemperNPT::TemperNPT(LAMMPS *lmp) : Pointers(lmp) {} + +/* ---------------------------------------------------------------------- */ + +TemperNPT::~TemperNPT() +{ + MPI_Comm_free(&roots); + if (ranswap) delete ranswap; + delete ranboltz; + delete [] set_temp; + delete [] temp2world; + delete [] world2temp; + delete [] world2root; +} + +/* ---------------------------------------------------------------------- + perform tempering with inter-world swaps +------------------------------------------------------------------------- */ + +void TemperNPT::command(int narg, char **arg) +{ + if (universe->nworlds == 1) + error->all(FLERR,"Must have more than one processor partition to temper"); + if (domain->box_exist == 0) + error->all(FLERR,"temper/npt command before simulation box is defined"); + if (narg != 7 && narg != 8) + error->universe_all(FLERR,"Illegal temper/npt command"); + + int nsteps = force->inumeric(FLERR,arg[0]); + nevery = force->inumeric(FLERR,arg[1]); + double temp = force->numeric(FLERR,arg[2]); + double press_set = force->numeric(FLERR,arg[6]); + + for (whichfix = 0; whichfix < modify->nfix; whichfix++) + if (strcmp(arg[3],modify->fix[whichfix]->id) == 0) break; + if (whichfix == modify->nfix) + error->universe_all(FLERR,"Tempering fix ID is not defined"); + + seed_swap = force->inumeric(FLERR,arg[4]); + seed_boltz = force->inumeric(FLERR,arg[5]); + + my_set_temp = universe->iworld; + if (narg == 8) my_set_temp = force->inumeric(FLERR,arg[6]); + + // swap frequency must evenly divide total # of timesteps + + if (nevery <= 0) + error->universe_all(FLERR,"Invalid frequency in temper/npt command"); + nswaps = nsteps/nevery; + if (nswaps*nevery != nsteps) + error->universe_all(FLERR,"Non integer # of swaps in temper/npt command"); + + // fix style must be appropriate for temperature and pressure control, + // i.e. it needs to provide a working Fix::reset_target() and must also + // change the volume. This currently only applies to fix npt and + // fix rigid/npt variants + + if ((strncmp(modify->fix[whichfix]->style,"npt",3) == 0) + || (strncmp(modify->fix[whichfix]->style,"rigid/npt",9) == 0)) + error->universe_all(FLERR,"Tempering temperature fix is not supported"); + + // setup for long tempering run + + update->whichflag = 1; + update->nsteps = nsteps; + update->beginstep = update->firststep = update->ntimestep; + update->endstep = update->laststep = update->firststep + nsteps; + if (update->laststep < 0) + error->all(FLERR,"Too many timesteps"); + + lmp->init(); + + // local storage + + me_universe = universe->me; + MPI_Comm_rank(world,&me); + nworlds = universe->nworlds; + iworld = universe->iworld; + boltz = force->boltz; + nktv2p = force->nktv2p; + + // pe_compute = ptr to thermo_pe compute + // notify compute it will be called at first swap + + int id = modify->find_compute("thermo_pe"); + if (id < 0) error->all(FLERR,"Tempering could not find thermo_pe compute"); + Compute *pe_compute = modify->compute[id]; + pe_compute->addstep(update->ntimestep + nevery); + + // create MPI communicator for root proc from each world + + int color; + if (me == 0) color = 0; + else color = 1; + MPI_Comm_split(universe->uworld,color,0,&roots); + + // RNGs for swaps and Boltzmann test + // warm up Boltzmann RNG + + if (seed_swap) ranswap = new RanPark(lmp,seed_swap); + else ranswap = NULL; + ranboltz = new RanPark(lmp,seed_boltz + me_universe); + for (int i = 0; i < 100; i++) ranboltz->uniform(); + + // world2root[i] = global proc that is root proc of world i + + world2root = new int[nworlds]; + if (me == 0) + MPI_Allgather(&me_universe,1,MPI_INT,world2root,1,MPI_INT,roots); + MPI_Bcast(world2root,nworlds,MPI_INT,0,world); + + // create static list of set temperatures + // allgather tempering arg "temp" across root procs + // bcast from each root to other procs in world + + set_temp = new double[nworlds]; + if (me == 0) MPI_Allgather(&temp,1,MPI_DOUBLE,set_temp,1,MPI_DOUBLE,roots); + MPI_Bcast(set_temp,nworlds,MPI_DOUBLE,0,world); + + // create world2temp only on root procs from my_set_temp + // create temp2world on root procs from world2temp, + // then bcast to all procs within world + + world2temp = new int[nworlds]; + temp2world = new int[nworlds]; + if (me == 0) { + MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots); + for (int i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i; + } + MPI_Bcast(temp2world,nworlds,MPI_INT,0,world); + + // if restarting tempering, reset temp target of Fix to current my_set_temp + + if (narg == 8) { + double new_temp = set_temp[my_set_temp]; + modify->fix[whichfix]->reset_target(new_temp); + } + + // setup tempering runs + + int i,which,partner,swap,partner_set_temp,partner_world; + double pe,pe_partner, delr,boltz_factor,new_temp, press_units; + + if (me_universe == 0 && universe->uscreen) + fprintf(universe->uscreen,"Setting up tempering ...\n"); + + update->integrate->setup(); + + if (me_universe == 0) { + if (universe->uscreen) { + fprintf(universe->uscreen,"Step"); + for (int i = 0; i < nworlds; i++) + fprintf(universe->uscreen," T%d",i); + fprintf(universe->uscreen,"\n"); + } + if (universe->ulogfile) { + fprintf(universe->ulogfile,"Step"); + for (int i = 0; i < nworlds; i++) + fprintf(universe->ulogfile," T%d",i); + fprintf(universe->ulogfile,"\n"); + } + print_status(); + } + + timer->init(); + timer->barrier_start(); + + for (int iswap = 0; iswap < nswaps; iswap++) { + + // run for nevery timesteps + + update->integrate->run(nevery); + + // compute PE + // notify compute it will be called at next swap + + pe = pe_compute->compute_scalar(); + pe_compute->addstep(update->ntimestep + nevery); + double boxlox=domain->boxlo[0]; + double boxhix=domain->boxhi[0]; + double boxloy=domain->boxlo[1]; + double boxhiy=domain->boxhi[1]; + double boxloz=domain->boxlo[2]; + double boxhiz=domain->boxhi[2]; + double vol = (boxhix - boxlox)*(boxhiy - boxloy)*(boxhiz - boxloz); + double vol_partner = vol; + // which = which of 2 kinds of swaps to do (0,1) + + if (!ranswap) which = iswap % 2; + else if (ranswap->uniform() < 0.5) which = 0; + else which = 1; + + // partner_set_temp = which set temp I am partnering with for this swap + + if (which == 0) { + if (my_set_temp % 2 == 0) partner_set_temp = my_set_temp + 1; + else partner_set_temp = my_set_temp - 1; + } else { + if (my_set_temp % 2 == 1) partner_set_temp = my_set_temp + 1; + else partner_set_temp = my_set_temp - 1; + } + + // partner = proc ID to swap with + // if partner = -1, then I am not a proc that swaps + + partner = -1; + if (me == 0 && partner_set_temp >= 0 && partner_set_temp < nworlds) { + partner_world = temp2world[partner_set_temp]; + partner = world2root[partner_world]; + } + + // swap with a partner, only root procs in each world participate + // hi proc sends PE to low proc + // lo proc make Boltzmann decision on whether to swap + // lo proc communicates decision back to hi proc + + swap = 0; + if (partner != -1) { + if (me_universe > partner) { + MPI_Send(&pe,1,MPI_DOUBLE,partner,0,universe->uworld); + } + else { + MPI_Recv(&pe_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE); + } + if (me_universe > partner) { + MPI_Send(&vol,1, MPI_DOUBLE,partner,0,universe->uworld); + } + else { + MPI_Recv(&vol_partner,1,MPI_DOUBLE,partner,0,universe->uworld,MPI_STATUS_IGNORE); + } + // Acceptance criteria changed for NPT ensemble + if (me_universe < partner) { + press_units = press_set/nktv2p; + delr = (pe_partner - pe)*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp])) + press_units*(1.0/(boltz*set_temp[my_set_temp]) - 1.0/(boltz*set_temp[partner_set_temp]))*(vol_partner - vol); + boltz_factor = -delr; + if (boltz_factor >= 0.0) swap = 1; + else if (ranboltz->uniform() < exp(boltz_factor)) swap = 1; + } + + if (me_universe < partner) + MPI_Send(&swap,1,MPI_INT,partner,0,universe->uworld); + else + MPI_Recv(&swap,1,MPI_INT,partner,0,universe->uworld,MPI_STATUS_IGNORE); +#ifdef TEMPER_DEBUG + if (me_universe < partner) + fprintf(universe->uscreen,"SWAP %d & %d: yes = %d,Ts = %d %d, PEs = %g %g, Bz = %g %g, vol = %g %g\n", + me_universe,partner,swap,my_set_temp,partner_set_temp, + pe,pe_partner,boltz_factor,exp(boltz_factor), vol, vol_partner); +#endif + + } + + // bcast swap result to other procs in my world + + MPI_Bcast(&swap,1,MPI_INT,0,world); + + // rescale kinetic energy via velocities if move is accepted + + if (swap) scale_velocities(partner_set_temp,my_set_temp); + + // if my world swapped, all procs in world reset temp target of Fix + + if (swap) { + new_temp = set_temp[partner_set_temp]; + modify->fix[whichfix]->reset_target(new_temp); + } + + // update my_set_temp and temp2world on every proc + // root procs update their value if swap took place + // allgather across root procs + // bcast within my world + + if (swap) my_set_temp = partner_set_temp; + if (me == 0) { + MPI_Allgather(&my_set_temp,1,MPI_INT,world2temp,1,MPI_INT,roots); + for (i = 0; i < nworlds; i++) temp2world[world2temp[i]] = i; + } + MPI_Bcast(temp2world,nworlds,MPI_INT,0,world); + + // print out current swap status + + if (me_universe == 0) print_status(); + } + + timer->barrier_stop(); + + update->integrate->cleanup(); + + Finish finish(lmp); + finish.end(1); + + update->whichflag = 0; + update->firststep = update->laststep = 0; + update->beginstep = update->endstep = 0; +} + +/* ---------------------------------------------------------------------- + scale kinetic energy via velocities a la Sugita +------------------------------------------------------------------------- */ + +void TemperNPT::scale_velocities(int t_partner, int t_me) +{ + double sfactor = sqrt(set_temp[t_partner]/set_temp[t_me]); + + double **v = atom->v; + int nlocal = atom->nlocal; + + for (int i = 0; i < nlocal; i++) { + v[i][0] = v[i][0]*sfactor; + v[i][1] = v[i][1]*sfactor; + v[i][2] = v[i][2]*sfactor; + } +} + +/* ---------------------------------------------------------------------- + proc 0 prints current tempering status +------------------------------------------------------------------------- */ + +void TemperNPT::print_status() +{ + if (universe->uscreen) { + fprintf(universe->uscreen,BIGINT_FORMAT,update->ntimestep); + for (int i = 0; i < nworlds; i++) + fprintf(universe->uscreen," %d",world2temp[i]); + fprintf(universe->uscreen,"\n"); + } + if (universe->ulogfile) { + fprintf(universe->ulogfile,BIGINT_FORMAT,update->ntimestep); + for (int i = 0; i < nworlds; i++) + fprintf(universe->ulogfile," %d",world2temp[i]); + fprintf(universe->ulogfile,"\n"); + fflush(universe->ulogfile); + } +} diff --git a/src/USER-MISC/temper_npt.h b/src/USER-MISC/temper_npt.h new file mode 100644 index 000000000..cbc434599 --- /dev/null +++ b/src/USER-MISC/temper_npt.h @@ -0,0 +1,108 @@ +/* -*- 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 COMMAND_CLASS + +CommandStyle(temper/npt,TemperNPT) + +#else + +#ifndef LMP_TEMPERNPT_H +#define LMP_TEMPERNPT_H + +#include "pointers.h" + +namespace LAMMPS_NS { + +class TemperNPT : protected Pointers { + public: + TemperNPT(class LAMMPS *); + ~TemperNPT(); + void command(int, char **); + + private: + int me,me_universe; // my proc ID in world and universe + int iworld,nworlds; // world info + double boltz; // copy from output->boltz + double nktv2p; + MPI_Comm roots; // MPI comm with 1 root proc from each world + class RanPark *ranswap,*ranboltz; // RNGs for swapping and Boltz factor + int nevery; // # of timesteps between swaps + int nswaps; // # of tempering swaps to perform + int seed_swap; // 0 = toggle swaps, n = RNG for swap direction + int seed_boltz; // seed for Boltz factor comparison + int whichfix; // index of temperature fix to use + int fixstyle; // what kind of temperature fix is used + + int my_set_temp; // which set temp I am simulating + double *set_temp; // static list of replica set temperatures + int *temp2world; // temp2world[i] = world simulating set temp i + int *world2temp; // world2temp[i] = temp simulated by world i + int *world2root; // world2root[i] = root proc of world i + + void scale_velocities(int, int); + void print_status(); +}; + +} + +#endif +#endif + +/* ERROR/WARNING messages: + +E: Must have more than one processor partition to temper + +Cannot use the temper command with only one processor partition. Use +the -partition command-line option. + +E: temper/npt command before simulation box is defined + +The temper/npt command cannot be used before a read_data, read_restart, +or create_box command. + +E: Illegal ... command + +Self-explanatory. Check the input script syntax and compare to the +documentation for the command. You can use -echo screen as a +command-line option when running LAMMPS to see the offending line. + +E: Tempering fix ID is not defined + +The fix ID specified by the temper/npt command does not exist. + +E: Invalid frequency in temper/npt command + +Nevery must be > 0. + +E: Non integer # of swaps in temper/npt command + +Swap frequency in temper/npt command must evenly divide the total +# of timesteps. + +E: Tempering temperature fix is not valid + +The fix specified by the temper command is not one that controls +temperature and pressure (npt). + +E: Too many timesteps + +The cummulative timesteps must fit in a 64-bit integer. + +E: Tempering could not find thermo_pe compute + +This compute is created by the thermo command. It must have been +explicitly deleted by a uncompute command. + +*/