forked from lijiext/lammps
Merge pull request #538 from akohlmey/collected-small-changes
Collected small changes and bugfixes
This commit is contained in:
sjplimp
GitHub
commit
4fc3f4f7e5
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@ -1073,7 +1073,7 @@ package"_Section_start.html#start_3.
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"table/rx"_pair_table_rx.html,
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"tersoff/table (o)"_pair_tersoff.html,
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"thole"_pair_thole.html,
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"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
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"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c)
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:line
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@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including
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which quantities can be queried by name:
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void *lammps_extract_global(void *, char *)
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void lammps_extract_box(void *, double *, double *,
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void lammps_extract_box(void *, double *, double *,
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double *, double *, double *, int *, int *)
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void *lammps_extract_atom(void *, char *)
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void *lammps_extract_compute(void *, char *, int, int)
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@ -2682,14 +2682,14 @@ bond_coeff 2 25.724 0.0 :pre
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When running dynamics with the adiabatic core/shell model, the
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following issues should be considered. The relative motion of
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the core and shell particles corresponds to the polarization,
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hereby an instantaneous relaxation of the shells is approximated
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the core and shell particles corresponds to the polarization,
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hereby an instantaneous relaxation of the shells is approximated
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and a fast core/shell spring frequency ensures a nearly constant
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internal kinetic energy during the simulation.
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internal kinetic energy during the simulation.
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Thermostats can alter this polarization behaviour, by scaling the
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internal kinetic energy, meaning the shell will not react freely to
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its electrostatic environment.
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Therefore it is typically desirable to decouple the relative motion of
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internal kinetic energy, meaning the shell will not react freely to
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its electrostatic environment.
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Therefore it is typically desirable to decouple the relative motion of
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the core/shell pair, which is an imaginary degree of freedom, from the
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real physical system. To do that, the "compute
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temp/cs"_compute_temp_cs.html command can be used, in conjunction with
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@ -2721,13 +2721,13 @@ fix thermostatequ all nve # integrator as needed f
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fix_modify thermoberendsen temp CSequ
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thermo_modify temp CSequ # output of center-of-mass derived temperature :pre
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The pressure for the core/shell system is computed via the regular
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LAMMPS convention by "treating the cores and shells as individual
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particles"_#MitchellFincham2. For the thermo output of the pressure
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as well as for the application of a barostat, it is necessary to
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use an additional "pressure"_compute_pressure compute based on the
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default "temperature"_compute_temp and specifying it as a second
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argument in "fix modify"_fix_modify.html and
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The pressure for the core/shell system is computed via the regular
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LAMMPS convention by "treating the cores and shells as individual
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particles"_#MitchellFincham2. For the thermo output of the pressure
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as well as for the application of a barostat, it is necessary to
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use an additional "pressure"_compute_pressure compute based on the
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default "temperature"_compute_temp and specifying it as a second
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argument in "fix modify"_fix_modify.html and
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"thermo_modify"_thermo_modify.html resulting in:
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(...)
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@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the
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velocity all create 1427 134 bias yes temp CSequ
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velocity all scale 1427 temp CSequ :pre
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To maintain the correct polarizability of the core/shell pairs, the
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kinetic energy of the internal motion shall remain nearly constant.
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Therefore the choice of spring force and mass ratio need to ensure
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much faster relative motion of the 2 atoms within the core/shell pair
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than their center-of-mass velocity. This allows the shells to
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effectively react instantaneously to the electrostatic environment and
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To maintain the correct polarizability of the core/shell pairs, the
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kinetic energy of the internal motion shall remain nearly constant.
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Therefore the choice of spring force and mass ratio need to ensure
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much faster relative motion of the 2 atoms within the core/shell pair
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than their center-of-mass velocity. This allows the shells to
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effectively react instantaneously to the electrostatic environment and
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limits energy transfer to or from the core/shell oscillators.
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This fast movement also dictates the timestep that can be used.
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The primary literature of the adiabatic core/shell model suggests that
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the fast relative motion of the core/shell pairs only allows negligible
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energy transfer to the environment.
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energy transfer to the environment.
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The mentioned energy transfer will typically lead to a small drift
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in total energy over time. This internal energy can be monitored
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using the "compute chunk/atom"_compute_chunk_atom.html and "compute
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@ -2790,7 +2790,7 @@ pairs as chunks.
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For example if core/shell pairs are the only molecules:
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read_data NaCl_CS_x0.1_prop.data
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read_data NaCl_CS_x0.1_prop.data
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compute prop all property/atom molecule
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compute cs_chunk all chunk/atom c_prop
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compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
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@ -585,7 +585,7 @@ do not recommend building with other acceleration packages installed
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make yes-kokkos
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make machine :pre
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make no-kokkos
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make machine :pre
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@ -839,13 +839,13 @@ written and read in parallel.
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Note that MPIIO is part of the standard message-passing interface
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(MPI) library, so you should not need any additional compiler or link
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settings, beyond what LAMMPS normally uses for MPI on your system.
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make yes-mpiio
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make machine :pre
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make no-mpiio
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make machine :pre
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[Supporting info:]
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src/MPIIO: filenames -> commands
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@ -855,7 +855,7 @@ src/MPIIO: filenames -> commands
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"read_restart"_read_restart.html :ul
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:line
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MSCG package :link(mscg),h4
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[Contents:]
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@ -914,7 +914,7 @@ lib/mscg/README
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examples/mscg :ul
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:line
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OPT package :link(OPT),h4
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[Contents:]
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@ -1387,7 +1387,7 @@ atomic information to continuum fields.
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[Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
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[Install or un-install:]
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Before building LAMMPS with this package, you must first build the ATC
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library in lib/atc. You can do this manually if you prefer; follow
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the instructions in lib/atc/README. You can also do it in one step
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@ -1420,10 +1420,10 @@ usual manner:
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make yes-user-atc
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make machine :pre
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make no-user-atc
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make machine :pre
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[Supporting info:]
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src/USER-ATC: filenames -> commands
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@ -1446,7 +1446,7 @@ model.
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[Author:] Ilya Valuev (JIHT, Russia).
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[Install or un-install:]
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Before building LAMMPS with this package, you must first build the
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AWPMD library in lib/awpmd. You can do this manually if you prefer;
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follow the instructions in lib/awpmd/README. You can also do it in
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@ -1479,10 +1479,10 @@ usual manner:
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make yes-user-awpmd
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make machine :pre
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make no-user-awpmd
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make machine :pre
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[Supporting info:]
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src/USER-AWPMD: filenames -> commands
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@ -1505,13 +1505,13 @@ stability.
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[Author:] Oliver Henrich (University of Strathclyde, Glasgow).
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[Install or un-install:]
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||||
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|
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make yes-user-cgdna
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make machine :pre
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make no-user-cgdna
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make machine :pre
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|
||||
|
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[Supporting info:]
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src/USER-CGDNA: filenames -> commands
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@ -1536,13 +1536,13 @@ acids.
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[Author:] Axel Kohlmeyer (Temple U).
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[Install or un-install:]
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||||
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||||
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make yes-user-cgsdk
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make machine :pre
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||||
|
||||
|
||||
make no-user-cgsdk
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make machine :pre
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||||
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||||
|
||||
[Supporting info:]
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||||
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src/USER-CGSDK: filenames -> commands
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|
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@ -1570,7 +1570,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and
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Jerome Henin (LISM, CNRS, Marseille, France).
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|
||||
[Install or un-install:]
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||||
|
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Before building LAMMPS with this package, you must first build the
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COLVARS library in lib/colvars. You can do this manually if you
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prefer; follow the instructions in lib/colvars/README. You can also
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|
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@ -1594,10 +1594,10 @@ usual manner:
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make yes-user-colvars
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make machine :pre
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||||
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||||
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make no-user-colvars
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make machine :pre
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||||
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[Supporting info:]
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||||
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src/USER-COLVARS: filenames -> commands
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||||
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@ -1619,13 +1619,13 @@ intensities based on kinematic diffraction theory.
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[Author:] Shawn Coleman while at the U Arkansas.
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|
||||
[Install or un-install:]
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|
||||
|
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make yes-user-diffraction
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make machine :pre
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||||
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||||
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||||
make no-user-diffraction
|
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make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
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||||
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src/USER-DIFFRACTION: filenames -> commands
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@ -1654,13 +1654,13 @@ algorithm.
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|||
Brennan (ARL).
|
||||
|
||||
[Install or un-install:]
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||||
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||||
|
||||
make yes-user-dpd
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make machine :pre
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||||
|
||||
|
||||
make no-user-dpd
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make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-DPD: filenames -> commands
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||||
|
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@ -1696,13 +1696,13 @@ tools/drude.
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Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
|
||||
|
||||
[Install or un-install:]
|
||||
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||||
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||||
make yes-user-drude
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make machine :pre
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||||
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||||
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||||
make no-user-drude
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||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-DRUDE: filenames -> commands
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||||
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@ -1734,13 +1734,13 @@ tools/eff; see its README file.
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|||
[Author:] Andres Jaramillo-Botero (CalTech).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-eff
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-eff
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||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-EFF: filenames -> commands
|
||||
|
|
@ -1773,13 +1773,13 @@ for using this package in tools/fep; see its README file.
|
|||
[Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-fep
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-fep
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-FEP: filenames -> commands
|
||||
|
|
@ -1836,13 +1836,13 @@ file.
|
|||
|
||||
You can then install/un-install the package and build LAMMPS in the
|
||||
usual manner:
|
||||
|
||||
|
||||
make yes-user-h5md
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-h5md
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-H5MD: filenames -> commands
|
||||
|
|
@ -1908,7 +1908,7 @@ explained in "Section 5.3.2"_accelerate_intel.html.
|
|||
|
||||
make yes-user-intel yes-user-omp
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-intel no-user-omp
|
||||
make machine :pre
|
||||
|
||||
|
|
@ -1938,13 +1938,13 @@ can be used to model MD particles influenced by hydrodynamic forces.
|
|||
Ontario).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-lb
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-lb
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-LB: filenames -> commands
|
||||
|
|
@ -1972,13 +1972,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL.
|
|||
[Authors:] Tomas Oppelstrup and John Moriarty (LLNL).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-mgpt
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-mgpt
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MGPT: filenames -> commands
|
||||
|
|
@ -2000,13 +2000,13 @@ dihedral, improper, or command style.
|
|||
src/USER-MISC/README file.
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-misc
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-misc
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MISC: filenames -> commands
|
||||
|
|
@ -2031,13 +2031,13 @@ n = grad(g).
|
|||
Netherlands; since 2017: Brandeis University, Waltham, MA, USA)
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-manifold
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-manifold
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MANIFOLD: filenames -> commands
|
||||
|
|
@ -2080,7 +2080,7 @@ at
|
|||
[Author:] Axel Kohlmeyer (Temple U).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
Note that the lib/molfile/Makefile.lammps file has a setting for a
|
||||
dynamic loading library libdl.a that should is typically present on
|
||||
all systems, which is required for LAMMPS to link with this package.
|
||||
|
|
@ -2090,10 +2090,10 @@ lib/molfile/Makefile.lammps for details.
|
|||
|
||||
make yes-user-molfile
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-molfile
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-MOLFILE: filenames -> commands
|
||||
|
|
@ -2128,7 +2128,7 @@ tools:
|
|||
[Author:] Lars Pastewka (Karlsruhe Institute of Technology).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
Note that to follow these steps, you need the standard NetCDF software
|
||||
package installed on your system. The lib/netcdf/Makefile.lammps file
|
||||
has settings for NetCDF include and library files that LAMMPS needs to
|
||||
|
|
@ -2138,7 +2138,7 @@ lib/netcdf/README for details.
|
|||
|
||||
make yes-user-netcdf
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-netcdf
|
||||
make machine :pre
|
||||
|
||||
|
|
@ -2178,10 +2178,10 @@ Once you have an appropriate Makefile.machine, you can
|
|||
install/un-install the package and build LAMMPS in the usual manner:
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-omp
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-omp
|
||||
make machine :pre
|
||||
|
||||
|
|
@ -2213,13 +2213,13 @@ relations, directly from molecular dynamics simulations.
|
|||
[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-phonon
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-phonon
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-PHONON: filenames -> commands
|
||||
|
|
@ -2235,7 +2235,7 @@ USER-QMMM package :link(USER-QMMM),h4
|
|||
|
||||
A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a
|
||||
QM/MM simulation, currently only in combination with the "Quantum
|
||||
ESPRESSO"_espresso package.
|
||||
ESPRESSO"_espresso package.
|
||||
|
||||
:link(espresso,http://www.quantum-espresso.org)
|
||||
|
||||
|
|
@ -2275,7 +2275,7 @@ usual manner:
|
|||
|
||||
make yes-user-qmmm
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-qmmm
|
||||
make machine :pre
|
||||
|
||||
|
|
@ -2284,7 +2284,7 @@ for a QM/MM simulation. You must also build Quantum ESPRESSO and
|
|||
create a new executable which links LAMMPS and Quanutm ESPRESSO
|
||||
together. These are steps 3 and 4 described in the lib/qmmm/README
|
||||
file.
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-QMMM: filenames -> commands
|
||||
|
|
@ -2312,13 +2312,13 @@ simulation.
|
|||
[Author:] Yuan Shen (Stanford U).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-qtb
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-qtb
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-QTB: filenames -> commands
|
||||
|
|
@ -2362,10 +2362,10 @@ usual manner:
|
|||
|
||||
make yes-user-quip
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-quip
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-QUIP: filenames -> commands
|
||||
|
|
@ -2388,13 +2388,13 @@ for monitoring molecules as bonds are created and destroyed.
|
|||
[Author:] Hasan Metin Aktulga (MSU) while at Purdue University.
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-reaxc
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-reaxc
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-REAXC: filenames -> commands
|
||||
|
|
@ -2451,10 +2451,10 @@ usual manner:
|
|||
|
||||
make yes-user-smd
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-smd
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-SMD: filenames -> commands
|
||||
|
|
@ -2477,13 +2477,13 @@ ionocovalent bonds in oxides.
|
|||
Tetot (LAAS-CNRS, France).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-smtbq
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-smtbq
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-SMTBQ: filenames -> commands
|
||||
|
|
@ -2516,13 +2516,13 @@ property/atom"_compute_property_atom.html command.
|
|||
Dynamics, Ernst Mach Institute, Germany).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-sph
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-sph
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-SPH: filenames -> commands
|
||||
|
|
@ -2544,13 +2544,13 @@ stress, etc) about individual interactions.
|
|||
[Author:] Axel Kohlmeyer (Temple U).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
make yes-user-tally
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-tally
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-TALLY: filenames -> commands
|
||||
|
|
@ -2577,7 +2577,7 @@ system.
|
|||
[Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing).
|
||||
|
||||
[Install or un-install:]
|
||||
|
||||
|
||||
The lib/vtk/Makefile.lammps file has settings for accessing VTK files
|
||||
and its library, which are required for LAMMPS to build and link with
|
||||
this package. If the settings are not valid for your system, check if
|
||||
|
|
@ -2590,10 +2590,10 @@ usual manner:
|
|||
|
||||
make yes-user-vtk
|
||||
make machine :pre
|
||||
|
||||
|
||||
make no-user-vtk
|
||||
make machine :pre
|
||||
|
||||
|
||||
[Supporting info:]
|
||||
|
||||
src/USER-VTK: filenames -> commands
|
||||
|
|
|
|||
|
|
@ -714,7 +714,7 @@ stored in the "image" property. All three image flags are stored in
|
|||
a packed format in a single integer, so count would be 1 to retrieve
|
||||
that integer, however also a count value of 3 can be used and then
|
||||
the image flags will be unpacked into 3 individual integers, ordered
|
||||
in a similar fashion as coordinates.
|
||||
in a similar fashion as coordinates.
|
||||
|
||||
Note that the data structure gather_atoms("x") returns is different
|
||||
from the data structure returned by extract_atom("x") in four ways.
|
||||
|
|
|
|||
|
|
@ -42,11 +42,11 @@ precision mode. Performance improvements are shown compared to
|
|||
LAMMPS {without using other acceleration packages} as these are
|
||||
under active development (and subject to performance changes). The
|
||||
measurements were performed using the input files available in
|
||||
the src/USER-INTEL/TEST directory with the provided run script.
|
||||
These are scalable in size; the results given are with 512K
|
||||
particles (524K for Liquid Crystal). Most of the simulations are
|
||||
the src/USER-INTEL/TEST directory with the provided run script.
|
||||
These are scalable in size; the results given are with 512K
|
||||
particles (524K for Liquid Crystal). Most of the simulations are
|
||||
standard LAMMPS benchmarks (indicated by the filename extension in
|
||||
parenthesis) with modifications to the run length and to add a
|
||||
parenthesis) with modifications to the run length and to add a
|
||||
warmup run (for use with offload benchmarks).
|
||||
|
||||
:c,image(JPG/user_intel.png)
|
||||
|
|
@ -64,30 +64,30 @@ simulation rates and instructions to reproduce.
|
|||
|
||||
In most molecular dynamics software, parallelization parameters
|
||||
(# of MPI, OpenMP, and vectorization) can change the results due
|
||||
to changing the order of operations with finite-precision
|
||||
to changing the order of operations with finite-precision
|
||||
calculations. The USER-INTEL package is deterministic. This means
|
||||
that the results should be reproducible from run to run with the
|
||||
{same} parallel configurations and when using determinstic
|
||||
{same} parallel configurations and when using determinstic
|
||||
libraries or library settings (MPI, OpenMP, FFT). However, there
|
||||
are differences in the USER-INTEL package that can change the
|
||||
order of operations compared to LAMMPS without acceleration:
|
||||
|
||||
Neighbor lists can be created in a different order :ulb,l
|
||||
Bins used for sorting atoms can be oriented differently :l
|
||||
The default stencil order for PPPM is 7. By default, LAMMPS will
|
||||
calculate other PPPM parameters to fit the desired acuracy with
|
||||
The default stencil order for PPPM is 7. By default, LAMMPS will
|
||||
calculate other PPPM parameters to fit the desired acuracy with
|
||||
this order :l
|
||||
The {newton} setting applies to all atoms, not just atoms shared
|
||||
between MPI tasks :l
|
||||
Vectorization can change the order for adding pairwise forces :l
|
||||
:ule
|
||||
|
||||
The precision mode (described below) used with the USER-INTEL
|
||||
package can change the {accuracy} of the calculations. For the
|
||||
default {mixed} precision option, calculations between pairs or
|
||||
triplets of atoms are performed in single precision, intended to
|
||||
The precision mode (described below) used with the USER-INTEL
|
||||
package can change the {accuracy} of the calculations. For the
|
||||
default {mixed} precision option, calculations between pairs or
|
||||
triplets of atoms are performed in single precision, intended to
|
||||
be within the inherent error of MD simulations. All accumulation
|
||||
is performed in double precision to prevent the error from growing
|
||||
is performed in double precision to prevent the error from growing
|
||||
with the number of atoms in the simulation. {Single} precision
|
||||
mode should not be used without appropriate validation.
|
||||
|
||||
|
|
@ -106,7 +106,7 @@ $t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l
|
|||
For some of the simple 2-body potentials without long-range
|
||||
electrostatics, performance and scalability can be better with
|
||||
the "newton off" setting added to the input script :l
|
||||
If using {kspace_style pppm} in the input script, add
|
||||
If using {kspace_style pppm} in the input script, add
|
||||
"kspace_modify diff ad" for better performance :l
|
||||
:ule
|
||||
|
||||
|
|
@ -115,12 +115,12 @@ For Intel Xeon Phi CPUs:
|
|||
Runs should be performed using MCDRAM. :ulb,l
|
||||
:ule
|
||||
|
||||
For simulations using {kspace_style pppm} on Intel CPUs
|
||||
For simulations using {kspace_style pppm} on Intel CPUs
|
||||
supporting AVX-512:
|
||||
|
||||
Add "kspace_modify diff ad" to the input script :ulb,l
|
||||
The command-line option should be changed to
|
||||
"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
|
||||
The command-line option should be changed to
|
||||
"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of
|
||||
threads minus 1. :l
|
||||
Do not use thread affinity (set KMP_AFFINITY=none) :l
|
||||
The "newton off" setting may provide better scalability :l
|
||||
|
|
@ -352,7 +352,7 @@ follow in the input script.
|
|||
|
||||
NOTE: The USER-INTEL package will perform better with modifications
|
||||
to the input script when "PPPM"_kspace_style.html is used:
|
||||
"kspace_modify diff ad"_kspace_modify.html should be added to the
|
||||
"kspace_modify diff ad"_kspace_modify.html should be added to the
|
||||
input script.
|
||||
|
||||
Long-Range Thread (LRT) mode is an option to the "package
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential
|
|||
|
||||
to define a modified finite extensible nonlinear elastic (FENE) potential
|
||||
"(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone
|
||||
in the oxDNA force field for coarse-grained modelling of DNA.
|
||||
in the oxDNA force field for coarse-grained modelling of DNA.
|
||||
|
||||
The following coefficients must be defined for the bond type via the
|
||||
"bond_coeff"_bond_coeff.html command as given in the above example, or in
|
||||
|
|
@ -43,8 +43,8 @@ r0 (distance) :ul
|
|||
|
||||
NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles
|
||||
for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
|
||||
and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
|
||||
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
|
||||
and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of
|
||||
"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair
|
||||
style {oxdna2/dh} have to be defined.
|
||||
The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
|
||||
|
|
@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
|
||||
"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -42,7 +42,7 @@ where the index {j} goes over the {n}i nearest neighbors of atom
|
|||
{i}, and the index {k} goes over the {n}ij common nearest neighbors
|
||||
between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom
|
||||
{k} to atoms {i} and {j}. The quantity in the double sum is computed
|
||||
for each atom.
|
||||
for each atom.
|
||||
|
||||
The CNP calculation is sensitive to the specified cutoff value.
|
||||
You should ensure that the appropriate nearest neighbors of an atom are
|
||||
|
|
|
|||
|
|
@ -16,7 +16,7 @@ ID = user-assigned name for the dump
|
|||
group-ID = ID of the group of atoms to be dumped
|
||||
vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page)
|
||||
N = dump every this many timesteps
|
||||
file = name of file to write dump info to
|
||||
file = name of file to write dump info to
|
||||
args = same as arguments for "dump_style custom"_dump.html :ul
|
||||
|
||||
[Examples:]
|
||||
|
|
@ -83,7 +83,7 @@ Triclinic simulation boxes (non-orthogonal) are saved as
|
|||
hexahedrons in either legacy .vtk or .vtu XML format.
|
||||
|
||||
Style {vtk} allows you to specify a list of atom attributes to be
|
||||
written to the dump file for each atom. The list of possible attributes
|
||||
written to the dump file for each atom. The list of possible attributes
|
||||
is the same as for the "dump_style custom"_dump.html command; see
|
||||
its doc page for a listing and an explanation of each attribute.
|
||||
|
||||
|
|
|
|||
|
|
@ -245,7 +245,7 @@ appear the system is converging to your specified pressure. The
|
|||
solution for this is to either (a) zero the velocities of all atoms
|
||||
before performing the minimization, or (b) make sure you are
|
||||
monitoring the pressure without its kinetic component. The latter can
|
||||
be done by outputting the pressure from the pressure compute this
|
||||
be done by outputting the pressure from the pressure compute this
|
||||
command creates (see below) or a pressure compute you define yourself.
|
||||
|
||||
NOTE: Because pressure is often a very sensitive function of volume,
|
||||
|
|
|
|||
|
|
@ -45,14 +45,14 @@ species {j} in particle {i}, {u_j} is the internal energy of species j,
|
|||
{DeltaH_f,j} is the heat of formation of species {j}, N is the number of
|
||||
molecules represented by the coarse-grained particle, kb is the
|
||||
Boltzmann constant, and T is the temperature of the system. Additionally,
|
||||
it is possible to modify the concentration-dependent particle internal
|
||||
energy relation by adding an energy correction, temperature-dependent
|
||||
it is possible to modify the concentration-dependent particle internal
|
||||
energy relation by adding an energy correction, temperature-dependent
|
||||
correction, and/or a molecule-dependent correction. An energy correction can
|
||||
be specified as a constant (in energy units). A temperature correction can be
|
||||
specified by multiplying a temperature correction coefficient by the
|
||||
internal temperature. A molecular correction can be specified by
|
||||
by multiplying a molecule correction coefficient by the average number of
|
||||
product gas particles in the coarse-grain particle.
|
||||
be specified as a constant (in energy units). A temperature correction can be
|
||||
specified by multiplying a temperature correction coefficient by the
|
||||
internal temperature. A molecular correction can be specified by
|
||||
by multiplying a molecule correction coefficient by the average number of
|
||||
product gas particles in the coarse-grain particle.
|
||||
|
||||
Fix {eos/table/rx} creates interpolation tables of length {N} from {m}
|
||||
internal energy values of each species {u_j} listed in a file as a
|
||||
|
|
@ -72,12 +72,12 @@ The second filename specifies a file containing heat of formation
|
|||
{DeltaH_f,j} for each species.
|
||||
|
||||
In cases where the coarse-grain particle represents a single molecular
|
||||
species (i.e., no reactions occur and fix {rx} is not present in the input file),
|
||||
fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
|
||||
within a non-reactive DPD simulation. In this case, the heat of formation
|
||||
species (i.e., no reactions occur and fix {rx} is not present in the input file),
|
||||
fix {eos/table/rx} can be applied in a similar manner to fix {eos/table}
|
||||
within a non-reactive DPD simulation. In this case, the heat of formation
|
||||
filename is replaced with the heat of formation value for the single species.
|
||||
Additionally, the energy correction and temperature correction coefficients may
|
||||
also be specified as fix arguments.
|
||||
Additionally, the energy correction and temperature correction coefficients may
|
||||
also be specified as fix arguments.
|
||||
|
||||
:line
|
||||
|
||||
|
|
@ -138,8 +138,8 @@ used as the species name must correspond with the tags used to define
|
|||
the reactions with the "fix rx"_fix_rx.html command.
|
||||
|
||||
Alternatively, corrections to the EOS can be included by specifying
|
||||
three additional columns that correspond to the energy correction,
|
||||
the temperature correction coefficient and molecule correction
|
||||
three additional columns that correspond to the energy correction,
|
||||
the temperature correction coefficient and molecule correction
|
||||
coefficient. In this case, the format of the file is as follows:
|
||||
|
||||
# HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre
|
||||
|
|
|
|||
|
|
@ -70,8 +70,8 @@ minimization"_minimize.html.
|
|||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
Currently, it does not support "molecule templates"_molecule.html.
|
||||
|
|
|
|||
|
|
@ -406,7 +406,7 @@ the user for each subsequent fix gcmc command.
|
|||
[Default:]
|
||||
|
||||
The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0,
|
||||
fugacity_coeff = 1, and full_energy = no,
|
||||
fugacity_coeff = 1, and full_energy = no,
|
||||
except for the situations where full_energy is required, as
|
||||
listed above.
|
||||
|
||||
|
|
|
|||
|
|
@ -85,13 +85,13 @@ No information about this fix is written to "binary restart
|
|||
files"_restart.html.
|
||||
|
||||
The "thermo_modify"_thermo_modify.html {press} option is supported
|
||||
by this fix to add the rescaled kinetic pressure as part of
|
||||
by this fix to add the rescaled kinetic pressure as part of
|
||||
"thermodynamic output"_thermo_style.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
|
|
|||
|
|
@ -58,14 +58,14 @@ input are listed in the same order as in the data file of LAMMPS. The
|
|||
initial configuration is ignored, as it will be substituted with the
|
||||
coordinates received from i-PI before forces are ever evaluated.
|
||||
|
||||
A note of caution when using potentials that contain long-range
|
||||
A note of caution when using potentials that contain long-range
|
||||
electrostatics, or that contain parameters that depend on box size:
|
||||
all of these options will be initialized based on the cell size in the
|
||||
LAMMPS-side initial configuration and kept constant during the run.
|
||||
This is required to e.g. obtain reproducible and conserved forces.
|
||||
If the cell varies too wildly, it may be advisable to reinitialize
|
||||
these interactions at each call. This behavior can be requested by
|
||||
setting the {reset} switch.
|
||||
LAMMPS-side initial configuration and kept constant during the run.
|
||||
This is required to e.g. obtain reproducible and conserved forces.
|
||||
If the cell varies too wildly, it may be advisable to reinitialize
|
||||
these interactions at each call. This behavior can be requested by
|
||||
setting the {reset} switch.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
|
|
|||
|
|
@ -57,7 +57,7 @@ simulations is as follows:
|
|||
Perform all-atom simulations on the system to be coarse grained.
|
||||
Generate a trajectory mapped to the coarse-grained model.
|
||||
Create input files for the MS-CG library.
|
||||
Run the range finder functionality of the MS-CG library.
|
||||
Run the range finder functionality of the MS-CG library.
|
||||
Run the force matching functionality of the MS-CG library.
|
||||
Check the results of the force matching.
|
||||
Run coarse-grained simulations using the new coarse-grained potentials. :ol
|
||||
|
|
@ -70,7 +70,7 @@ Step 2 can be performed using a Python script (what is the name?)
|
|||
provided with the MS-CG library which defines the coarse-grained model
|
||||
and converts a standard LAMMPS dump file for an all-atom simulation
|
||||
(step 1) into a LAMMPS dump file which has the positions of and forces
|
||||
on the coarse-grained beads.
|
||||
on the coarse-grained beads.
|
||||
|
||||
In step 3, an input file named "control.in" is needed by the MS-CG
|
||||
library which sets parameters for the range finding and force matching
|
||||
|
|
|
|||
|
|
@ -23,13 +23,13 @@ fix 1 all nve/dot :pre
|
|||
[Description:]
|
||||
|
||||
Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1
|
||||
to a group of atoms, but without Langevin dynamics.
|
||||
to a group of atoms, but without Langevin dynamics.
|
||||
This command performs Molecular dynamics (MD)
|
||||
via a velocity-Verlet algorithm and an evolution operator that rotates
|
||||
the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
|
||||
via a velocity-Verlet algorithm and an evolution operator that rotates
|
||||
the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1.
|
||||
|
||||
This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
without damping and noise and can be used to determine the stability range
|
||||
without damping and noise and can be used to determine the stability range
|
||||
in a NVE ensemble prior to using the Langevin-type DOTC-integrator
|
||||
(see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html).
|
||||
The command is equivalent to the "fix nve"_fix_nve.html.
|
||||
|
|
|
|||
|
|
@ -28,20 +28,20 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
|
||||
Apply a rigid-body Langevin-type integrator of the kind "Langevin C"
|
||||
as described in "(Davidchack)"_#Davidchack2
|
||||
to a group of atoms, which models an interaction with an implicit background
|
||||
solvent. This command performs Brownian dynamics (BD)
|
||||
via a technique that splits the integration into a deterministic Hamiltonian
|
||||
part and the Ornstein-Uhlenbeck process for noise and damping.
|
||||
via a technique that splits the integration into a deterministic Hamiltonian
|
||||
part and the Ornstein-Uhlenbeck process for noise and damping.
|
||||
The quaternion degrees of freedom are updated though an evolution
|
||||
operator which performs a rotation in quaternion space, preserves
|
||||
the quaternion norm and is akin to "(Miller)"_#Miller2.
|
||||
|
||||
In terms of syntax this command has been closely modelled on the
|
||||
"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
|
||||
the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
|
||||
one single command. The main feature is improved stability
|
||||
In terms of syntax this command has been closely modelled on the
|
||||
"fix langevin"_fix_langevin.html and its {angmom} option. But it combines
|
||||
the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in
|
||||
one single command. The main feature is improved stability
|
||||
over the standard integrator, permitting slightly larger timestep sizes.
|
||||
|
||||
NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs
|
||||
|
|
@ -57,7 +57,7 @@ Fc is the conservative force computed via the usual inter-particle
|
|||
interactions ("pair_style"_pair_style.html,
|
||||
"bond_style"_bond_style.html, etc).
|
||||
|
||||
The Ff and Fr terms are implicitly taken into account by this fix
|
||||
The Ff and Fr terms are implicitly taken into account by this fix
|
||||
on a per-particle basis.
|
||||
|
||||
Ff is a frictional drag or viscous damping term proportional to the
|
||||
|
|
@ -77,7 +77,7 @@ a Gaussian random number) for speed.
|
|||
|
||||
:line
|
||||
|
||||
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
|
||||
{Tstart} and {Tstop} have to be constant values, i.e. they cannot
|
||||
be variables.
|
||||
|
||||
The {damp} parameter is specified in time units and determines how
|
||||
|
|
@ -98,16 +98,16 @@ different numbers of processors.
|
|||
|
||||
The keyword/value option has to be used in the following way:
|
||||
|
||||
This fix has to be used together with the {angmom} keyword. The
|
||||
particles are always considered to have a finite size.
|
||||
The keyword {angmom} enables thermostatting of the rotational degrees of
|
||||
freedom in addition to the usual translational degrees of freedom.
|
||||
This fix has to be used together with the {angmom} keyword. The
|
||||
particles are always considered to have a finite size.
|
||||
The keyword {angmom} enables thermostatting of the rotational degrees of
|
||||
freedom in addition to the usual translational degrees of freedom.
|
||||
|
||||
The scale factor after the {angmom} keyword gives the ratio of the rotational to
|
||||
The scale factor after the {angmom} keyword gives the ratio of the rotational to
|
||||
the translational friction coefficient.
|
||||
|
||||
An example input file can be found in /examples/USER/cgdna/examples/duplex2/.
|
||||
A technical report with more information on this integrator can be found
|
||||
A technical report with more information on this integrator can be found
|
||||
"here"_PDF/USER-CGDNA-overview.pdf.
|
||||
|
||||
:line
|
||||
|
|
@ -120,7 +120,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
|
||||
"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html,
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -27,7 +27,7 @@ timestep. V is volume; K is kinetic energy. This creates a system
|
|||
trajectory consistent with the isokinetic ensemble.
|
||||
|
||||
The equations of motion used are those of Minary et al in
|
||||
"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
|
||||
"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in
|
||||
"(Zhang)"_#nvk-Zhang.
|
||||
|
||||
The kinetic energy will be held constant at its value given when fix
|
||||
|
|
|
|||
|
|
@ -89,7 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
|
|||
group can straddle a periodic boundary. See the "dump"_dump.html doc
|
||||
page for a discussion of unwrapped coordinates. It also means that a
|
||||
spring connecting two groups or a group and the tether point can cross
|
||||
a periodic boundary and its length be calculated correctly.
|
||||
a periodic boundary and its length be calculated correctly.
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
|
|
|
|||
|
|
@ -144,7 +144,11 @@ this fix.
|
|||
|
||||
"fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html
|
||||
|
||||
[Restrictions:] none
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS was built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
|
||||
[Default:]
|
||||
|
||||
|
|
|
|||
|
|
@ -344,7 +344,7 @@ informations can help understanding what is going wrong. For instance
|
|||
when the path angle becomes accute the definition of tangent used in
|
||||
the NEB calculation is questionable and the NEB cannot may diverge
|
||||
"(Maras)"_#Maras2.
|
||||
|
||||
|
||||
|
||||
When running on multiple partitions, LAMMPS produces additional log
|
||||
files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a
|
||||
|
|
|
|||
|
|
@ -40,8 +40,8 @@ vectorial atomic forces.
|
|||
|
||||
Only a single pair_coeff command is used with the {agni} style which
|
||||
specifies an AGNI potential file containing the parameters of the
|
||||
force field for the needed elements. These are mapped to LAMMPS atom
|
||||
types by specifying N additional arguments after the filename in the
|
||||
force field for the needed elements. These are mapped to LAMMPS atom
|
||||
types by specifying N additional arguments after the filename in the
|
||||
pair_coeff command, where N is the number of LAMMPS atom types:
|
||||
|
||||
filename
|
||||
|
|
@ -52,13 +52,13 @@ to specify the path for the force field file.
|
|||
|
||||
An AGNI force field is fully specified by the filename which contains the
|
||||
parameters of the force field, i.e., the reference training environments
|
||||
used to construct the machine learning force field. Example force field
|
||||
and input files are provided in the examples/USER/misc/agni directory.
|
||||
used to construct the machine learning force field. Example force field
|
||||
and input files are provided in the examples/USER/misc/agni directory.
|
||||
|
||||
:line
|
||||
|
||||
Styles with {omp} suffix is functionally the same as the corresponding
|
||||
style without the suffix. They have been optimized to run faster, depending
|
||||
Styles with {omp} suffix is functionally the same as the corresponding
|
||||
style without the suffix. They have been optimized to run faster, depending
|
||||
on your available hardware, as discussed in "Section 5"_Section_accelerate.html
|
||||
of the manual. The accelerated style takes the same arguments and
|
||||
should produce the same results, except for round-off and precision
|
||||
|
|
|
|||
|
|
@ -75,7 +75,7 @@ Lennard-Jones 12/6) given by
|
|||
:c,image(Eqs/pair_buck.jpg)
|
||||
|
||||
where rho is an ionic-pair dependent length parameter, and Rc is the
|
||||
cutoff on both terms.
|
||||
cutoff on both terms.
|
||||
|
||||
The styles with {coul/cut} or {coul/long} or {coul/msm} add a
|
||||
Coulombic term as described for the "lj/cut"_pair_lj.html pair styles.
|
||||
|
|
|
|||
|
|
@ -55,33 +55,33 @@ defined in the reaction kinetics files specified with the "fix
|
|||
rx"_fix_rx.html command or they must correspond to the tag "1fluid",
|
||||
signifying interaction with a product species mixture determined
|
||||
through a one-fluid approximation. The interaction potential is
|
||||
weighted by the geometric average of either the mole fraction concentrations
|
||||
or the number of molecules associated with the interacting coarse-grained
|
||||
particles (see the {fractional} or {molecular} weighting pair style options).
|
||||
weighted by the geometric average of either the mole fraction concentrations
|
||||
or the number of molecules associated with the interacting coarse-grained
|
||||
particles (see the {fractional} or {molecular} weighting pair style options).
|
||||
The coarse-grained potential is stored before and after the
|
||||
reaction kinetics solver is applied, where the difference is defined
|
||||
to be the internal chemical energy (uChem).
|
||||
|
||||
The fourth argument specifies the type of scaling that will be used
|
||||
The fourth argument specifies the type of scaling that will be used
|
||||
to scale the EXP-6 parameters as reactions occur. Currently, there
|
||||
are three scaling options: {exponent}, {polynomial} and {none}.
|
||||
|
||||
Exponent scaling requires two additional arguments for scaling
|
||||
Exponent scaling requires two additional arguments for scaling
|
||||
the {Rm} and {epsilon} parameters, respectively. The scaling factor
|
||||
is computed by phi^exponent, where phi is the number of molecules
|
||||
represented by the coarse-grain particle and exponent is specified
|
||||
is computed by phi^exponent, where phi is the number of molecules
|
||||
represented by the coarse-grain particle and exponent is specified
|
||||
as a pair coefficient argument for {Rm} and {epsilon}, respectively.
|
||||
The {Rm} and {epsilon} parameters are multiplied by the scaling
|
||||
The {Rm} and {epsilon} parameters are multiplied by the scaling
|
||||
factor to give the scaled interaction parameters for the CG particle.
|
||||
|
||||
Polynomial scaling requires a filename to be specified as a pair
|
||||
Polynomial scaling requires a filename to be specified as a pair
|
||||
coeff argument. The file contains the coefficients to a fifth order
|
||||
polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
|
||||
upon phi (the number of molecules represented by the CG particle).
|
||||
polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend
|
||||
upon phi (the number of molecules represented by the CG particle).
|
||||
The format of a polynomial file is provided below.
|
||||
|
||||
The {none} option to the scaling does not have any additional pair coeff
|
||||
arguments. This is equivalent to specifying the {exponent} option with
|
||||
arguments. This is equivalent to specifying the {exponent} option with
|
||||
{Rm} and {epsilon} exponents of 0.0 and 0.0, respectively.
|
||||
|
||||
The final argument specifies the interaction cutoff (optional).
|
||||
|
|
@ -102,7 +102,7 @@ parenthesized comments):
|
|||
|
||||
# POLYNOMIAL FILE (one or more comment or blank lines) :pre
|
||||
# General Functional Form:
|
||||
# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
|
||||
# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F
|
||||
#
|
||||
# Parameter A B C D E F
|
||||
(blank)
|
||||
|
|
|
|||
|
|
@ -24,25 +24,25 @@ pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
|
||||
potential as described in "(KC05)"_#KC05. An important simplification is made,
|
||||
which is to take all normals along the z-axis.
|
||||
The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction
|
||||
potential as described in "(KC05)"_#KC05. An important simplification is made,
|
||||
which is to take all normals along the z-axis.
|
||||
|
||||
:c,image(Eqs/pair_kolmogorov_crespi_z.jpg)
|
||||
|
||||
It is important to have a suffiently large cutoff to ensure smooth forces.
|
||||
Energies are shifted so that they go continously to zero at the cutoff assuming
|
||||
It is important to have a suffiently large cutoff to ensure smooth forces.
|
||||
Energies are shifted so that they go continously to zero at the cutoff assuming
|
||||
that the exponential part of {Vij} (first term) decays sufficiently fast.
|
||||
This shift is achieved by the last term in the equation for {Vij} above.
|
||||
|
||||
This potential is intended for interactions between two layers of graphene.
|
||||
Therefore, to avoid interaction between layers in multi-layered materials,
|
||||
each layer should have a separate atom type and interactions should only
|
||||
This potential is intended for interactions between two layers of graphene.
|
||||
Therefore, to avoid interaction between layers in multi-layered materials,
|
||||
each layer should have a separate atom type and interactions should only
|
||||
be computed between atom types of neighbouring layers.
|
||||
|
||||
The parameter file (e.g. CC.KC), is intended for use with metal
|
||||
"units"_units.html, with energies in meV. An additional parameter, {S},
|
||||
is available to facilitate scaling of energies in accordance with
|
||||
The parameter file (e.g. CC.KC), is intended for use with metal
|
||||
"units"_units.html, with energies in meV. An additional parameter, {S},
|
||||
is available to facilitate scaling of energies in accordance with
|
||||
"(vanWijk)"_#vanWijk.
|
||||
|
||||
This potential must be used in combination with hybrid/overlay.
|
||||
|
|
@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info.
|
|||
|
||||
:line
|
||||
|
||||
:link(KC05)
|
||||
:link(KC05)
|
||||
[(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005)
|
||||
|
||||
:link(vanWijk)
|
||||
|
|
|
|||
|
|
@ -97,9 +97,9 @@ tags must either correspond to the species defined in the reaction
|
|||
kinetics files specified with the "fix rx"_fix_rx.html command or they
|
||||
must correspond to the tag "1fluid", signifying interaction with a
|
||||
product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
|
||||
stored before and after the reaction kinetics solver is applied, where
|
||||
the difference is defined to be the internal chemical energy (uChem).
|
||||
|
|
|
|||
|
|
@ -39,17 +39,17 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1
|
|||
|
||||
[Description:]
|
||||
|
||||
The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk}
|
||||
and coaxial stacking interaction {oxdna/coaxstk} as well
|
||||
as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on
|
||||
opposite strands.
|
||||
|
||||
The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
|
||||
in the above example. The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients
|
||||
in the above example. The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1
|
||||
for a detailed description of the oxDNA force field.
|
||||
|
||||
|
|
@ -57,8 +57,8 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty
|
|||
{oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
|
||||
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
|
||||
The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example).
|
||||
When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html
|
||||
or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
||||
|
|
@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|||
|
||||
[Related commands:]
|
||||
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html
|
||||
|
||||
[Default:] none
|
||||
|
|
|
|||
|
|
@ -45,17 +45,17 @@ pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre
|
|||
|
||||
[Description:]
|
||||
|
||||
The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field
|
||||
for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the
|
||||
excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk}
|
||||
and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh}
|
||||
as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on
|
||||
opposite strands.
|
||||
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
The exact functional form of the pair styles is rather complex.
|
||||
The individual potentials consist of products of modulation factors,
|
||||
which themselves are constructed from a number of more basic potentials
|
||||
(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms.
|
||||
We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2
|
||||
and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field.
|
||||
|
||||
|
|
@ -63,7 +63,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st
|
|||
{oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients
|
||||
in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
|
||||
Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
|
||||
Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients
|
||||
after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat
|
||||
e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html
|
||||
the temperature coefficients have to be matched to the one used in the fix.
|
||||
|
|
@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages.
|
|||
[Related commands:]
|
||||
|
||||
"bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html,
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
|
||||
"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html
|
||||
|
||||
[Default:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -85,9 +85,9 @@ tags must either correspond to the species defined in the reaction
|
|||
kinetics files specified with the "fix rx"_fix_rx.html command or they
|
||||
must correspond to the tag "1fluid", signifying interaction with a
|
||||
product species mixture determined through a one-fluid approximation.
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
The interaction potential is weighted by the geometric average of
|
||||
either the mole fraction concentrations or the number of molecules
|
||||
associated with the interacting coarse-grained particles (see the
|
||||
{fractional} or {molecular} weighting pair style options). The coarse-grained potential is
|
||||
stored before and after the reaction kinetics solver is applied, where
|
||||
the difference is defined to be the internal chemical energy (uChem).
|
||||
|
|
|
|||
|
|
@ -489,7 +489,7 @@ python"_Section_python.html. Note that it is important that the
|
|||
stand-alone LAMMPS executable and the LAMMPS shared library be
|
||||
consistent (built from the same source code files) in order for this
|
||||
to work. If the two have been built at different times using
|
||||
different source files, problems may occur.
|
||||
different source files, problems may occur.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
|
|
|
|||
|
|
@ -86,7 +86,7 @@ machine via HTTPS:
|
|||
or, if you have set up your GitHub account for using SSH keys, via SSH:
|
||||
|
||||
$ git clone git@github.com:<your user name>/lammps.git :pre
|
||||
|
||||
|
||||
You can find the proper URL by clicking the "Clone or download"-button:
|
||||
|
||||
:c,image(JPG/tutorial_https_block.png)
|
||||
|
|
|
|||
|
|
@ -36,7 +36,7 @@ lammps.PyLammps :h4
|
|||
|
||||
higher-level abstraction built on top of original C-Types interface
|
||||
manipulation of Python objects
|
||||
communication with LAMMPS is hidden from API user
|
||||
communication with LAMMPS is hidden from API user
|
||||
shorter, more concise Python
|
||||
better IPython integration, designed for quick prototyping :ul
|
||||
|
||||
|
|
@ -328,7 +328,7 @@ IPyLammps Examples :h2
|
|||
|
||||
Examples of IPython notebooks can be found in the python/examples/pylammps
|
||||
subdirectory. To open these notebooks launch {jupyter notebook} inside this
|
||||
directory and navigate to one of them. If you compiled and installed
|
||||
directory and navigate to one of them. If you compiled and installed
|
||||
a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
|
||||
you should be able to rerun all of these notebooks.
|
||||
|
||||
|
|
@ -399,19 +399,19 @@ natoms = L.system.natoms :pre
|
|||
for i in range(niterations):
|
||||
iatom = random.randrange(0, natoms)
|
||||
current_atom = L.atoms\[iatom\] :pre
|
||||
|
||||
|
||||
x0, y0 = current_atom.position :pre
|
||||
|
||||
|
||||
dx = deltamove * random.uniform(-1, 1)
|
||||
dy = deltamove * random.uniform(-1, 1) :pre
|
||||
|
||||
|
||||
current_atom.position = (x0+dx, y0+dy) :pre
|
||||
|
||||
|
||||
L.run(1, "pre no post no") :pre
|
||||
|
||||
|
||||
e = L.eval("pe")
|
||||
energies.append(e) :pre
|
||||
|
||||
|
||||
if e <= elast:
|
||||
naccept += 1
|
||||
elast = e
|
||||
|
|
@ -460,4 +460,4 @@ Feedback and Contributing :h2
|
|||
If you find this Python interface useful, please feel free to provide feedback
|
||||
and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also
|
||||
want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
|
||||
and maybe their latest research results.
|
||||
and maybe their latest research results.
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1337,8 +1337,8 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
|
|||
fH[1] = 0.5 * alpha * fd[1];
|
||||
fH[2] = 0.5 * alpha * fd[2];
|
||||
|
||||
xH1 = x[jH1];
|
||||
xH2 = x[jH2];
|
||||
xH1 = x[iH1];
|
||||
xH2 = x[iH2];
|
||||
v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
|
||||
v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
|
||||
v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
|
||||
|
|
|
|||
|
|
@ -1271,7 +1271,7 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
|
|||
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
|
||||
double cross321[3],cross234[3],prefactor,SpN;
|
||||
double fcijpc,fcikpc,fcjlpc,fcjkpc,fcilpc;
|
||||
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
|
||||
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa2,at2,cw,cwnum,cwnom;
|
||||
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
|
||||
double dctik,dctjk,dctjl,dctij,dctji,dctil,rik2i,rjl2i,sink2i,sinl2i;
|
||||
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
|
||||
|
|
@ -1856,8 +1856,6 @@ double PairAIREBO::bondorder(int i, int j, double rij[3],
|
|||
|
||||
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa1 = -prefactor*(1.0-square(om1234)) *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
|
||||
at2 = aa*cwnum;
|
||||
|
||||
|
|
@ -2107,7 +2105,7 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
|
|||
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
|
||||
double cross321[3],cross234[3],prefactor,SpN;
|
||||
double fcikpc,fcjlpc,fcjkpc,fcilpc;
|
||||
double dt2dik[3],dt2djl[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
|
||||
double dt2dik[3],dt2djl[3],aa,aaa2,at2,cw,cwnum,cwnom;
|
||||
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
|
||||
double dctik,dctjk,dctjl,dctil,rik2i,rjl2i,sink2i,sinl2i;
|
||||
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil;
|
||||
|
|
@ -2800,8 +2798,6 @@ double PairAIREBO::bondorderLJ(int i, int j, double rij[3], double rijmag,
|
|||
|
||||
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa1 = -prefactor*(1.0-square(om1234)) *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
|
||||
at2 = aa*cwnum;
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -50,7 +50,7 @@ enum{NCOMMON};
|
|||
|
||||
ComputeCNPAtom::ComputeCNPAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
Compute(lmp, narg, arg),
|
||||
nearest(NULL), nnearest(NULL), cnpv(NULL)
|
||||
list(NULL), nearest(NULL), nnearest(NULL), cnpv(NULL)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR,"Illegal compute cnp/atom command");
|
||||
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -1038,7 +1038,7 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
|
|||
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
|
||||
double cross321[3],cross234[3],prefactor,SpN;
|
||||
double fcijpc,fcikpc,fcjlpc,fcjkpc,fcilpc;
|
||||
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
|
||||
double dt2dik[3],dt2djl[3],dt2dij[3],aa,aaa2,at2,cw,cwnum,cwnom;
|
||||
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
|
||||
double dctik,dctjk,dctjl,dctij,dctji,dctil,rik2i,rjl2i,sink2i,sinl2i;
|
||||
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil,dt1dij;
|
||||
|
|
@ -1628,8 +1628,6 @@ double PairAIREBOOMP::bondorder_thr(int i, int j, double rij[3], double rijmag,
|
|||
|
||||
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa1 = -prefactor*(1.0-square(om1234)) *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
|
||||
at2 = aa*cwnum;
|
||||
|
||||
|
|
@ -1879,7 +1877,7 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
|
|||
double w21,dw21,r34[3],r34mag,cos234,w34,dw34;
|
||||
double cross321[3],cross234[3],prefactor,SpN;
|
||||
double fcikpc,fcjlpc,fcjkpc,fcilpc;
|
||||
double dt2dik[3],dt2djl[3],aa,aaa1,aaa2,at2,cw,cwnum,cwnom;
|
||||
double dt2dik[3],dt2djl[3],aa,aaa2,at2,cw,cwnum,cwnom;
|
||||
double sin321,sin234,rr,rijrik,rijrjl,rjk2,rik2,ril2,rjl2;
|
||||
double dctik,dctjk,dctjl,dctil,rik2i,rjl2i,sink2i,sinl2i;
|
||||
double rjk[3],ril[3],dt1dik,dt1djk,dt1djl,dt1dil;
|
||||
|
|
@ -2572,8 +2570,6 @@ double PairAIREBOOMP::bondorderLJ_thr(int i, int j, double rij[3], double rijmag
|
|||
|
||||
aa = (prefactor*2.0*cw/cwnom)*w21*w34 *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa1 = -prefactor*(1.0-square(om1234)) *
|
||||
(1.0-tspjik)*(1.0-tspijl);
|
||||
aaa2 = -prefactor*(1.0-square(om1234)) * w21*w34;
|
||||
at2 = aa*cwnum;
|
||||
|
||||
|
|
|
|||
|
|
@ -572,17 +572,18 @@ void PairReaxCOMP::read_reax_forces(int vflag)
|
|||
|
||||
void PairReaxCOMP::FindBond()
|
||||
{
|
||||
int i, ii, j, pj, jtag, nj, jtmp, jj;
|
||||
double bo_tmp, bo_cut, rij, rsq;
|
||||
|
||||
bond_data *bo_ij;
|
||||
bo_cut = 0.10;
|
||||
const double bo_cut = 0.10;
|
||||
int i;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel for schedule(static) default(shared) \
|
||||
private(i, nj, pj, bo_ij, j, bo_tmp)
|
||||
private(i)
|
||||
#endif
|
||||
for (i = 0; i < system->n; i++) {
|
||||
int j, pj, nj;
|
||||
double bo_tmp;
|
||||
bond_data *bo_ij;
|
||||
|
||||
nj = 0;
|
||||
for( pj = Start_Index(i, lists); pj < End_Index(i, lists); ++pj ) {
|
||||
bo_ij = &( lists->select.bond_list[pj] );
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
|
|
|||
|
|
@ -55,7 +55,6 @@ void Add_dBond_to_ForcesOMP( reax_system *system, int i, int pj,
|
|||
long reductionOffset = (system->N * tid);
|
||||
|
||||
/* Virial Tallying variables */
|
||||
double f_scaler;
|
||||
rvec fi_tmp, fj_tmp, fk_tmp, delij, delji, delki, delkj, temp;
|
||||
|
||||
/* Initializations */
|
||||
|
|
@ -229,14 +228,11 @@ void Add_dBond_to_Forces_NPTOMP( reax_system *system, int i, int pj, simulation_
|
|||
ivec rel_box;
|
||||
int pk, k, j;
|
||||
|
||||
PairReaxCOMP *pair_reax_ptr = static_cast<class PairReaxCOMP*>(system->pair_ptr);
|
||||
|
||||
#if defined(_OPENMP)
|
||||
int tid = omp_get_thread_num();
|
||||
#else
|
||||
int tid = 0;
|
||||
#endif
|
||||
ThrData *thr = pair_reax_ptr->getFixOMP()->get_thr(tid);
|
||||
long reductionOffset = (system->N * tid);
|
||||
|
||||
/* Initializations */
|
||||
|
|
@ -430,12 +426,9 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
|
|||
#endif
|
||||
|
||||
double p_lp1 = system->reax_param.gp.l[15];
|
||||
int num_bonds = 0;
|
||||
double p_boc1 = system->reax_param.gp.l[0];
|
||||
double p_boc2 = system->reax_param.gp.l[1];
|
||||
reax_list *bonds = (*lists) + BONDS;
|
||||
int natoms = system->N;
|
||||
int nthreads = control->nthreads;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel default(shared)
|
||||
|
|
@ -454,11 +447,6 @@ void BOOMP( reax_system *system, control_params *control, simulation_data *data,
|
|||
two_body_parameters *twbp;
|
||||
bond_order_data *bo_ij, *bo_ji;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
int tid = omp_get_thread_num();
|
||||
#else
|
||||
int tid = 0;
|
||||
#endif
|
||||
/* Calculate Deltaprime, Deltaprime_boc values */
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp for schedule(static)
|
||||
|
|
|
|||
|
|
@ -49,14 +49,13 @@ void BondsOMP( reax_system *system, control_params *control,
|
|||
startTimeBase = MPI_Wtime();
|
||||
#endif
|
||||
|
||||
int natoms = system->n;
|
||||
int nthreads = control->nthreads;
|
||||
const int natoms = system->n;
|
||||
reax_list *bonds = (*lists) + BONDS;
|
||||
double gp3 = system->reax_param.gp.l[3];
|
||||
double gp4 = system->reax_param.gp.l[4];
|
||||
double gp7 = system->reax_param.gp.l[7];
|
||||
double gp10 = system->reax_param.gp.l[10];
|
||||
double gp37 = (int) system->reax_param.gp.l[37];
|
||||
const double gp3 = system->reax_param.gp.l[3];
|
||||
const double gp4 = system->reax_param.gp.l[4];
|
||||
const double gp7 = system->reax_param.gp.l[7];
|
||||
const double gp10 = system->reax_param.gp.l[10];
|
||||
const int gp37 = (int) system->reax_param.gp.l[37];
|
||||
double total_Ebond = 0.0;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
|
|
@ -66,9 +65,8 @@ void BondsOMP( reax_system *system, control_params *control,
|
|||
int i, j, pj;
|
||||
int start_i, end_i;
|
||||
int type_i, type_j;
|
||||
double ebond, ebond_thr=0.0, pow_BOs_be2, exp_be12, CEbo;
|
||||
double gp3, gp4, gp7, gp10, gp37;
|
||||
double exphu, exphua1, exphub1, exphuov, hulpov, estriph, estriph_thr=0.0;
|
||||
double ebond, pow_BOs_be2, exp_be12, CEbo;
|
||||
double exphu, exphua1, exphub1, exphuov, hulpov, estriph;
|
||||
double decobdbo, decobdboua, decobdboub;
|
||||
single_body_parameters *sbp_i, *sbp_j;
|
||||
two_body_parameters *twbp;
|
||||
|
|
|
|||
|
|
@ -265,7 +265,6 @@ void Validate_ListsOMP( reax_system *system, storage *workspace, reax_list **lis
|
|||
{
|
||||
int i, comp, Hindex;
|
||||
reax_list *bonds, *hbonds;
|
||||
reallocate_data *realloc = &(workspace->realloc);
|
||||
double saferzone = system->saferzone;
|
||||
|
||||
#if defined(_OPENMP)
|
||||
|
|
@ -335,25 +334,21 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
|
|||
startTimeBase = MPI_Wtime();
|
||||
#endif
|
||||
|
||||
int i, j, pi, pj;
|
||||
int start_i, end_i, start_j, end_j;
|
||||
int i, j, pj;
|
||||
int start_i, end_i;
|
||||
int type_i, type_j;
|
||||
int ihb, jhb, ihb_top, jhb_top;
|
||||
int local, flag;
|
||||
double r_ij, cutoff;
|
||||
double cutoff;
|
||||
single_body_parameters *sbp_i, *sbp_j;
|
||||
two_body_parameters *twbp;
|
||||
far_neighbor_data *nbr_pj;
|
||||
reax_atom *atom_i, *atom_j;
|
||||
bond_data *ibond, *jbond;
|
||||
reax_list *far_nbrs = *lists + FAR_NBRS;
|
||||
reax_list *bonds = *lists + BONDS;
|
||||
reax_list *hbonds = *lists + HBONDS;
|
||||
int num_bonds = 0;
|
||||
int num_hbonds = 0;
|
||||
int btop_i = 0;
|
||||
int btop_j = 0;
|
||||
int renbr = (data->step-data->prev_steps) % control->reneighbor == 0;
|
||||
|
||||
// We will use CdDeltaReduction as a temporary (double) buffer to accumulate total_bond_order
|
||||
// This is safe because CdDeltaReduction is currently zeroed and its accumulation doesn't start until BondsOMP()
|
||||
|
|
@ -368,8 +363,8 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
|
|||
|
||||
#if defined(_OPENMP)
|
||||
#pragma omp parallel default(shared) \
|
||||
private(i, atom_i, type_i, pi, start_i, end_i, sbp_i, btop_i, ibond, ihb, ihb_top, \
|
||||
j, atom_j, type_j, pj, start_j, end_j, sbp_j, nbr_pj, jbond, jhb, twbp)
|
||||
private(i, atom_i, type_i, start_i, end_i, sbp_i, btop_i, ihb, ihb_top, \
|
||||
j, atom_j, type_j, pj, sbp_j, nbr_pj, jhb, twbp)
|
||||
#endif
|
||||
{
|
||||
|
||||
|
|
@ -417,7 +412,6 @@ void Init_Forces_noQEq_OMP( reax_system *system, control_params *control,
|
|||
// outside of critical section.
|
||||
|
||||
// Start top portion of BOp()
|
||||
int jj = nbr_pj->nbr;
|
||||
double C12, C34, C56;
|
||||
double BO, BO_s, BO_pi, BO_pi2;
|
||||
double bo_cut = control->bo_cut;
|
||||
|
|
@ -602,7 +596,6 @@ void Compute_ForcesOMP( reax_system *system, control_params *control,
|
|||
reax_list **lists, output_controls *out_control,
|
||||
mpi_datatypes *mpi_data )
|
||||
{
|
||||
int qeq_flag;
|
||||
MPI_Comm comm = mpi_data->world;
|
||||
|
||||
// Init Forces
|
||||
|
|
|
|||
|
|
@ -50,16 +50,14 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
|
|||
#endif
|
||||
|
||||
/* Initialize parameters */
|
||||
double p_lp1 = system->reax_param.gp.l[15];
|
||||
double p_lp3 = system->reax_param.gp.l[5];
|
||||
double p_ovun3 = system->reax_param.gp.l[32];
|
||||
double p_ovun4 = system->reax_param.gp.l[31];
|
||||
double p_ovun6 = system->reax_param.gp.l[6];
|
||||
double p_ovun7 = system->reax_param.gp.l[8];
|
||||
double p_ovun8 = system->reax_param.gp.l[9];
|
||||
const double p_lp3 = system->reax_param.gp.l[5];
|
||||
const double p_ovun3 = system->reax_param.gp.l[32];
|
||||
const double p_ovun4 = system->reax_param.gp.l[31];
|
||||
const double p_ovun6 = system->reax_param.gp.l[6];
|
||||
const double p_ovun7 = system->reax_param.gp.l[8];
|
||||
const double p_ovun8 = system->reax_param.gp.l[9];
|
||||
|
||||
int natoms = system->n;
|
||||
int nthreads = control->nthreads;
|
||||
const int natoms = system->n;
|
||||
reax_list *bonds = (*lists) + BONDS;
|
||||
|
||||
double total_Elp = 0.0;
|
||||
|
|
@ -79,11 +77,11 @@ void Atom_EnergyOMP( reax_system *system, control_params *control,
|
|||
double exp_ovun2n, exp_ovun6, exp_ovun8;
|
||||
double inv_exp_ovun1, inv_exp_ovun2, inv_exp_ovun2n, inv_exp_ovun8;
|
||||
double e_un, CEunder1, CEunder2, CEunder3, CEunder4;
|
||||
double eng_tmp, f_tmp;
|
||||
double eng_tmp;
|
||||
double p_lp2, p_ovun2, p_ovun5;
|
||||
int numbonds;
|
||||
|
||||
single_body_parameters *sbp_i, *sbp_j;
|
||||
single_body_parameters *sbp_i;
|
||||
two_body_parameters *twbp;
|
||||
bond_data *pbond;
|
||||
bond_order_data *bo_ij;
|
||||
|
|
|
|||
|
|
@ -48,8 +48,6 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
|
|||
reax_list **lists, output_controls *out_control ) {
|
||||
|
||||
int natoms = system->n;
|
||||
int nthreads = control->nthreads;
|
||||
long totalReductionSize = system->N * nthreads;
|
||||
reax_list *far_nbrs = (*lists) + FAR_NBRS;
|
||||
double p_vdW1 = system->reax_param.gp.l[28];
|
||||
double p_vdW1i = 1.0 / p_vdW1;
|
||||
|
|
@ -71,7 +69,8 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
|
|||
double tmp, r_ij, fn13, exp1, exp2;
|
||||
double Tap, dTap, dfn13, CEvd, CEclmb, de_core;
|
||||
double dr3gamij_1, dr3gamij_3;
|
||||
double e_ele, e_ele_thr, e_vdW, e_vdW_thr, e_core, SMALL = 0.0001;
|
||||
double e_ele, e_vdW, e_core;
|
||||
const double SMALL = 0.0001;
|
||||
double e_lg, de_lg, r_ij5, r_ij6, re6;
|
||||
rvec temp, ext_press;
|
||||
two_body_parameters *twbp;
|
||||
|
|
@ -92,7 +91,6 @@ void vdW_Coulomb_Energy_OMP( reax_system *system, control_params *control,
|
|||
system->pair_ptr->vatom, thr);
|
||||
e_core = 0;
|
||||
e_vdW = 0;
|
||||
e_vdW_thr = 0;
|
||||
e_lg = 0;
|
||||
de_lg = 0.0;
|
||||
|
||||
|
|
@ -263,8 +261,6 @@ void Tabulated_vdW_Coulomb_Energy_OMP(reax_system *system,control_params *contro
|
|||
double SMALL = 0.0001;
|
||||
int natoms = system->n;
|
||||
reax_list *far_nbrs = (*lists) + FAR_NBRS;
|
||||
int nthreads = control->nthreads;
|
||||
long totalReductionSize = system->N * nthreads;
|
||||
double total_EvdW = 0.;
|
||||
double total_Eele = 0.;
|
||||
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
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Reference in New Issue