new CHARMM pair styles with force swithing/shifting
This commit is contained in:
Steve Plimpton
@ -940,6 +940,8 @@ KOKKOS, o = USER-OMP, t = OPT.
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"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
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"lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
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"lj/charmm/coul/long (giko)"_pair_charmm.html,
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"lj/charmm/coul/long (giko)"_pair_charmm.html,
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"lj/charmm/coul/msm"_pair_charmm.html,
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"lj/charmm/coul/msm"_pair_charmm.html,
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"lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
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"lj/charmmfsw/coul/long"_pair_charmm.html,
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"lj/class2 (gko)"_pair_class2.html,
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"lj/class2 (gko)"_pair_class2.html,
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"lj/class2/coul/cut (ko)"_pair_class2.html,
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"lj/class2/coul/cut (ko)"_pair_class2.html,
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"lj/class2/coul/long (gko)"_pair_class2.html,
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"lj/class2/coul/long (gko)"_pair_class2.html,
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@ -1148,6 +1150,7 @@ USER-OMP, t = OPT.
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"zero"_dihedral_zero.html,
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"zero"_dihedral_zero.html,
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"hybrid"_dihedral_hybrid.html,
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"hybrid"_dihedral_hybrid.html,
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"charmm (ko)"_dihedral_charmm.html,
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"charmm (ko)"_dihedral_charmm.html,
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"charmmfsh"_dihedral_charmm.html,
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"class2 (ko)"_dihedral_class2.html,
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"class2 (ko)"_dihedral_class2.html,
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"harmonic (io)"_dihedral_harmonic.html,
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"harmonic (io)"_dihedral_harmonic.html,
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"helix (o)"_dihedral_helix.html,
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"helix (o)"_dihedral_helix.html,
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@ -51,9 +51,11 @@ Lowercase directories :h4
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accelerate: run with various acceleration options (OpenMP, GPU, Phi)
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accelerate: run with various acceleration options (OpenMP, GPU, Phi)
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balance: dynamic load balancing, 2d system
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balance: dynamic load balancing, 2d system
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body: body particles, 2d system
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body: body particles, 2d system
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cmap: CMAP 5-body contributions to CHARMM force field
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colloid: big colloid particles in a small particle solvent, 2d system
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colloid: big colloid particles in a small particle solvent, 2d system
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comb: models using the COMB potential
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comb: models using the COMB potential
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coreshell: core/shell model using CORESHELL package
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coreshell: core/shell model using CORESHELL package
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controller: use of fix controller as a thermostat
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crack: crack propagation in a 2d solid
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crack: crack propagation in a 2d solid
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deposit: deposit atoms and molecules on a surface
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deposit: deposit atoms and molecules on a surface
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dipole: point dipolar particles, 2d system
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dipole: point dipolar particles, 2d system
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@ -62,6 +64,8 @@ eim: NaCl using the EIM potential
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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ellipse: ellipsoidal particles in spherical solvent, 2d system
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flow: Couette and Poiseuille flow in a 2d channel
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flow: Couette and Poiseuille flow in a 2d channel
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friction: frictional contact of spherical asperities between 2d surfaces
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friction: frictional contact of spherical asperities between 2d surfaces
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gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
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granregion: use of fix wall/region/gran as boundary on granular particles
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hugoniostat: Hugoniostat shock dynamics
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hugoniostat: Hugoniostat shock dynamics
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indent: spherical indenter into a 2d solid
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indent: spherical indenter into a 2d solid
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kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
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kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
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@ -69,6 +73,7 @@ meam: MEAM test for SiC and shear (same as shear examples)
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melt: rapid melt of 3d LJ system
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melt: rapid melt of 3d LJ system
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
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micelle: self-assembly of small lipid-like molecules into 2d bilayers
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min: energy minimization of 2d LJ melt
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min: energy minimization of 2d LJ melt
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mscg: parameterize a multi-scale coarse-graining (MSCG) model
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msst: MSST shock dynamics
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msst: MSST shock dynamics
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nb3b: use of nonbonded 3-body harmonic pair style
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nb3b: use of nonbonded 3-body harmonic pair style
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neb: nudged elastic band (NEB) calculation for barrier finding
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neb: nudged elastic band (NEB) calculation for barrier finding
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@ -87,7 +92,8 @@ snap: NVE dynamics for BCC tantalum crystal using SNAP potential
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srd: stochastic rotation dynamics (SRD) particles as solvent
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srd: stochastic rotation dynamics (SRD) particles as solvent
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streitz: use of Streitz/Mintmire potential with charge equilibration
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streitz: use of Streitz/Mintmire potential with charge equilibration
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
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vashishta: use of the Vashishta potential :tb(s=:)
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vashishta: use of the Vashishta potential
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voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:)
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Here is how you can run and visualize one of the sample problems:
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Here is how you can run and visualize one of the sample problems:
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@ -204,7 +204,10 @@ documentation for the formula it computes.
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"bond_style"_bond_harmonic.html harmonic
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"bond_style"_bond_harmonic.html harmonic
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"angle_style"_angle_charmm.html charmm
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"angle_style"_angle_charmm.html charmm
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"dihedral_style"_dihedral_charmm.html charmmfsh
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"dihedral_style"_dihedral_charmm.html charmm
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"dihedral_style"_dihedral_charmm.html charmm
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"pair_style"_pair_charmm.html lj/charmmfsw/coul/charmmfsh
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"pair_style"_pair_charmm.html lj/charmmfsw/coul/long
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"pair_style"_pair_charmm.html lj/charmm/coul/charmm
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"pair_style"_pair_charmm.html lj/charmm/coul/charmm
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"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
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"pair_style"_pair_charmm.html lj/charmm/coul/charmm/implicit
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"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
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"pair_style"_pair_charmm.html lj/charmm/coul/long :ul
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@ -212,6 +215,12 @@ documentation for the formula it computes.
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"special_bonds"_special_bonds.html charmm
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"special_bonds"_special_bonds.html charmm
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"special_bonds"_special_bonds.html amber :ul
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"special_bonds"_special_bonds.html amber :ul
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NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were
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released in March 2017. We recommend they be used instead of the
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older {charmm} styles. See discussion of the differences on the "pair
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charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
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doc pages.
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DREIDING is a generic force field developed by the "Goddard
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DREIDING is a generic force field developed by the "Goddard
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group"_http://www.wag.caltech.edu at Caltech and is useful for
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group"_http://www.wag.caltech.edu at Caltech and is useful for
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predicting structures and dynamics of organic, biological and
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predicting structures and dynamics of organic, biological and
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@ -19,7 +19,7 @@ keyword = {extra/dof} or {extra} or {dynamic/dof} or {dynamic} :l
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N = # of extra degrees of freedom to subtract
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N = # of extra degrees of freedom to subtract
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{extra} syntax is identical to {extra/dof}, will be disabled at some point
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{extra} syntax is identical to {extra/dof}, will be disabled at some point
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{dynamic/dof} value = {yes} or {no}
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{dynamic/dof} value = {yes} or {no}
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yes/no = do or do not recompute the number of atoms contributing to the temperature
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yes/no = do or do not recompute the number of degrees of freedom (DOF) contributing to the temperature
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{dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
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{dynamic} syntax is identical to {dynamic/dof}, will be disabled at some point :pre
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:ule
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:ule
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@ -46,13 +46,16 @@ degrees-of-freedom. See the "compute
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temp/asphere"_compute_temp_asphere.html command for an example.
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temp/asphere"_compute_temp_asphere.html command for an example.
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The {dynamic/dof} or {dynamic} keyword determines whether the number
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The {dynamic/dof} or {dynamic} keyword determines whether the number
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of atoms N in the compute group is re-computed each time a temperature
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of atoms N in the compute group and their associated degrees of
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is computed. Only compute styles that calculate a temperature use
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freedom are re-computed each time a temperature is computed. Only
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this option. By default, N is assumed to be constant. If you are
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compute styles that calculate a temperature use this option. By
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adding atoms to the system (see the "fix pour"_fix_pour.html, "fix
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default, N and their DOF are assumed to be constant. If you are
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deposit"_fix_deposit.html and "fix gcmc"_fix_gcmc.html commands) or
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adding atoms or molecules to the system (see the "fix
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expect atoms to be lost (e.g. due to evaporation), then this option
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pour"_fix_pour.html, "fix deposit"_fix_deposit.html, and "fix
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should be used to insure the temperature is correctly normalized.
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gcmc"_fix_gcmc.html commands) or expect atoms or molecules to be lost
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(e.g. due to exiting the simulation box or via "fix
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evaporation"_fix_evaporation.html), then this option should be used to
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insure the temperature is correctly normalized.
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NOTE: The {extra} and {dynamic} keywords should not be used as they
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NOTE: The {extra} and {dynamic} keywords should not be used as they
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are deprecated (March 2017) and will eventually be disabled. Instead,
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are deprecated (March 2017) and will eventually be disabled. Instead,
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@ -10,21 +10,25 @@ dihedral_style charmm command :h3
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dihedral_style charmm/intel command :h3
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dihedral_style charmm/intel command :h3
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dihedral_style charmm/kk command :h3
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dihedral_style charmm/kk command :h3
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dihedral_style charmm/omp command :h3
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dihedral_style charmm/omp command :h3
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dihedral_style charmmfsh command :h3
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[Syntax:]
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[Syntax:]
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dihedral_style charmm :pre
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dihedral_style style :pre
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style = {charmm} or {charmmfsh} :ul
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[Examples:]
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[Examples:]
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dihedral_style charmm
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dihedral_style charmm
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dihedral_style charmmfsh
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dihedral_coeff 1 0.2 1 180 1.0
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dihedral_coeff 1 0.2 1 180 1.0
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dihedral_coeff 2 1.8 1 0 1.0
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dihedral_coeff 2 1.8 1 0 1.0
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dihedral_coeff 1 3.1 2 180 0.5 :pre
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dihedral_coeff 1 3.1 2 180 0.5 :pre
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[Description:]
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[Description:]
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The {charmm} dihedral style uses the potential
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The {charmm} and {charmmfsh} dihedral styles use the potential
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:c,image(Eqs/dihedral_charmm.jpg)
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:c,image(Eqs/dihedral_charmm.jpg)
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@ -34,6 +38,11 @@ field (see comment on weighting factors below). See
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"(Cornell)"_#dihedral-Cornell for a description of the AMBER force
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"(Cornell)"_#dihedral-Cornell for a description of the AMBER force
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field.
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field.
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NOTE: The newer {charmmfsh} style was released in March 2017. We
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recommend it be used instead of the older {charmm} style when running
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a simulation with the CHARMM force field. See the discussion below
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and more details on the "pair_style charmm"_pair_charmm.html doc page.
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The following coefficients must be defined for each dihedral type via the
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The following coefficients must be defined for each dihedral type via the
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"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
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"dihedral_coeff"_dihedral_coeff.html command as in the example above, or in
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the data file or restart files read by the "read_data"_read_data.html
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the data file or restart files read by the "read_data"_read_data.html
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@ -73,13 +82,23 @@ special_bonds 1-4 scaling factor to 0.0 (which is the
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default). Otherwise 1-4 non-bonded interactions in dihedrals will be
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default). Otherwise 1-4 non-bonded interactions in dihedrals will be
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computed twice.
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computed twice.
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Also note that for AMBER force fields, which use pair styles with
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For simulations using the CHARMM force field, the difference between
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"lj/cut", the special_bonds 1-4 scaling factor should be set to the
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the {charmm} and {charmmfsh} styles is in the computation of the 1-4
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AMBER defaults (1/2 and 5/6) and all the dihedral weighting factors
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non-bond interactions, if the distance between the two atoms is within
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(4th coeff above) must be set to 0.0. In this case, you can use any
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the switching distance of the pairwise potential defined by the
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pair style you wish, since the dihedral does not need any
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corresponding CHARMM pair style, i.e. between the inner and outer
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Lennard-Jones parameter information and will not compute any 1-4
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cutoffs specified for the pair style. See the discussion on the
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non-bonded interactions.
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"CHARMM pair_style"_pair_charmm.html doc page for details.
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Note that for AMBER force fields, which use pair styles with "lj/cut",
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the special_bonds 1-4 scaling factor should be set to the AMBER
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defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
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coeff above) must be set to 0.0. In this case, you can use any pair
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style you wish, since the dihedral does not need any Lennard-Jones
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parameter information and will not compute any 1-4 non-bonded
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interactions. Likewise the {charmm} or {charmmfsh} styles are
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identical in this case since no 1-4 non-bonded interactions are
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computed.
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:line
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:line
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@ -182,13 +182,13 @@ currently support the -DFFT_SINGLE compiler switch.
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:line
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:line
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The {msm} style invokes a multi-level summation method MSM solver,
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The {msm} style invokes a multi-level summation method MSM solver,
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"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge to a 3d
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"(Hardy)"_#Hardy2006 or "(Hardy2)"_#Hardy2009, which maps atom charge
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mesh, and uses a multi-level hierarchy of coarser and coarser meshes
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to a 3d mesh, and uses a multi-level hierarchy of coarser and coarser
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on which direct coulomb solves are done. This method does not use
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meshes on which direct coulomb solves are done. This method does not
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FFTs and scales as N. It may therefore be faster than the other
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use FFTs and scales as N. It may therefore be faster than the other
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K-space solvers for relatively large problems when running on large
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K-space solvers for relatively large problems when running on large
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core counts. MSM can also be used for non-periodic boundary conditions and
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core counts. MSM can also be used for non-periodic boundary conditions
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for mixed periodic and non-periodic boundaries.
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and for mixed periodic and non-periodic boundaries.
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MSM is most competitive versus Ewald and PPPM when only relatively
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MSM is most competitive versus Ewald and PPPM when only relatively
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low accuracy forces, about 1e-4 relative error or less accurate,
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low accuracy forces, about 1e-4 relative error or less accurate,
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@ -17,12 +17,14 @@ pair_style lj/charmm/coul/long/opt command :h3
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pair_style lj/charmm/coul/long/omp command :h3
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pair_style lj/charmm/coul/long/omp command :h3
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pair_style lj/charmm/coul/msm command :h3
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pair_style lj/charmm/coul/msm command :h3
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pair_style lj/charmm/coul/msm/omp command :h3
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pair_style lj/charmm/coul/msm/omp command :h3
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pair_style lj/charmmfsw/coul/charmmfsh command :h3
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pair_style lj/charmmfsw/coul/long command :h3
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[Syntax:]
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[Syntax:]
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pair_style style args :pre
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pair_style style args :pre
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style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm}
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style = {lj/charmm/coul/charmm} or {lj/charmm/coul/charmm/implicit} or {lj/charmm/coul/long} or {lj/charmm/coul/msm} or {lj/charmmfsw/coul/charmmfsh} or {lj/charmmfsw/coul/long}
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args = list of arguments for a particular style :ul
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args = list of arguments for a particular style :ul
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{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
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{lj/charmm/coul/charmm} args = inner outer (inner2) (outer2)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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inner, outer = global switching cutoffs for Lennard Jones (and Coulombic if only 2 args)
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@ -35,12 +37,20 @@ args = list of arguments for a particular style :ul
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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{lj/charmm/coul/msm} args = inner outer (cutoff)
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{lj/charmm/coul/msm} args = inner outer (cutoff)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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inner, outer = global switching cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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{lj/charmmfsw/coul/charmmfsh} args = inner outer (cutoff)
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inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args)
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{lj/charmmfsw/coul/long} args = inner outer (cutoff)
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inner, outer = global cutoffs for LJ (and Coulombic if only 2 args)
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
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cutoff = global cutoff for Coulombic (optional, outer is Coulombic cutoff if only 2 args) :pre
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[Examples:]
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[Examples:]
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pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_style lj/charmm/coul/charmm 8.0 10.0 7.0 9.0
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pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0
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pair_style lj/charmmfsw/coul/charmmfsh 8.0 10.0 7.0 9.0
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pair_coeff * * 100.0 2.0
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pair_coeff * * 100.0 2.0
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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@ -51,6 +61,8 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_style lj/charmm/coul/long 8.0 10.0
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pair_style lj/charmm/coul/long 8.0 10.0 9.0
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pair_style lj/charmm/coul/long 8.0 10.0 9.0
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||||||
|
pair_style lj/charmmfsw/coul/long 8.0 10.0
|
||||||
|
pair_style lj/charmmfsw/coul/long 8.0 10.0 9.0
|
||||||
pair_coeff * * 100.0 2.0
|
pair_coeff * * 100.0 2.0
|
||||||
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
|
pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
|
||||||
|
|
||||||
@ -61,21 +73,55 @@ pair_coeff 1 1 100.0 2.0 150.0 3.5 :pre
|
|||||||
|
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
The {lj/charmm} styles compute LJ and Coulombic interactions with an
|
These pair styles compute Lennard Jones (LJ) and Coulombic
|
||||||
additional switching function S(r) that ramps the energy and force
|
interactions with additional switching or shifting functions that ramp
|
||||||
smoothly to zero between an inner and outer cutoff. It is a widely
|
the energy and/or force smoothly to zero between an inner and outer
|
||||||
used potential in the "CHARMM"_http://www.scripps.edu/brooks MD code.
|
cutoff. They are implementations of the widely used CHARMM force
|
||||||
See "(MacKerell)"_#pair-MacKerell for a description of the CHARMM force
|
field used in the "CHARMM"_http://www.scripps.edu/brooks MD code (and
|
||||||
field.
|
others). See "(MacKerell)"_#pair-MacKerell for a description of the
|
||||||
|
CHARMM force field.
|
||||||
|
|
||||||
|
The styles with {charmm} (not {charmmfsw} or {charmmfsh}) in their
|
||||||
|
name are the older, original LAMMPS implemetations. They compute the
|
||||||
|
LJ and Coulombic interactions with an energy switching function (esw,
|
||||||
|
a cubic polynomial), which ramps the energy smoothly to zero between
|
||||||
|
the inner and outer cutoff. This can cause irregularities in
|
||||||
|
pair-wise forces (due to the discontinuous 2nd derivative of energy at
|
||||||
|
the boundaries of the switching region), which in some cases can
|
||||||
|
result in substantial artifacts in an MD simulation.
|
||||||
|
|
||||||
|
The newer styles with {charmmfsw} or {charmmfsh} in their name replace
|
||||||
|
the energy switching with force switching (fsw) and force shifting
|
||||||
|
(fsh) functions, for LJ and Coulombic interactions respectively.
|
||||||
|
These follow the formulas and description given in
|
||||||
|
"(Steinbach)"_#Steinbach and "(Brooks)"_#Brooks to minimize these
|
||||||
|
artifacts.
|
||||||
|
|
||||||
|
NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
|
||||||
|
March 2017. We recommend they be used instead of the older {charmm}
|
||||||
|
styles. Eventually code from the new styles will propagate into the
|
||||||
|
related pair styles (e.g. implicit, accelerator, free energy
|
||||||
|
variants).
|
||||||
|
|
||||||
|
The general CHARMM formulas are as follows
|
||||||
|
|
||||||
:c,image(Eqs/pair_charmm.jpg)
|
:c,image(Eqs/pair_charmm.jpg)
|
||||||
|
|
||||||
Both the LJ and Coulombic terms require an inner and outer cutoff.
|
where the specific form of the switching or shifting function S(r) is
|
||||||
They can be the same for both formulas or different depending on
|
given in the "(Steinbach)"_#Steinbach paper.
|
||||||
whether 2 or 4 arguments are used in the pair_style command. In each
|
|
||||||
case, the inner cutoff distance must be less than the outer cutoff.
|
When using the {lj/charmm/coul/charmm styles}, both the LJ and
|
||||||
It it typical to make the difference between the 2 cutoffs about 1.0
|
Coulombic terms require an inner and outer cutoff. They can be the
|
||||||
Angstrom.
|
same for both formulas or different depending on whether 2 or 4
|
||||||
|
arguments are used in the pair_style command. For the
|
||||||
|
{lj/charmmfsw/coul/charmmfsh} style, the LJ term requires both an
|
||||||
|
inner and outer cutoff, while the Coulombic term requires only one
|
||||||
|
cutoff. If the Coulomb cutoff is not specified (2 instead of 3
|
||||||
|
arguments), the LJ outer cutoff is used for the Coulombic cutoff. In
|
||||||
|
all cases where an inner and outer cutoff are specified, the inner
|
||||||
|
cutoff distance must be less than the outer cutoff. It is typical to
|
||||||
|
make the difference between the inner and outer cutoffs about 2.0
|
||||||
|
Angstroms.
|
||||||
|
|
||||||
Style {lj/charmm/coul/charmm/implicit} computes the same formulas as
|
Style {lj/charmm/coul/charmm/implicit} computes the same formulas as
|
||||||
style {lj/charmm/coul/charmm} except that an additional 1/r term is
|
style {lj/charmm/coul/charmm} except that an additional 1/r term is
|
||||||
@ -86,12 +132,18 @@ screening. It is designed for use in a simulation of an unsolvated
|
|||||||
biomolecule (no explicit water molecules).
|
biomolecule (no explicit water molecules).
|
||||||
|
|
||||||
Styles {lj/charmm/coul/long} and {lj/charmm/coul/msm} compute the same
|
Styles {lj/charmm/coul/long} and {lj/charmm/coul/msm} compute the same
|
||||||
formulas as style {lj/charmm/coul/charmm} except that an additional
|
formulas as style {lj/charmm/coul/charmm} and style
|
||||||
damping factor is applied to the Coulombic term, as described for the
|
{lj/charmmfsw/coul/long} computes the same formulas as style
|
||||||
"lj/cut"_pair_lj.html pair styles. Only one Coulombic cutoff is
|
{lj/charmmfsw/coul/charmmfsh}, except that an additional damping
|
||||||
specified for {lj/charmm/coul/long} and {lj/charmm/coul/msm}; if only
|
factor is applied to the Coulombic term, so it can be used in
|
||||||
2 arguments are used in the pair_style command, then the outer LJ
|
conjunction with the "kspace_style"_kspace_style.html command and its
|
||||||
cutoff is used as the single Coulombic cutoff.
|
{ewald} or {pppm} or {msm} option. Only one Coulombic cutoff is
|
||||||
|
specified for these styles; if only 2 arguments are used in the
|
||||||
|
pair_style command, then the outer LJ cutoff is used as the single
|
||||||
|
Coulombic cutoff. The Coulombic cutoff specified for these styles
|
||||||
|
means that pairwise interactions within this distance are computed
|
||||||
|
directly; interactions outside that distance are computed in
|
||||||
|
reciprocal space.
|
||||||
|
|
||||||
The following coefficients must be defined for each pair of atoms
|
The following coefficients must be defined for each pair of atoms
|
||||||
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
types via the "pair_coeff"_pair_coeff.html command as in the examples
|
||||||
@ -111,7 +163,7 @@ sigma.
|
|||||||
The latter 2 coefficients are optional. If they are specified, they
|
The latter 2 coefficients are optional. If they are specified, they
|
||||||
are used in the LJ formula between 2 atoms of these types which are
|
are used in the LJ formula between 2 atoms of these types which are
|
||||||
also first and fourth atoms in any dihedral. No cutoffs are specified
|
also first and fourth atoms in any dihedral. No cutoffs are specified
|
||||||
because this CHARMM force field does not allow varying cutoffs for
|
because the CHARMM force field does not allow varying cutoffs for
|
||||||
individual atom pairs; all pairs use the global cutoff(s) specified in
|
individual atom pairs; all pairs use the global cutoff(s) specified in
|
||||||
the pair_style command.
|
the pair_style command.
|
||||||
|
|
||||||
@ -148,38 +200,41 @@ mixed. The default mix value is {arithmetic} to coincide with the
|
|||||||
usual settings for the CHARMM force field. See the "pair_modify"
|
usual settings for the CHARMM force field. See the "pair_modify"
|
||||||
command for details.
|
command for details.
|
||||||
|
|
||||||
None of the lj/charmm pair styles support the
|
None of the {lj/charmm} or {lj/charmmfsw} pair styles support the
|
||||||
"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
|
"pair_modify"_pair_modify.html shift option, since the Lennard-Jones
|
||||||
portion of the pair interaction is smoothed to 0.0 at the cutoff.
|
portion of the pair interaction is smoothed to 0.0 at the cutoff.
|
||||||
|
|
||||||
The {lj/charmm/coul/long} style supports the
|
The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} styles support
|
||||||
"pair_modify"_pair_modify.html table option since it can tabulate the
|
the "pair_modify"_pair_modify.html table option since they can
|
||||||
short-range portion of the long-range Coulombic interaction.
|
tabulate the short-range portion of the long-range Coulombic
|
||||||
|
interaction.
|
||||||
|
|
||||||
None of the lj/charmm pair styles support the
|
None of the {lj/charmm} or {lj/charmmfsw} pair styles support the
|
||||||
"pair_modify"_pair_modify.html tail option for adding long-range tail
|
"pair_modify"_pair_modify.html tail option for adding long-range tail
|
||||||
corrections to energy and pressure, since the Lennard-Jones portion of
|
corrections to energy and pressure, since the Lennard-Jones portion of
|
||||||
the pair interaction is smoothed to 0.0 at the cutoff.
|
the pair interaction is smoothed to 0.0 at the cutoff.
|
||||||
|
|
||||||
All of the lj/charmm pair styles write their information to "binary
|
All of the {lj/charmm} and {lj/charmmfsw} pair styles write their
|
||||||
restart files"_restart.html, so pair_style and pair_coeff commands do
|
information to "binary restart files"_restart.html, so pair_style and
|
||||||
not need to be specified in an input script that reads a restart file.
|
pair_coeff commands do not need to be specified in an input script
|
||||||
|
that reads a restart file.
|
||||||
|
|
||||||
The lj/charmm/coul/long pair style supports the use of the {inner},
|
The {lj/charmm/coul/long} and {lj/charmmfsw/coul/long} pair styles
|
||||||
{middle}, and {outer} keywords of the "run_style respa"_run_style.html
|
support the use of the {inner}, {middle}, and {outer} keywords of the
|
||||||
command, meaning the pairwise forces can be partitioned by distance at
|
"run_style respa"_run_style.html command, meaning the pairwise forces
|
||||||
different levels of the rRESPA hierarchy. The other styles only
|
can be partitioned by distance at different levels of the rRESPA
|
||||||
support the {pair} keyword of run_style respa. See the
|
hierarchy. The other styles only support the {pair} keyword of
|
||||||
"run_style"_run_style.html command for details.
|
run_style respa. See the "run_style"_run_style.html command for
|
||||||
|
details.
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
[Restrictions:]
|
[Restrictions:]
|
||||||
|
|
||||||
The {lj/charmm/coul/charmm} and {lj/charmm/coul/charmm/implicit}
|
All the styles with {coul/charmm} or {coul/charmmfsh} styles are part
|
||||||
styles are part of the MOLECULE package. The {lj/charmm/coul/long}
|
of the MOLECULE package. All the styles with {coul/long} style are
|
||||||
style is part of the KSPACE package. They are only enabled if LAMMPS
|
part of the KSPACE package. They are only enabled if LAMMPS was built
|
||||||
was built with those packages. See the "Making
|
with those packages. See the "Making
|
||||||
LAMMPS"_Section_start.html#start_3 section for more info. Note that
|
LAMMPS"_Section_start.html#start_3 section for more info. Note that
|
||||||
the MOLECULE and KSPACE packages are installed by default.
|
the MOLECULE and KSPACE packages are installed by default.
|
||||||
|
|
||||||
@ -191,6 +246,13 @@ the MOLECULE and KSPACE packages are installed by default.
|
|||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
|
:link(Brooks)
|
||||||
|
[(Brooks)] Brooks, et al, J Comput Chem, 30, 1545 (2009).
|
||||||
|
|
||||||
:link(pair-MacKerell)
|
:link(pair-MacKerell)
|
||||||
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
[(MacKerell)] MacKerell, Bashford, Bellott, Dunbrack, Evanseck, Field,
|
||||||
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
Fischer, Gao, Guo, Ha, et al, J Phys Chem, 102, 3586 (1998).
|
||||||
|
|
||||||
|
:link(Stenibach)
|
||||||
|
[(Steinbach)] Steinbach, Brooks, J Comput Chem, 15, 667 (1994).
|
||||||
|
|
||||||
|
|||||||
@ -25,18 +25,19 @@ pair_coeff 1 2 momb 0.0 1.0 1.0 10.2847 2.361 :pre
|
|||||||
|
|
||||||
[Description:]
|
[Description:]
|
||||||
|
|
||||||
Style {momb} computes pairwise van der Waals (vdW) and short-range interactions using the
|
Style {momb} computes pairwise van der Waals (vdW) and short-range
|
||||||
Morse potential and "(Grimme)"_#Grimme method implemented in the Many-Body
|
interactions using the Morse potential and "(Grimme)"_#Grimme method
|
||||||
Metal-Organic (MOMB) force field described comprehensively in "(Fichthorn)"_#Fichthorn and
|
implemented in the Many-Body Metal-Organic (MOMB) force field
|
||||||
"(Zhou)"_#Zhou4. Grimme's method is widely used to correct for dispersion
|
described comprehensively in "(Fichthorn)"_#Fichthorn and
|
||||||
in density functional theory calculations.
|
"(Zhou)"_#Zhou4. Grimme's method is widely used to correct for
|
||||||
|
dispersion in density functional theory calculations.
|
||||||
|
|
||||||
:c,image(Eqs/pair_momb.jpg)
|
:c,image(Eqs/pair_momb.jpg)
|
||||||
|
|
||||||
For the {momb} pair style, the following coefficients must be defined for each
|
For the {momb} pair style, the following coefficients must be defined
|
||||||
pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the
|
for each pair of atoms types via the "pair_coeff"_pair_coeff.html
|
||||||
examples above, or in the data file or restart files read by the
|
command as in the examples above, or in the data file or restart files
|
||||||
"read_data"_read_data.html as described below:
|
read by the "read_data"_read_data.html as described below:
|
||||||
|
|
||||||
D0 (energy units)
|
D0 (energy units)
|
||||||
alpha (1/distance units)
|
alpha (1/distance units)
|
||||||
|
|||||||
@ -63,8 +63,8 @@ balance: dynamic load balancing, 2d system
|
|||||||
body: body particles, 2d system
|
body: body particles, 2d system
|
||||||
cmap: CMAP 5-body contributions to CHARMM force field
|
cmap: CMAP 5-body contributions to CHARMM force field
|
||||||
colloid: big colloid particles in a small particle solvent, 2d system
|
colloid: big colloid particles in a small particle solvent, 2d system
|
||||||
coreshell: adiabatic core/shell model
|
|
||||||
comb: models using the COMB potential
|
comb: models using the COMB potential
|
||||||
|
coreshell: adiabatic core/shell model
|
||||||
controller: use of fix controller as a thermostat
|
controller: use of fix controller as a thermostat
|
||||||
crack: crack propagation in a 2d solid
|
crack: crack propagation in a 2d solid
|
||||||
deposit: deposition of atoms and molecules onto a 3d substrate
|
deposit: deposition of atoms and molecules onto a 3d substrate
|
||||||
@ -74,6 +74,7 @@ eim: NaCl using the EIM potential
|
|||||||
ellipse: ellipsoidal particles in spherical solvent, 2d system
|
ellipse: ellipsoidal particles in spherical solvent, 2d system
|
||||||
flow: Couette and Poiseuille flow in a 2d channel
|
flow: Couette and Poiseuille flow in a 2d channel
|
||||||
friction: frictional contact of spherical asperities between 2d surfaces
|
friction: frictional contact of spherical asperities between 2d surfaces
|
||||||
|
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
|
||||||
granregion: use of fix wall/region/gran as boundary on granular particles
|
granregion: use of fix wall/region/gran as boundary on granular particles
|
||||||
hugoniostat: Hugoniostat shock dynamics
|
hugoniostat: Hugoniostat shock dynamics
|
||||||
indent: spherical indenter into a 2d solid
|
indent: spherical indenter into a 2d solid
|
||||||
@ -103,7 +104,7 @@ snap: NVE dynamics for BCC tantalum crystal using SNAP potential
|
|||||||
streitz: Streitz-Mintmire potential for Al2O3
|
streitz: Streitz-Mintmire potential for Al2O3
|
||||||
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
|
||||||
vashishta: models using the Vashishta potential
|
vashishta: models using the Vashishta potential
|
||||||
voronoi: test of Voronoi tesselation in compute voronoi/atom
|
voronoi: Voronoi tesselation via compute voronoi/atom command
|
||||||
|
|
||||||
Here is a src/Make.py command which will perform a parallel build of a
|
Here is a src/Make.py command which will perform a parallel build of a
|
||||||
LAMMPS executable "lmp_mpi" with all the packages needed by all the
|
LAMMPS executable "lmp_mpi" with all the packages needed by all the
|
||||||
|
|||||||
44
examples/gcmc/CO2.txt
Normal file
44
examples/gcmc/CO2.txt
Normal file
@ -0,0 +1,44 @@
|
|||||||
|
# CO2 molecule file. TraPPE model.
|
||||||
|
|
||||||
|
3 atoms
|
||||||
|
2 bonds
|
||||||
|
1 angles
|
||||||
|
|
||||||
|
Coords
|
||||||
|
|
||||||
|
1 0.0 0.0 0.0
|
||||||
|
2 -1.16 0.0 0.0
|
||||||
|
3 1.16 0.0 0.0
|
||||||
|
|
||||||
|
Types
|
||||||
|
|
||||||
|
1 1
|
||||||
|
2 2
|
||||||
|
3 2
|
||||||
|
|
||||||
|
Charges
|
||||||
|
|
||||||
|
1 0.7
|
||||||
|
2 -0.35
|
||||||
|
3 -0.35
|
||||||
|
|
||||||
|
Bonds
|
||||||
|
|
||||||
|
1 1 1 2
|
||||||
|
2 1 1 3
|
||||||
|
|
||||||
|
Angles
|
||||||
|
|
||||||
|
1 1 2 1 3
|
||||||
|
|
||||||
|
Special Bond Counts
|
||||||
|
|
||||||
|
1 2 0 0
|
||||||
|
2 1 1 0
|
||||||
|
3 1 1 0
|
||||||
|
|
||||||
|
Special Bonds
|
||||||
|
|
||||||
|
1 2 3
|
||||||
|
2 1 3
|
||||||
|
3 1 2
|
||||||
83
examples/gcmc/in.gcmc.co2
Normal file
83
examples/gcmc/in.gcmc.co2
Normal file
@ -0,0 +1,83 @@
|
|||||||
|
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
|
||||||
|
# Rigid CO2 TraPPE model
|
||||||
|
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
|
||||||
|
# mixtures containing alkanes, carbon dioxide and
|
||||||
|
# nitrogen AIChE J., 47,1676-1682 (2001)].
|
||||||
|
|
||||||
|
# variables available on command line
|
||||||
|
|
||||||
|
variable mu index -8.1
|
||||||
|
variable disp index 0.5
|
||||||
|
variable temp index 338.0
|
||||||
|
variable lbox index 10.0
|
||||||
|
variable spacing index 5.0
|
||||||
|
|
||||||
|
# global model settings
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
boundary p p p
|
||||||
|
pair_style lj/cut/coul/long 14
|
||||||
|
pair_modify mix arithmetic tail yes
|
||||||
|
kspace_style ewald 0.0001
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
|
||||||
|
# box, start molecules on simple cubic lattice
|
||||||
|
|
||||||
|
lattice sc ${spacing}
|
||||||
|
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
|
||||||
|
create_box 2 box &
|
||||||
|
bond/types 1 &
|
||||||
|
angle/types 1 &
|
||||||
|
extra/bond/per/atom 2 &
|
||||||
|
extra/angle/per/atom 1 &
|
||||||
|
extra/special/per/atom 2
|
||||||
|
molecule co2mol CO2.txt
|
||||||
|
create_atoms 0 box mol co2mol 464563 units box
|
||||||
|
|
||||||
|
# rigid CO2 TraPPE model
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.053649 2.8
|
||||||
|
pair_coeff 2 2 0.156973 3.05
|
||||||
|
bond_coeff 1 0 1.16
|
||||||
|
angle_coeff 1 0 180
|
||||||
|
|
||||||
|
# masses
|
||||||
|
|
||||||
|
mass 1 12.0107
|
||||||
|
mass 2 15.9994
|
||||||
|
|
||||||
|
# MD settings
|
||||||
|
|
||||||
|
group co2 type 1 2
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
velocity all create ${temp} 54654
|
||||||
|
timestep 1.0
|
||||||
|
|
||||||
|
# rigid constraints with thermostat
|
||||||
|
|
||||||
|
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
|
||||||
|
fix_modify myrigidnvt dynamic/dof no
|
||||||
|
|
||||||
|
# gcmc
|
||||||
|
|
||||||
|
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 ${temp} ${mu} ${disp} mol &
|
||||||
|
co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||||
|
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||||
|
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||||
|
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||||
|
compute_modify thermo_temp dynamic/dof yes
|
||||||
|
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# run
|
||||||
|
|
||||||
|
run 20000
|
||||||
|
|
||||||
42
examples/gcmc/in.gcmc.lj
Normal file
42
examples/gcmc/in.gcmc.lj
Normal file
@ -0,0 +1,42 @@
|
|||||||
|
# GCMC for LJ simple fluid, no dynamics
|
||||||
|
|
||||||
|
# variables available on command line
|
||||||
|
|
||||||
|
variable mu index -21.0
|
||||||
|
variable disp index 1.0
|
||||||
|
variable temp index 2.0
|
||||||
|
variable lbox index 10.0
|
||||||
|
|
||||||
|
# global model settings
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
pair_style lj/cut 3.0
|
||||||
|
pair_modify tail yes
|
||||||
|
|
||||||
|
# box
|
||||||
|
|
||||||
|
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
|
||||||
|
create_box 1 box
|
||||||
|
|
||||||
|
# lj parameters
|
||||||
|
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
# gcmc
|
||||||
|
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||||
|
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||||
|
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||||
|
compute_modify thermo_temp dynamic yes
|
||||||
|
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# run
|
||||||
|
|
||||||
|
run 1000
|
||||||
177
examples/gcmc/log.24Mar17.gcmc.co2.g++.1
Normal file
177
examples/gcmc/log.24Mar17.gcmc.co2.g++.1
Normal file
@ -0,0 +1,177 @@
|
|||||||
|
LAMMPS (17 Mar 2017)
|
||||||
|
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
|
||||||
|
# Rigid CO2 TraPPE model
|
||||||
|
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
|
||||||
|
# mixtures containing alkanes, carbon dioxide and
|
||||||
|
# nitrogen AIChE J., 47,1676-1682 (2001)].
|
||||||
|
|
||||||
|
# variables available on command line
|
||||||
|
|
||||||
|
variable mu index -8.1
|
||||||
|
variable disp index 0.5
|
||||||
|
variable temp index 338.0
|
||||||
|
variable lbox index 10.0
|
||||||
|
variable spacing index 5.0
|
||||||
|
|
||||||
|
# global model settings
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
boundary p p p
|
||||||
|
pair_style lj/cut/coul/long 14
|
||||||
|
pair_modify mix arithmetic tail yes
|
||||||
|
kspace_style ewald 0.0001
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
|
||||||
|
# box, start molecules on simple cubic lattice
|
||||||
|
|
||||||
|
lattice sc ${spacing}
|
||||||
|
lattice sc 5.0
|
||||||
|
Lattice spacing in x,y,z = 5 5 5
|
||||||
|
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
|
||||||
|
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
|
||||||
|
region box block 0 10.0 0 10.0 0 ${lbox} units box
|
||||||
|
region box block 0 10.0 0 10.0 0 10.0 units box
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||||
|
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
molecule co2mol CO2.txt
|
||||||
|
Read molecule co2mol:
|
||||||
|
3 atoms with 2 types
|
||||||
|
2 bonds with 1 types
|
||||||
|
1 angles with 1 types
|
||||||
|
0 dihedrals with 0 types
|
||||||
|
0 impropers with 0 types
|
||||||
|
create_atoms 0 box mol co2mol 464563 units box
|
||||||
|
Created 24 atoms
|
||||||
|
|
||||||
|
# rigid CO2 TraPPE model
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.053649 2.8
|
||||||
|
pair_coeff 2 2 0.156973 3.05
|
||||||
|
bond_coeff 1 0 1.16
|
||||||
|
angle_coeff 1 0 180
|
||||||
|
|
||||||
|
# masses
|
||||||
|
|
||||||
|
mass 1 12.0107
|
||||||
|
mass 2 15.9994
|
||||||
|
|
||||||
|
# MD settings
|
||||||
|
|
||||||
|
group co2 type 1 2
|
||||||
|
24 atoms in group co2
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
velocity all create ${temp} 54654
|
||||||
|
velocity all create 338.0 54654
|
||||||
|
timestep 1.0
|
||||||
|
|
||||||
|
# rigid constraints with thermostat
|
||||||
|
|
||||||
|
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
|
||||||
|
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
|
||||||
|
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
|
||||||
|
8 rigid bodies with 24 atoms
|
||||||
|
1.16 = max distance from body owner to body atom
|
||||||
|
fix_modify myrigidnvt dynamic/dof no
|
||||||
|
|
||||||
|
# gcmc
|
||||||
|
|
||||||
|
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||||
|
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||||
|
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||||
|
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||||
|
compute_modify thermo_temp dynamic/dof yes
|
||||||
|
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# run
|
||||||
|
|
||||||
|
run 20000
|
||||||
|
Ewald initialization ...
|
||||||
|
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||||
|
G vector (1/distance) = 0.164636
|
||||||
|
estimated absolute RMS force accuracy = 0.0332064
|
||||||
|
estimated relative force accuracy = 0.0001
|
||||||
|
KSpace vectors: actual max1d max3d = 16 2 62
|
||||||
|
kxmax kymax kzmax = 2 2 2
|
||||||
|
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:439)
|
||||||
|
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
|
||||||
|
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
|
||||||
|
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 16
|
||||||
|
ghost atom cutoff = 16
|
||||||
|
binsize = 8, bins = 2 2 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 15.61 | 15.61 | 15.61 Mbytes
|
||||||
|
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
|
||||||
|
0 364.27579 4238.8631 -9.6809388 13.391989 0.5846359 24 0 0 0 0
|
||||||
|
1000 311.39835 -327.93481 -8.6795381 9.9010062 0.51155641 21 0.13302848 0.12331626 0.6894397 0.90997852
|
||||||
|
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
|
||||||
|
2000 905.66812 319.43347 -0.50350961 6.2991241 0.14615898 6 0.20952183 0.20430213 0.71797992 0.92626683
|
||||||
|
3000 275.57393 -719.89718 -26.534978 14.238181 0.80387436 33 0.21291069 0.20460696 0.72899202 0.9133259
|
||||||
|
4000 254.70771 -245.01902 -20.981537 13.160079 0.80387436 33 0.17245726 0.16974613 0.70145764 0.90542759
|
||||||
|
5000 96.073601 -517.98124 -34.019065 5.441166 0.87695385 36 0.14174575 0.13607057 0.6776754 0.90155771
|
||||||
|
6000 397.57265 148.92645 -7.2012893 10.665797 0.43847693 18 0.12299956 0.1202471 0.66165464 0.90274793
|
||||||
|
7000 455.4271 -347.44181 -5.9244703 12.217875 0.43847693 18 0.15182038 0.14791307 0.67904236 0.90560829
|
||||||
|
8000 301.03124 -627.45324 -13.251012 11.066909 0.5846359 24 0.16687346 0.16315516 0.6936719 0.91129375
|
||||||
|
9000 256.5747 -565.67983 -17.814128 11.981874 0.73079488 30 0.15458482 0.15131825 0.68966283 0.90993975
|
||||||
|
10000 443.60076 89.586912 -6.077863 11.900606 0.43847693 18 0.16092552 0.16020353 0.69882461 0.91422145
|
||||||
|
11000 436.43777 64.412921 -6.7128469 11.708443 0.43847693 18 0.17453966 0.17480683 0.70679243 0.91369445
|
||||||
|
12000 594.42207 849.07743 -3.3708621 10.040536 0.29231795 12 0.17461606 0.17568622 0.71175869 0.91333367
|
||||||
|
13000 426.85849 -1093.1334 -17.524618 17.813377 0.65771539 27 0.17742896 0.17792831 0.71363306 0.91450124
|
||||||
|
14000 317.75995 336.31107 -10.46774 11.681912 0.5846359 24 0.18331181 0.18427921 0.71715557 0.91652256
|
||||||
|
15000 272.65129 317.50536 -26.428336 14.087176 0.80387436 33 0.17449167 0.175957 0.71122398 0.91528038
|
||||||
|
16000 344.28567 -577.91079 -18.177927 16.077919 0.73079488 30 0.1661682 0.16781514 0.70485136 0.91508882
|
||||||
|
17000 134.55928 -193.5668 -30.297136 7.6208177 0.87695385 36 0.15965609 0.1605036 0.69658104 0.9140445
|
||||||
|
18000 231.87302 -446.07671 -14.875027 9.6763722 0.65771539 27 0.15270985 0.15351831 0.69002918 0.91372795
|
||||||
|
19000 328.6835 -280.22365 -20.001303 16.982214 0.80387436 33 0.15201017 0.15272181 0.69023195 0.91272534
|
||||||
|
20000 0 -20.39554 -0.14872889 -0 0 0 0.15600204 0.15750795 0.69503275 0.9138765
|
||||||
|
Loop time of 30.9008 on 1 procs for 20000 steps with 0 atoms
|
||||||
|
|
||||||
|
Performance: 55.921 ns/day, 0.429 hours/ns, 647.233 timesteps/s
|
||||||
|
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.1985 | 2.1985 | 2.1985 | 0.0 | 7.11
|
||||||
|
Bond | 0.029596 | 0.029596 | 0.029596 | 0.0 | 0.10
|
||||||
|
Kspace | 0.23123 | 0.23123 | 0.23123 | 0.0 | 0.75
|
||||||
|
Neigh | 0.16141 | 0.16141 | 0.16141 | 0.0 | 0.52
|
||||||
|
Comm | 0.20628 | 0.20628 | 0.20628 | 0.0 | 0.67
|
||||||
|
Output | 0.00068831 | 0.00068831 | 0.00068831 | 0.0 | 0.00
|
||||||
|
Modify | 28.022 | 28.022 | 28.022 | 0.0 | 90.69
|
||||||
|
Other | | 0.05058 | | | 0.16
|
||||||
|
|
||||||
|
Nlocal: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 0
|
||||||
|
Neighbor list builds = 40367
|
||||||
|
Dangerous builds = 118
|
||||||
|
|
||||||
|
Total wall time: 0:00:30
|
||||||
179
examples/gcmc/log.24Mar17.gcmc.co2.g++.4
Normal file
179
examples/gcmc/log.24Mar17.gcmc.co2.g++.4
Normal file
@ -0,0 +1,179 @@
|
|||||||
|
LAMMPS (17 Mar 2017)
|
||||||
|
# GCMC for CO2 molecular fluid, rigid/small/nvt dynamics
|
||||||
|
# Rigid CO2 TraPPE model
|
||||||
|
# [Potoff and J.I. Siepmann, Vapor-liquid equilibria of
|
||||||
|
# mixtures containing alkanes, carbon dioxide and
|
||||||
|
# nitrogen AIChE J., 47,1676-1682 (2001)].
|
||||||
|
|
||||||
|
# variables available on command line
|
||||||
|
|
||||||
|
variable mu index -8.1
|
||||||
|
variable disp index 0.5
|
||||||
|
variable temp index 338.0
|
||||||
|
variable lbox index 10.0
|
||||||
|
variable spacing index 5.0
|
||||||
|
|
||||||
|
# global model settings
|
||||||
|
|
||||||
|
units real
|
||||||
|
atom_style full
|
||||||
|
boundary p p p
|
||||||
|
pair_style lj/cut/coul/long 14
|
||||||
|
pair_modify mix arithmetic tail yes
|
||||||
|
kspace_style ewald 0.0001
|
||||||
|
bond_style harmonic
|
||||||
|
angle_style harmonic
|
||||||
|
|
||||||
|
# box, start molecules on simple cubic lattice
|
||||||
|
|
||||||
|
lattice sc ${spacing}
|
||||||
|
lattice sc 5.0
|
||||||
|
Lattice spacing in x,y,z = 5 5 5
|
||||||
|
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox} units box
|
||||||
|
region box block 0 10.0 0 ${lbox} 0 ${lbox} units box
|
||||||
|
region box block 0 10.0 0 10.0 0 ${lbox} units box
|
||||||
|
region box block 0 10.0 0 10.0 0 10.0 units box
|
||||||
|
create_box 2 box bond/types 1 angle/types 1 extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
|
||||||
|
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
molecule co2mol CO2.txt
|
||||||
|
Read molecule co2mol:
|
||||||
|
3 atoms with 2 types
|
||||||
|
2 bonds with 1 types
|
||||||
|
1 angles with 1 types
|
||||||
|
0 dihedrals with 0 types
|
||||||
|
0 impropers with 0 types
|
||||||
|
create_atoms 0 box mol co2mol 464563 units box
|
||||||
|
Created 24 atoms
|
||||||
|
|
||||||
|
# rigid CO2 TraPPE model
|
||||||
|
|
||||||
|
pair_coeff 1 1 0.053649 2.8
|
||||||
|
pair_coeff 2 2 0.156973 3.05
|
||||||
|
bond_coeff 1 0 1.16
|
||||||
|
angle_coeff 1 0 180
|
||||||
|
|
||||||
|
# masses
|
||||||
|
|
||||||
|
mass 1 12.0107
|
||||||
|
mass 2 15.9994
|
||||||
|
|
||||||
|
# MD settings
|
||||||
|
|
||||||
|
group co2 type 1 2
|
||||||
|
24 atoms in group co2
|
||||||
|
neighbor 2.0 bin
|
||||||
|
neigh_modify every 1 delay 10 check yes
|
||||||
|
velocity all create ${temp} 54654
|
||||||
|
velocity all create 338.0 54654
|
||||||
|
timestep 1.0
|
||||||
|
|
||||||
|
# rigid constraints with thermostat
|
||||||
|
|
||||||
|
fix myrigidnvt all rigid/nvt/small molecule temp ${temp} ${temp} 100 mol co2mol
|
||||||
|
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 ${temp} 100 mol co2mol
|
||||||
|
fix myrigidnvt all rigid/nvt/small molecule temp 338.0 338.0 100 mol co2mol
|
||||||
|
8 rigid bodies with 24 atoms
|
||||||
|
1.16 = max distance from body owner to body atom
|
||||||
|
fix_modify myrigidnvt dynamic/dof no
|
||||||
|
|
||||||
|
# gcmc
|
||||||
|
|
||||||
|
variable tfac equal 5.0/3.0 # (3 trans + 2 rot)/(3 trans)
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 ${temp} ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 ${mu} ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 ${disp} mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert ${tfac} group co2 rigid myrigidnvt
|
||||||
|
fix mygcmc all gcmc 100 100 100 0 54341 338.0 -8.1 0.5 mol co2mol tfac_insert 1.66666666666667 group co2 rigid myrigidnvt
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||||
|
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||||
|
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||||
|
variable racc equal f_mygcmc[8]/(f_mygcmc[7]+0.1)
|
||||||
|
compute_modify thermo_temp dynamic/dof yes
|
||||||
|
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc v_racc
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
# run
|
||||||
|
|
||||||
|
run 20000
|
||||||
|
Ewald initialization ...
|
||||||
|
WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321)
|
||||||
|
G vector (1/distance) = 0.164636
|
||||||
|
estimated absolute RMS force accuracy = 0.0332064
|
||||||
|
estimated relative force accuracy = 0.0001
|
||||||
|
KSpace vectors: actual max1d max3d = 16 2 62
|
||||||
|
kxmax kymax kzmax = 2 2 2
|
||||||
|
WARNING: Fix gcmc using full_energy option (../fix_gcmc.cpp:439)
|
||||||
|
0 atoms in group FixGCMC:gcmc_exclusion_group:mygcmc
|
||||||
|
0 atoms in group FixGCMC:rotation_gas_atoms:mygcmc
|
||||||
|
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:472)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 16
|
||||||
|
ghost atom cutoff = 16
|
||||||
|
binsize = 8, bins = 2 2 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut/coul/long, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 15.4 | 15.4 | 15.4 Mbytes
|
||||||
|
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc v_racc
|
||||||
|
0 386.52184 23582.465 -3.2433417 14.209828 0.5846359 24 0 0 0 0
|
||||||
|
WARNING: Using kspace solver on system with no charge (../kspace.cpp:289)
|
||||||
|
1000 760.80877 -39.270882 -3.5239626 12.851016 0.29231795 12 0.24161633 0.22984103 0.71087092 0.85283311
|
||||||
|
2000 308.0739 -255.061 -20.411926 14.386853 0.73079488 30 0.26075352 0.24898725 0.73128383 0.88590474
|
||||||
|
3000 432.34358 -1361.3278 -12.644057 15.894387 0.5846359 24 0.21121583 0.21051229 0.70036003 0.86735027
|
||||||
|
4000 631.524 -63.488785 -3.6517158 13.804656 0.36539744 15 0.22486443 0.22886173 0.72358173 0.87172606
|
||||||
|
5000 730.61244 -1029.284 -6.2144028 19.600352 0.43847693 18 0.23017182 0.22740779 0.72281887 0.87820845
|
||||||
|
6000 752.43412 503.4547 -3.7053679 16.447663 0.36539744 15 0.22943971 0.226183 0.71450085 0.87447436
|
||||||
|
7000 660.68448 828.51735 -10.592278 21.006666 0.51155641 21 0.24702096 0.24218506 0.71815602 0.8740222
|
||||||
|
8000 331.58822 -621.22187 -5.3705759 7.2482776 0.36539744 15 0.23211903 0.22906813 0.70281376 0.86269411
|
||||||
|
9000 413.91538 869.51669 -11.28701 15.216905 0.5846359 24 0.23246466 0.22923961 0.70832684 0.86244176
|
||||||
|
10000 242.20861 -808.23311 -5.4533937 5.2945044 0.36539744 15 0.22024676 0.22031775 0.70785097 0.85712561
|
||||||
|
11000 348.20046 -372.16895 -3.4663358 7.6114092 0.36539744 15 0.2252033 0.22688969 0.71513402 0.86123263
|
||||||
|
12000 251.99682 303.30092 -18.58289 11.768089 0.73079488 30 0.20916844 0.21068047 0.694787 0.84635875
|
||||||
|
13000 306.83592 -1582.0137 -20.810287 14.329041 0.73079488 30 0.19494837 0.196527 0.67554784 0.83056119
|
||||||
|
14000 476.57411 268.94927 -14.185859 19.888076 0.65771539 27 0.19779631 0.20016859 0.67957528 0.83375167
|
||||||
|
15000 267.03534 730.71183 -9.3348616 9.8171066 0.5846359 24 0.19468305 0.19814971 0.68032974 0.83810439
|
||||||
|
16000 639.83235 2190.3244 -9.6666503 26.701062 0.65771539 27 0.19520687 0.19848997 0.68514387 0.84100361
|
||||||
|
17000 2237.1203 -222.59057 -0.18248834 4.4456205 0.073079488 3 0.20412446 0.20757814 0.69175318 0.8434939
|
||||||
|
18000 754.44841 205.54694 -10.501943 27.736031 0.5846359 24 0.2129422 0.21508015 0.69665031 0.84758331
|
||||||
|
19000 1610.1148 1293.6003 -0.20849836 3.1996309 0.073079488 3 0.22061668 0.22356929 0.69949369 0.84851405
|
||||||
|
20000 231.61458 -39.696514 -4.6452226 5.0629266 0.36539744 15 0.21984893 0.22246517 0.69914635 0.85058457
|
||||||
|
Loop time of 21.1019 on 4 procs for 20000 steps with 15 atoms
|
||||||
|
|
||||||
|
Performance: 81.888 ns/day, 0.293 hours/ns, 947.781 timesteps/s
|
||||||
|
98.9% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.31897 | 0.41973 | 0.49748 | 10.1 | 1.99
|
||||||
|
Bond | 0.014808 | 0.015063 | 0.015289 | 0.2 | 0.07
|
||||||
|
Kspace | 0.3813 | 0.46228 | 0.56585 | 9.8 | 2.19
|
||||||
|
Neigh | 0.049173 | 0.050043 | 0.050868 | 0.3 | 0.24
|
||||||
|
Comm | 0.9755 | 0.99686 | 1.0205 | 1.9 | 4.72
|
||||||
|
Output | 0.0014546 | 0.0015051 | 0.0016098 | 0.2 | 0.01
|
||||||
|
Modify | 19.043 | 19.062 | 19.085 | 0.4 | 90.33
|
||||||
|
Other | | 0.09438 | | | 0.45
|
||||||
|
|
||||||
|
Nlocal: 3.75 ave 6 max 3 min
|
||||||
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 876.5 ave 937 max 818 min
|
||||||
|
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||||
|
Neighs: 490.5 ave 647 max 363 min
|
||||||
|
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 1962
|
||||||
|
Ave neighs/atom = 130.8
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 40070
|
||||||
|
Dangerous builds = 115
|
||||||
|
|
||||||
|
Total wall time: 0:00:21
|
||||||
103
examples/gcmc/log.24Mar17.gcmc.lj.g++.1
Normal file
103
examples/gcmc/log.24Mar17.gcmc.lj.g++.1
Normal file
@ -0,0 +1,103 @@
|
|||||||
|
LAMMPS (17 Mar 2017)
|
||||||
|
# GCMC for LJ simple fluid, no dynamics
|
||||||
|
|
||||||
|
# variables available on command line
|
||||||
|
|
||||||
|
variable mu index -21.0
|
||||||
|
variable disp index 1.0
|
||||||
|
variable temp index 2.0
|
||||||
|
variable lbox index 10.0
|
||||||
|
|
||||||
|
# global model settings
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
pair_style lj/cut 3.0
|
||||||
|
pair_modify tail yes
|
||||||
|
|
||||||
|
# box
|
||||||
|
|
||||||
|
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
|
||||||
|
region box block 0 10.0 0 ${lbox} 0 ${lbox}
|
||||||
|
region box block 0 10.0 0 10.0 0 ${lbox}
|
||||||
|
region box block 0 10.0 0 10.0 0 10.0
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
|
||||||
|
# lj parameters
|
||||||
|
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
# gcmc
|
||||||
|
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 ${disp}
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 1.0
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||||
|
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||||
|
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||||
|
compute_modify thermo_temp dynamic yes
|
||||||
|
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# run
|
||||||
|
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 0.4369 | 0.4369 | 0.4369 Mbytes
|
||||||
|
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc
|
||||||
|
0 0 0 0 -0 0 0 0 0 0
|
||||||
|
100 1.9042848 0.39026453 -1.7692765 2.8466449 0.292 292 0.3619855 0.30247792 0.40278761
|
||||||
|
200 1.8651924 0.47815517 -1.8494955 2.7886155 0.305 305 0.34021109 0.30357196 0.37759189
|
||||||
|
300 2.0626994 0.52068504 -1.8197295 3.0834166 0.291 291 0.32055605 0.3003043 0.36103862
|
||||||
|
400 2.0394818 0.53751435 -1.7636699 3.0482184 0.278 278 0.31698808 0.29995864 0.35441275
|
||||||
|
500 1.9628066 0.54594742 -1.7145336 2.9339513 0.287 287 0.31211861 0.29724228 0.35161407
|
||||||
|
600 1.9845913 0.40846162 -1.8199325 2.9669308 0.299 299 0.30976643 0.29612711 0.34933559
|
||||||
|
700 1.8582606 0.53445462 -1.7869306 2.777974 0.296 296 0.30642103 0.29446478 0.34633665
|
||||||
|
800 2.0340641 0.66057698 -1.7075279 3.0403148 0.283 283 0.30730979 0.29746793 0.34768045
|
||||||
|
900 2.0830765 0.63731971 -1.894775 3.114911 0.322 322 0.30636338 0.29737705 0.34737644
|
||||||
|
1000 1.9688933 0.50024802 -1.7013944 2.9428299 0.281 281 0.3053174 0.29772245 0.34788254
|
||||||
|
Loop time of 3.98286 on 1 procs for 1000 steps with 281 atoms
|
||||||
|
|
||||||
|
Performance: 108464.750 tau/day, 251.076 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.10563 | 0.10563 | 0.10563 | 0.0 | 2.65
|
||||||
|
Neigh | 0.33428 | 0.33428 | 0.33428 | 0.0 | 8.39
|
||||||
|
Comm | 0.027969 | 0.027969 | 0.027969 | 0.0 | 0.70
|
||||||
|
Output | 0.00017285 | 0.00017285 | 0.00017285 | 0.0 | 0.00
|
||||||
|
Modify | 3.5096 | 3.5096 | 3.5096 | 0.0 | 88.12
|
||||||
|
Other | | 0.005197 | | | 0.13
|
||||||
|
|
||||||
|
Nlocal: 281 ave 281 max 281 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 977 ave 977 max 977 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 5902 ave 5902 max 5902 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 5902
|
||||||
|
Ave neighs/atom = 21.0036
|
||||||
|
Neighbor list builds = 1000
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:03
|
||||||
103
examples/gcmc/log.24Mar17.gcmc.lj.g++.4
Normal file
103
examples/gcmc/log.24Mar17.gcmc.lj.g++.4
Normal file
@ -0,0 +1,103 @@
|
|||||||
|
LAMMPS (17 Mar 2017)
|
||||||
|
# GCMC for LJ simple fluid, no dynamics
|
||||||
|
|
||||||
|
# variables available on command line
|
||||||
|
|
||||||
|
variable mu index -21.0
|
||||||
|
variable disp index 1.0
|
||||||
|
variable temp index 2.0
|
||||||
|
variable lbox index 10.0
|
||||||
|
|
||||||
|
# global model settings
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style atomic
|
||||||
|
pair_style lj/cut 3.0
|
||||||
|
pair_modify tail yes
|
||||||
|
|
||||||
|
# box
|
||||||
|
|
||||||
|
region box block 0 ${lbox} 0 ${lbox} 0 ${lbox}
|
||||||
|
region box block 0 10.0 0 ${lbox} 0 ${lbox}
|
||||||
|
region box block 0 10.0 0 10.0 0 ${lbox}
|
||||||
|
region box block 0 10.0 0 10.0 0 10.0
|
||||||
|
create_box 1 box
|
||||||
|
Created orthogonal box = (0 0 0) to (10 10 10)
|
||||||
|
1 by 2 by 2 MPI processor grid
|
||||||
|
|
||||||
|
# lj parameters
|
||||||
|
|
||||||
|
pair_coeff * * 1.0 1.0
|
||||||
|
mass * 1.0
|
||||||
|
|
||||||
|
# gcmc
|
||||||
|
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 ${temp} ${mu} ${disp}
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 2.0 ${mu} ${disp}
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 ${disp}
|
||||||
|
fix mygcmc all gcmc 1 100 100 1 29494 2.0 -21.0 1.0
|
||||||
|
|
||||||
|
# output
|
||||||
|
|
||||||
|
variable tacc equal f_mygcmc[2]/(f_mygcmc[1]+0.1)
|
||||||
|
variable iacc equal f_mygcmc[4]/(f_mygcmc[3]+0.1)
|
||||||
|
variable dacc equal f_mygcmc[6]/(f_mygcmc[5]+0.1)
|
||||||
|
compute_modify thermo_temp dynamic yes
|
||||||
|
thermo_style custom step temp press pe ke density atoms v_iacc v_dacc v_tacc
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
# run
|
||||||
|
|
||||||
|
run 1000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.3
|
||||||
|
ghost atom cutoff = 3.3
|
||||||
|
binsize = 1.65, bins = 7 7 7
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair lj/cut, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d/newton
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 0.434 | 0.434 | 0.434 Mbytes
|
||||||
|
Step Temp Press PotEng KinEng Density Atoms v_iacc v_dacc v_tacc
|
||||||
|
0 0 0 0 -0 0 0 0 0 0
|
||||||
|
100 2.0328045 0.58661762 -1.6812724 3.0385824 0.287 287 0.35917318 0.30067507 0.38663622
|
||||||
|
200 1.9594279 0.50682399 -1.7308396 2.9287927 0.284 284 0.33788365 0.30337335 0.37300293
|
||||||
|
300 2.0602937 0.7028247 -1.9278541 3.0806296 0.315 315 0.31882007 0.29697498 0.36167185
|
||||||
|
400 1.995183 0.4328246 -1.8715454 2.983026 0.307 307 0.31527654 0.29681901 0.35673374
|
||||||
|
500 2.1390101 0.48232215 -1.554138 3.1960306 0.257 257 0.31372975 0.30003067 0.35558858
|
||||||
|
600 2.0584244 0.4929049 -1.6995569 3.0767263 0.283 283 0.31114213 0.29801665 0.35160109
|
||||||
|
700 1.9155066 0.49654243 -1.5770611 2.8624174 0.265 265 0.31056419 0.29944173 0.35157337
|
||||||
|
800 2.0883562 0.52731947 -1.8261112 3.1220925 0.3 300 0.30730979 0.29704354 0.34898892
|
||||||
|
900 2.0470677 0.5605993 -2.0130053 3.0610656 0.322 322 0.30484441 0.29586719 0.34678883
|
||||||
|
1000 2.004135 0.50642204 -1.6956257 2.9955798 0.283 283 0.30396929 0.29634309 0.34770304
|
||||||
|
Loop time of 3.688 on 4 procs for 1000 steps with 283 atoms
|
||||||
|
|
||||||
|
Performance: 117136.751 tau/day, 271.150 timesteps/s
|
||||||
|
99.2% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.024644 | 0.026027 | 0.027483 | 0.6 | 0.71
|
||||||
|
Neigh | 0.085449 | 0.088998 | 0.092893 | 0.9 | 2.41
|
||||||
|
Comm | 0.045756 | 0.051296 | 0.056578 | 1.7 | 1.39
|
||||||
|
Output | 0.00028491 | 0.00030857 | 0.00035262 | 0.0 | 0.01
|
||||||
|
Modify | 3.5189 | 3.5191 | 3.5194 | 0.0 | 95.42
|
||||||
|
Other | | 0.002221 | | | 0.06
|
||||||
|
|
||||||
|
Nlocal: 70.75 ave 77 max 68 min
|
||||||
|
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||||
|
Nghost: 514.25 ave 520 max 507 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 1 0 1
|
||||||
|
Neighs: 1483.5 ave 1715 max 1359 min
|
||||||
|
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 5934
|
||||||
|
Ave neighs/atom = 20.9682
|
||||||
|
Neighbor list builds = 1000
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:03
|
||||||
1078
src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
Normal file
1078
src/KSPACE/pair_lj_charmmfsw_coul_long.cpp
Normal file
File diff suppressed because it is too large
Load Diff
110
src/KSPACE/pair_lj_charmmfsw_coul_long.h
Normal file
110
src/KSPACE/pair_lj_charmmfsw_coul_long.h
Normal file
@ -0,0 +1,110 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef PAIR_CLASS
|
||||||
|
|
||||||
|
PairStyle(lj/charmmfsw/coul/long,PairLJCharmmfswCoulLong)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_H
|
||||||
|
#define LMP_PAIR_LJ_CHARMMFSW_COUL_LONG_H
|
||||||
|
|
||||||
|
#include "pair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class PairLJCharmmfswCoulLong : public Pair {
|
||||||
|
public:
|
||||||
|
PairLJCharmmfswCoulLong(class LAMMPS *);
|
||||||
|
virtual ~PairLJCharmmfswCoulLong();
|
||||||
|
|
||||||
|
virtual void compute(int, int);
|
||||||
|
virtual void settings(int, char **);
|
||||||
|
void coeff(int, char **);
|
||||||
|
virtual void init_style();
|
||||||
|
void init_list(int, class NeighList *);
|
||||||
|
virtual double init_one(int, int);
|
||||||
|
void write_restart(FILE *);
|
||||||
|
void read_restart(FILE *);
|
||||||
|
void write_restart_settings(FILE *);
|
||||||
|
void read_restart_settings(FILE *);
|
||||||
|
void write_data(FILE *);
|
||||||
|
void write_data_all(FILE *);
|
||||||
|
virtual double single(int, int, int, int, double, double, double, double &);
|
||||||
|
|
||||||
|
void compute_inner();
|
||||||
|
void compute_middle();
|
||||||
|
virtual void compute_outer(int, int);
|
||||||
|
virtual void *extract(const char *, int &);
|
||||||
|
|
||||||
|
protected:
|
||||||
|
int implicit;
|
||||||
|
int dihedflag;
|
||||||
|
|
||||||
|
double cut_lj_inner,cut_lj,cut_ljinv,cut_lj_innerinv;
|
||||||
|
double cut_lj_innersq,cut_ljsq;
|
||||||
|
double cut_lj3inv,cut_lj_inner3inv,cut_lj3,cut_lj_inner3;
|
||||||
|
double cut_lj6inv,cut_lj_inner6inv,cut_lj6,cut_lj_inner6;
|
||||||
|
double cut_coul,cut_coulsq;
|
||||||
|
double cut_bothsq;
|
||||||
|
double denom_lj,denom_lj12,denom_lj6;
|
||||||
|
double **epsilon,**sigma,**eps14,**sigma14;
|
||||||
|
double **lj1,**lj2,**lj3,**lj4,**offset;
|
||||||
|
double **lj14_1,**lj14_2,**lj14_3,**lj14_4;
|
||||||
|
double *cut_respa;
|
||||||
|
double g_ewald;
|
||||||
|
|
||||||
|
virtual void allocate();
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: Incorrect args for pair coefficients
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
|
E: Pair style lj/charmmfsw/coul/long requires atom attribute q
|
||||||
|
|
||||||
|
The atom style defined does not have these attributes.
|
||||||
|
|
||||||
|
E: Pair inner cutoff >= Pair outer cutoff
|
||||||
|
|
||||||
|
The specified cutoffs for the pair style are inconsistent.
|
||||||
|
|
||||||
|
E: Pair cutoff < Respa interior cutoff
|
||||||
|
|
||||||
|
One or more pairwise cutoffs are too short to use with the specified
|
||||||
|
rRESPA cutoffs.
|
||||||
|
|
||||||
|
E: Pair inner cutoff < Respa interior cutoff
|
||||||
|
|
||||||
|
One or more pairwise cutoffs are too short to use with the specified
|
||||||
|
rRESPA cutoffs.
|
||||||
|
|
||||||
|
E: Pair style requires a KSpace style
|
||||||
|
|
||||||
|
No kspace style is defined.
|
||||||
|
|
||||||
|
*/
|
||||||
@ -3183,7 +3183,9 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
|
|||||||
for (i=0; i<64; i++) coeffs[i]=0.0;
|
for (i=0; i<64; i++) coeffs[i]=0.0;
|
||||||
|
|
||||||
if (typei==0 && typej==0) {
|
if (typei==0 && typej==0) {
|
||||||
|
|
||||||
// if the inputs are out of bounds set them back to a point in bounds
|
// if the inputs are out of bounds set them back to a point in bounds
|
||||||
|
|
||||||
if (Nij<piCCdom[0][0]) Nij=piCCdom[0][0];
|
if (Nij<piCCdom[0][0]) Nij=piCCdom[0][0];
|
||||||
if (Nij>piCCdom[0][1]) Nij=piCCdom[0][1];
|
if (Nij>piCCdom[0][1]) Nij=piCCdom[0][1];
|
||||||
if (Nji<piCCdom[1][0]) Nji=piCCdom[1][0];
|
if (Nji<piCCdom[1][0]) Nji=piCCdom[1][0];
|
||||||
@ -3213,10 +3215,10 @@ double PairAIREBO::piRCSpline(double Nij, double Nji, double Nijconj,
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
// CH interaction
|
// CH interaction
|
||||||
|
|
||||||
if ((typei==0 && typej==1) || (typei==1 && typej==0)) {
|
if ((typei==0 && typej==1) || (typei==1 && typej==0)) {
|
||||||
|
|
||||||
// if the inputs are out of bounds set them back to a point in bounds
|
// if the inputs are out of bounds set them back to a point in bounds
|
||||||
|
|
||||||
if (Nij<piCHdom[0][0] || Nij>piCHdom[0][1] ||
|
if (Nij<piCHdom[0][0] || Nij>piCHdom[0][1] ||
|
||||||
|
|||||||
482
src/MOLECULE/dihedral_charmmfsh.cpp
Normal file
482
src/MOLECULE/dihedral_charmmfsh.cpp
Normal file
@ -0,0 +1,482 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Contributing author: Paul Crozier (SNL)
|
||||||
|
The force-shifted sections were provided by Robert Meissner
|
||||||
|
and Lucio Colombi Ciacchi of Bremen University, Bremen, Germany,
|
||||||
|
with additional assistance from Robert A. Latour, Clemson University
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include <mpi.h>
|
||||||
|
#include <math.h>
|
||||||
|
#include <stdlib.h>
|
||||||
|
#include "dihedral_charmmfsh.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "pair.h"
|
||||||
|
#include "update.h"
|
||||||
|
#include "math_const.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
using namespace MathConst;
|
||||||
|
|
||||||
|
#define TOLERANCE 0.05
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)
|
||||||
|
{
|
||||||
|
weightflag = 0;
|
||||||
|
writedata = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
DihedralCharmmfsh::~DihedralCharmmfsh()
|
||||||
|
{
|
||||||
|
if (allocated && !copymode) {
|
||||||
|
memory->destroy(setflag);
|
||||||
|
memory->destroy(k);
|
||||||
|
memory->destroy(multiplicity);
|
||||||
|
memory->destroy(shift);
|
||||||
|
memory->destroy(cos_shift);
|
||||||
|
memory->destroy(sin_shift);
|
||||||
|
memory->destroy(weight);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DihedralCharmmfsh::compute(int eflag, int vflag)
|
||||||
|
{
|
||||||
|
int i1,i2,i3,i4,i,m,n,type;
|
||||||
|
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
|
||||||
|
double edihedral,f1[3],f2[3],f3[3],f4[3];
|
||||||
|
double ax,ay,az,bx,by,bz,rasq,rbsq,rgsq,rg,rginv,ra2inv,rb2inv,rabinv;
|
||||||
|
double df,df1,ddf1,fg,hg,fga,hgb,gaa,gbb;
|
||||||
|
double dtfx,dtfy,dtfz,dtgx,dtgy,dtgz,dthx,dthy,dthz;
|
||||||
|
double c,s,p,sx2,sy2,sz2;
|
||||||
|
int itype,jtype;
|
||||||
|
double delx,dely,delz,rsq,r2inv,r6inv,r;
|
||||||
|
double forcecoul,forcelj,fpair,ecoul,evdwl;
|
||||||
|
|
||||||
|
edihedral = evdwl = ecoul = 0.0;
|
||||||
|
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||||
|
else evflag = 0;
|
||||||
|
|
||||||
|
// insure pair->ev_tally() will use 1-4 virial contribution
|
||||||
|
|
||||||
|
if (weightflag && vflag_global == 2)
|
||||||
|
force->pair->vflag_either = force->pair->vflag_global = 1;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double **f = atom->f;
|
||||||
|
double *q = atom->q;
|
||||||
|
int *atomtype = atom->type;
|
||||||
|
int **dihedrallist = neighbor->dihedrallist;
|
||||||
|
int ndihedrallist = neighbor->ndihedrallist;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
int newton_bond = force->newton_bond;
|
||||||
|
double qqrd2e = force->qqrd2e;
|
||||||
|
|
||||||
|
for (n = 0; n < ndihedrallist; n++) {
|
||||||
|
i1 = dihedrallist[n][0];
|
||||||
|
i2 = dihedrallist[n][1];
|
||||||
|
i3 = dihedrallist[n][2];
|
||||||
|
i4 = dihedrallist[n][3];
|
||||||
|
type = dihedrallist[n][4];
|
||||||
|
|
||||||
|
// 1st bond
|
||||||
|
|
||||||
|
vb1x = x[i1][0] - x[i2][0];
|
||||||
|
vb1y = x[i1][1] - x[i2][1];
|
||||||
|
vb1z = x[i1][2] - x[i2][2];
|
||||||
|
|
||||||
|
// 2nd bond
|
||||||
|
|
||||||
|
vb2x = x[i3][0] - x[i2][0];
|
||||||
|
vb2y = x[i3][1] - x[i2][1];
|
||||||
|
vb2z = x[i3][2] - x[i2][2];
|
||||||
|
|
||||||
|
vb2xm = -vb2x;
|
||||||
|
vb2ym = -vb2y;
|
||||||
|
vb2zm = -vb2z;
|
||||||
|
|
||||||
|
// 3rd bond
|
||||||
|
|
||||||
|
vb3x = x[i4][0] - x[i3][0];
|
||||||
|
vb3y = x[i4][1] - x[i3][1];
|
||||||
|
vb3z = x[i4][2] - x[i3][2];
|
||||||
|
|
||||||
|
ax = vb1y*vb2zm - vb1z*vb2ym;
|
||||||
|
ay = vb1z*vb2xm - vb1x*vb2zm;
|
||||||
|
az = vb1x*vb2ym - vb1y*vb2xm;
|
||||||
|
bx = vb3y*vb2zm - vb3z*vb2ym;
|
||||||
|
by = vb3z*vb2xm - vb3x*vb2zm;
|
||||||
|
bz = vb3x*vb2ym - vb3y*vb2xm;
|
||||||
|
|
||||||
|
rasq = ax*ax + ay*ay + az*az;
|
||||||
|
rbsq = bx*bx + by*by + bz*bz;
|
||||||
|
rgsq = vb2xm*vb2xm + vb2ym*vb2ym + vb2zm*vb2zm;
|
||||||
|
rg = sqrt(rgsq);
|
||||||
|
|
||||||
|
rginv = ra2inv = rb2inv = 0.0;
|
||||||
|
if (rg > 0) rginv = 1.0/rg;
|
||||||
|
if (rasq > 0) ra2inv = 1.0/rasq;
|
||||||
|
if (rbsq > 0) rb2inv = 1.0/rbsq;
|
||||||
|
rabinv = sqrt(ra2inv*rb2inv);
|
||||||
|
|
||||||
|
c = (ax*bx + ay*by + az*bz)*rabinv;
|
||||||
|
s = rg*rabinv*(ax*vb3x + ay*vb3y + az*vb3z);
|
||||||
|
|
||||||
|
// error check
|
||||||
|
|
||||||
|
if (c > 1.0 + TOLERANCE || c < (-1.0 - TOLERANCE)) {
|
||||||
|
int me;
|
||||||
|
MPI_Comm_rank(world,&me);
|
||||||
|
if (screen) {
|
||||||
|
char str[128];
|
||||||
|
sprintf(str,"Dihedral problem: %d " BIGINT_FORMAT " "
|
||||||
|
TAGINT_FORMAT " " TAGINT_FORMAT " "
|
||||||
|
TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||||
|
me,update->ntimestep,
|
||||||
|
atom->tag[i1],atom->tag[i2],atom->tag[i3],atom->tag[i4]);
|
||||||
|
error->warning(FLERR,str,0);
|
||||||
|
fprintf(screen," 1st atom: %d %g %g %g\n",
|
||||||
|
me,x[i1][0],x[i1][1],x[i1][2]);
|
||||||
|
fprintf(screen," 2nd atom: %d %g %g %g\n",
|
||||||
|
me,x[i2][0],x[i2][1],x[i2][2]);
|
||||||
|
fprintf(screen," 3rd atom: %d %g %g %g\n",
|
||||||
|
me,x[i3][0],x[i3][1],x[i3][2]);
|
||||||
|
fprintf(screen," 4th atom: %d %g %g %g\n",
|
||||||
|
me,x[i4][0],x[i4][1],x[i4][2]);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (c > 1.0) c = 1.0;
|
||||||
|
if (c < -1.0) c = -1.0;
|
||||||
|
|
||||||
|
m = multiplicity[type];
|
||||||
|
p = 1.0;
|
||||||
|
ddf1 = df1 = 0.0;
|
||||||
|
|
||||||
|
for (i = 0; i < m; i++) {
|
||||||
|
ddf1 = p*c - df1*s;
|
||||||
|
df1 = p*s + df1*c;
|
||||||
|
p = ddf1;
|
||||||
|
}
|
||||||
|
|
||||||
|
p = p*cos_shift[type] + df1*sin_shift[type];
|
||||||
|
df1 = df1*cos_shift[type] - ddf1*sin_shift[type];
|
||||||
|
df1 *= -m;
|
||||||
|
p += 1.0;
|
||||||
|
|
||||||
|
if (m == 0) {
|
||||||
|
p = 1.0 + cos_shift[type];
|
||||||
|
df1 = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (eflag) edihedral = k[type] * p;
|
||||||
|
|
||||||
|
fg = vb1x*vb2xm + vb1y*vb2ym + vb1z*vb2zm;
|
||||||
|
hg = vb3x*vb2xm + vb3y*vb2ym + vb3z*vb2zm;
|
||||||
|
fga = fg*ra2inv*rginv;
|
||||||
|
hgb = hg*rb2inv*rginv;
|
||||||
|
gaa = -ra2inv*rg;
|
||||||
|
gbb = rb2inv*rg;
|
||||||
|
|
||||||
|
dtfx = gaa*ax;
|
||||||
|
dtfy = gaa*ay;
|
||||||
|
dtfz = gaa*az;
|
||||||
|
dtgx = fga*ax - hgb*bx;
|
||||||
|
dtgy = fga*ay - hgb*by;
|
||||||
|
dtgz = fga*az - hgb*bz;
|
||||||
|
dthx = gbb*bx;
|
||||||
|
dthy = gbb*by;
|
||||||
|
dthz = gbb*bz;
|
||||||
|
|
||||||
|
df = -k[type] * df1;
|
||||||
|
|
||||||
|
sx2 = df*dtgx;
|
||||||
|
sy2 = df*dtgy;
|
||||||
|
sz2 = df*dtgz;
|
||||||
|
|
||||||
|
f1[0] = df*dtfx;
|
||||||
|
f1[1] = df*dtfy;
|
||||||
|
f1[2] = df*dtfz;
|
||||||
|
|
||||||
|
f2[0] = sx2 - f1[0];
|
||||||
|
f2[1] = sy2 - f1[1];
|
||||||
|
f2[2] = sz2 - f1[2];
|
||||||
|
|
||||||
|
f4[0] = df*dthx;
|
||||||
|
f4[1] = df*dthy;
|
||||||
|
f4[2] = df*dthz;
|
||||||
|
|
||||||
|
f3[0] = -sx2 - f4[0];
|
||||||
|
f3[1] = -sy2 - f4[1];
|
||||||
|
f3[2] = -sz2 - f4[2];
|
||||||
|
|
||||||
|
// apply force to each of 4 atoms
|
||||||
|
|
||||||
|
if (newton_bond || i1 < nlocal) {
|
||||||
|
f[i1][0] += f1[0];
|
||||||
|
f[i1][1] += f1[1];
|
||||||
|
f[i1][2] += f1[2];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (newton_bond || i2 < nlocal) {
|
||||||
|
f[i2][0] += f2[0];
|
||||||
|
f[i2][1] += f2[1];
|
||||||
|
f[i2][2] += f2[2];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (newton_bond || i3 < nlocal) {
|
||||||
|
f[i3][0] += f3[0];
|
||||||
|
f[i3][1] += f3[1];
|
||||||
|
f[i3][2] += f3[2];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (newton_bond || i4 < nlocal) {
|
||||||
|
f[i4][0] += f4[0];
|
||||||
|
f[i4][1] += f4[1];
|
||||||
|
f[i4][2] += f4[2];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (evflag)
|
||||||
|
ev_tally(i1,i2,i3,i4,nlocal,newton_bond,edihedral,f1,f3,f4,
|
||||||
|
vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z);
|
||||||
|
|
||||||
|
// 1-4 LJ and Coulomb interactions
|
||||||
|
// tally energy/virial in pair, using newton_bond as newton flag
|
||||||
|
|
||||||
|
if (weight[type] > 0.0) {
|
||||||
|
itype = atomtype[i1];
|
||||||
|
jtype = atomtype[i4];
|
||||||
|
|
||||||
|
delx = x[i1][0] - x[i4][0];
|
||||||
|
dely = x[i1][1] - x[i4][1];
|
||||||
|
delz = x[i1][2] - x[i4][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
r2inv = 1.0/rsq;
|
||||||
|
r6inv = r2inv*r2inv*r2inv;
|
||||||
|
|
||||||
|
// modifying coul and LJ force and energies to apply
|
||||||
|
// force_shift and force_switch as in CHARMM pairwise
|
||||||
|
// LJ interactions between 1-4 atoms should usually be
|
||||||
|
// for r < cut_inner, so switching not applied
|
||||||
|
|
||||||
|
r = sqrt(rsq);
|
||||||
|
if (implicit) forcecoul = qqrd2e * q[i1]*q[i4]*r2inv;
|
||||||
|
else if (dihedflag) forcecoul = qqrd2e * q[i1]*q[i4]*sqrt(r2inv);
|
||||||
|
else forcecoul = qqrd2e * q[i1]*q[i4]*(sqrt(r2inv) -
|
||||||
|
r*cut_coulinv14*cut_coulinv14);
|
||||||
|
forcelj = r6inv * (lj14_1[itype][jtype]*r6inv - lj14_2[itype][jtype]);
|
||||||
|
fpair = weight[type] * (forcelj+forcecoul)*r2inv;
|
||||||
|
|
||||||
|
if (eflag) {
|
||||||
|
if (dihedflag) ecoul = weight[type] * forcecoul;
|
||||||
|
else ecoul = weight[type] * qqrd2e * q[i1]*q[i4] *
|
||||||
|
(sqrt(r2inv) + r*cut_coulinv14*cut_coulinv14 -
|
||||||
|
2.0*cut_coulinv14);
|
||||||
|
evdwl14_12 = r6inv*lj14_3[itype][jtype]*r6inv -
|
||||||
|
lj14_3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
|
||||||
|
evdwl14_6 = -lj14_4[itype][jtype]*r6inv +
|
||||||
|
lj14_4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
|
||||||
|
evdwl = evdwl14_12 + evdwl14_6;
|
||||||
|
evdwl *= weight[type];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (newton_bond || i1 < nlocal) {
|
||||||
|
f[i1][0] += delx*fpair;
|
||||||
|
f[i1][1] += dely*fpair;
|
||||||
|
f[i1][2] += delz*fpair;
|
||||||
|
}
|
||||||
|
if (newton_bond || i4 < nlocal) {
|
||||||
|
f[i4][0] -= delx*fpair;
|
||||||
|
f[i4][1] -= dely*fpair;
|
||||||
|
f[i4][2] -= delz*fpair;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (evflag) force->pair->ev_tally(i1,i4,nlocal,newton_bond,
|
||||||
|
evdwl,ecoul,fpair,delx,dely,delz);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DihedralCharmmfsh::allocate()
|
||||||
|
{
|
||||||
|
allocated = 1;
|
||||||
|
int n = atom->ndihedraltypes;
|
||||||
|
|
||||||
|
memory->create(k,n+1,"dihedral:k");
|
||||||
|
memory->create(multiplicity,n+1,"dihedral:k");
|
||||||
|
memory->create(shift,n+1,"dihedral:shift");
|
||||||
|
memory->create(cos_shift,n+1,"dihedral:cos_shift");
|
||||||
|
memory->create(sin_shift,n+1,"dihedral:sin_shift");
|
||||||
|
memory->create(weight,n+1,"dihedral:weight");
|
||||||
|
|
||||||
|
memory->create(setflag,n+1,"dihedral:setflag");
|
||||||
|
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
set coeffs for one type
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DihedralCharmmfsh::coeff(int narg, char **arg)
|
||||||
|
{
|
||||||
|
if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||||
|
if (!allocated) allocate();
|
||||||
|
|
||||||
|
int ilo,ihi;
|
||||||
|
force->bounds(FLERR,arg[0],atom->ndihedraltypes,ilo,ihi);
|
||||||
|
|
||||||
|
// require integer values of shift for backwards compatibility
|
||||||
|
// arbitrary phase angle shift could be allowed, but would break
|
||||||
|
// backwards compatibility and is probably not needed
|
||||||
|
|
||||||
|
double k_one = force->numeric(FLERR,arg[1]);
|
||||||
|
int multiplicity_one = force->inumeric(FLERR,arg[2]);
|
||||||
|
int shift_one = force->inumeric(FLERR,arg[3]);
|
||||||
|
double weight_one = force->numeric(FLERR,arg[4]);
|
||||||
|
|
||||||
|
if (multiplicity_one < 0)
|
||||||
|
error->all(FLERR,"Incorrect multiplicity arg for dihedral coefficients");
|
||||||
|
if (weight_one < 0.0 || weight_one > 1.0)
|
||||||
|
error->all(FLERR,"Incorrect weight arg for dihedral coefficients");
|
||||||
|
if (weight_one > 0.0) weightflag=1;
|
||||||
|
|
||||||
|
int count = 0;
|
||||||
|
for (int i = ilo; i <= ihi; i++) {
|
||||||
|
k[i] = k_one;
|
||||||
|
shift[i] = shift_one;
|
||||||
|
cos_shift[i] = cos(MY_PI*shift_one/180.0);
|
||||||
|
sin_shift[i] = sin(MY_PI*shift_one/180.0);
|
||||||
|
multiplicity[i] = multiplicity_one;
|
||||||
|
weight[i] = weight_one;
|
||||||
|
setflag[i] = 1;
|
||||||
|
count++;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (count == 0) error->all(FLERR,"Incorrect args for dihedral coefficients");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
error check and initialize all values needed for force computation
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DihedralCharmmfsh::init_style()
|
||||||
|
{
|
||||||
|
// insure use of CHARMM pair_style if any weight factors are non-zero
|
||||||
|
// set local ptrs to LJ 14 arrays setup by Pair
|
||||||
|
|
||||||
|
if (weightflag) {
|
||||||
|
int itmp;
|
||||||
|
if (force->pair == NULL)
|
||||||
|
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
|
||||||
|
lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
|
||||||
|
lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
|
||||||
|
lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
|
||||||
|
lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
|
||||||
|
int *ptr = (int *) force->pair->extract("implicit",itmp);
|
||||||
|
if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
|
||||||
|
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
|
||||||
|
implicit = *ptr;
|
||||||
|
}
|
||||||
|
|
||||||
|
// constants for applying force switch (LJ) and force_shift (coul)
|
||||||
|
// to 1/4 dihedral atoms to match CHARMM pairwise interactions
|
||||||
|
|
||||||
|
int itmp;
|
||||||
|
int *p_dihedflag = (int *) force->pair->extract("dihedflag",itmp);
|
||||||
|
double *p_cutljinner = (double *) force->pair->extract("cut_lj_inner",itmp);
|
||||||
|
double *p_cutlj = (double *) force->pair->extract("cut_lj",itmp);
|
||||||
|
double *p_cutcoul = (double *) force->pair->extract("cut_coul",itmp);
|
||||||
|
|
||||||
|
if (p_cutcoul == NULL || p_cutljinner == NULL ||
|
||||||
|
p_cutlj == NULL || p_dihedflag == NULL)
|
||||||
|
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
|
||||||
|
|
||||||
|
dihedflag = *p_dihedflag;
|
||||||
|
cut_coul14 = *p_cutcoul;
|
||||||
|
cut_lj_inner14 = *p_cutljinner;
|
||||||
|
cut_lj14 = *p_cutlj;
|
||||||
|
|
||||||
|
cut_coulinv14 = 1/cut_coul14;
|
||||||
|
cut_lj_inner3inv = (1/cut_lj_inner14) * (1/cut_lj_inner14) *
|
||||||
|
(1/cut_lj_inner14);
|
||||||
|
cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv;
|
||||||
|
cut_lj3inv = (1/cut_lj14) * (1/cut_lj14) * (1/cut_lj14);
|
||||||
|
cut_lj6inv = cut_lj3inv * cut_lj3inv;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes out coeffs to restart file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DihedralCharmmfsh::write_restart(FILE *fp)
|
||||||
|
{
|
||||||
|
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||||
|
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||||
|
fwrite(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||||
|
fwrite(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||||
|
fwrite(&weightflag,sizeof(int),1,fp);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 reads coeffs from restart file, bcasts them
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DihedralCharmmfsh::read_restart(FILE *fp)
|
||||||
|
{
|
||||||
|
allocate();
|
||||||
|
|
||||||
|
if (comm->me == 0) {
|
||||||
|
fread(&k[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||||
|
fread(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||||
|
fread(&shift[1],sizeof(int),atom->ndihedraltypes,fp);
|
||||||
|
fread(&weight[1],sizeof(double),atom->ndihedraltypes,fp);
|
||||||
|
fread(&weightflag,sizeof(int),1,fp);
|
||||||
|
}
|
||||||
|
MPI_Bcast(&k[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&multiplicity[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||||
|
MPI_Bcast(&shift[1],atom->ndihedraltypes,MPI_INT,0,world);
|
||||||
|
MPI_Bcast(&weight[1],atom->ndihedraltypes,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&weightflag,1,MPI_INT,0,world);
|
||||||
|
|
||||||
|
for (int i = 1; i <= atom->ndihedraltypes; i++) {
|
||||||
|
setflag[i] = 1;
|
||||||
|
cos_shift[i] = cos(MY_PI*shift[i]/180.0);
|
||||||
|
sin_shift[i] = sin(MY_PI*shift[i]/180.0);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes to data file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void DihedralCharmmfsh::write_data(FILE *fp)
|
||||||
|
{
|
||||||
|
for (int i = 1; i <= atom->ndihedraltypes; i++)
|
||||||
|
fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
|
||||||
|
}
|
||||||
|
|
||||||
81
src/MOLECULE/dihedral_charmmfsh.h
Normal file
81
src/MOLECULE/dihedral_charmmfsh.h
Normal file
@ -0,0 +1,81 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef DIHEDRAL_CLASS
|
||||||
|
|
||||||
|
DihedralStyle(charmmfsh,DihedralCharmmfsh)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_DIHEDRAL_CHARMMFSH_H
|
||||||
|
#define LMP_DIHEDRAL_CHARMMFSH_H
|
||||||
|
|
||||||
|
#include <stdio.h>
|
||||||
|
#include "dihedral.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class DihedralCharmmfsh : public Dihedral {
|
||||||
|
public:
|
||||||
|
DihedralCharmmfsh(class LAMMPS *);
|
||||||
|
virtual ~DihedralCharmmfsh();
|
||||||
|
virtual void compute(int, int);
|
||||||
|
virtual void coeff(int, char **);
|
||||||
|
virtual void init_style();
|
||||||
|
void write_restart(FILE *);
|
||||||
|
void read_restart(FILE *);
|
||||||
|
void write_data(FILE *);
|
||||||
|
|
||||||
|
protected:
|
||||||
|
int implicit,weightflag,dihedflag;
|
||||||
|
double cut_lj_inner14,cut_lj14,cut_coul14;
|
||||||
|
double evdwl14_12,evdwl14_6,cut_coulinv14;
|
||||||
|
double cut_lj_inner3inv,cut_lj_inner6inv,cut_lj3inv,cut_lj6inv;
|
||||||
|
|
||||||
|
double *k,*weight,*cos_shift,*sin_shift;
|
||||||
|
int *multiplicity,*shift;
|
||||||
|
double **lj14_1,**lj14_2,**lj14_3,**lj14_4;
|
||||||
|
|
||||||
|
virtual void allocate();
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
W: Dihedral problem: %d %ld %d %d %d %d
|
||||||
|
|
||||||
|
Conformation of the 4 listed dihedral atoms is extreme; you may want
|
||||||
|
to check your simulation geometry.
|
||||||
|
|
||||||
|
E: Incorrect args for dihedral coefficients
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
|
E: Incorrect multiplicity arg for dihedral coefficients
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
|
E: Incorrect weight arg for dihedral coefficients
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
|
E: Dihedral charmmfsh is incompatible with Pair style
|
||||||
|
|
||||||
|
Dihedral style charmmfsh must be used with a pair style charmm
|
||||||
|
in order for the 1-4 epsilon/sigma parameters to be defined.
|
||||||
|
|
||||||
|
*/
|
||||||
546
src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
Normal file
546
src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.cpp
Normal file
@ -0,0 +1,546 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Contributing author: Paul Crozier (SNL)
|
||||||
|
The lj-fsw/coul-fsh (force-switched and force-shifted) sections
|
||||||
|
were provided by Robert Meissner
|
||||||
|
and Lucio Colombi Ciacchi of Bremen University, Bremen, Germany,
|
||||||
|
with additional assistance from Robert A. Latour, Clemson University
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include <math.h>
|
||||||
|
#include <stdio.h>
|
||||||
|
#include <stdlib.h>
|
||||||
|
#include <string.h>
|
||||||
|
#include "pair_lj_charmmfsw_coul_charmmfsh.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
PairLJCharmmfswCoulCharmmfsh::PairLJCharmmfswCoulCharmmfsh(LAMMPS *lmp) :
|
||||||
|
Pair(lmp)
|
||||||
|
{
|
||||||
|
implicit = 0;
|
||||||
|
mix_flag = ARITHMETIC;
|
||||||
|
writedata = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
PairLJCharmmfswCoulCharmmfsh::~PairLJCharmmfswCoulCharmmfsh()
|
||||||
|
{
|
||||||
|
if (!copymode) {
|
||||||
|
if (allocated) {
|
||||||
|
memory->destroy(setflag);
|
||||||
|
memory->destroy(cutsq);
|
||||||
|
|
||||||
|
memory->destroy(epsilon);
|
||||||
|
memory->destroy(sigma);
|
||||||
|
memory->destroy(eps14);
|
||||||
|
memory->destroy(sigma14);
|
||||||
|
memory->destroy(lj1);
|
||||||
|
memory->destroy(lj2);
|
||||||
|
memory->destroy(lj3);
|
||||||
|
memory->destroy(lj4);
|
||||||
|
memory->destroy(lj14_1);
|
||||||
|
memory->destroy(lj14_2);
|
||||||
|
memory->destroy(lj14_3);
|
||||||
|
memory->destroy(lj14_4);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::compute(int eflag, int vflag)
|
||||||
|
{
|
||||||
|
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||||
|
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwl12,evdwl6,ecoul,fpair;
|
||||||
|
double r,rinv,r3inv,rsq,r2inv,r6inv,forcecoul,forcelj,factor_coul,factor_lj;
|
||||||
|
double switch1;
|
||||||
|
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||||
|
|
||||||
|
evdwl = ecoul = 0.0;
|
||||||
|
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||||
|
else evflag = vflag_fdotr = 0;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double **f = atom->f;
|
||||||
|
double *q = atom->q;
|
||||||
|
int *type = atom->type;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
double *special_coul = force->special_coul;
|
||||||
|
double *special_lj = force->special_lj;
|
||||||
|
int newton_pair = force->newton_pair;
|
||||||
|
double qqrd2e = force->qqrd2e;
|
||||||
|
|
||||||
|
inum = list->inum;
|
||||||
|
ilist = list->ilist;
|
||||||
|
numneigh = list->numneigh;
|
||||||
|
firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// loop over neighbors of my atoms
|
||||||
|
|
||||||
|
for (ii = 0; ii < inum; ii++) {
|
||||||
|
i = ilist[ii];
|
||||||
|
qtmp = q[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
itype = type[i];
|
||||||
|
jlist = firstneigh[i];
|
||||||
|
jnum = numneigh[i];
|
||||||
|
|
||||||
|
for (jj = 0; jj < jnum; jj++) {
|
||||||
|
j = jlist[jj];
|
||||||
|
factor_lj = special_lj[sbmask(j)];
|
||||||
|
factor_coul = special_coul[sbmask(j)];
|
||||||
|
j &= NEIGHMASK;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq < cut_bothsq) {
|
||||||
|
r2inv = 1.0/rsq;
|
||||||
|
r = sqrt(rsq);
|
||||||
|
|
||||||
|
if (rsq < cut_coulsq) {
|
||||||
|
forcecoul = qqrd2e * qtmp*q[j]*
|
||||||
|
(sqrt(r2inv) - r*cut_coulinv*cut_coulinv);
|
||||||
|
} else forcecoul = 0.0;
|
||||||
|
|
||||||
|
if (rsq < cut_ljsq) {
|
||||||
|
r6inv = r2inv*r2inv*r2inv;
|
||||||
|
jtype = type[j];
|
||||||
|
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||||
|
if (rsq > cut_lj_innersq) {
|
||||||
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
||||||
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
||||||
|
forcelj = forcelj*switch1;
|
||||||
|
}
|
||||||
|
} else forcelj = 0.0;
|
||||||
|
|
||||||
|
fpair = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
|
||||||
|
|
||||||
|
f[i][0] += delx*fpair;
|
||||||
|
f[i][1] += dely*fpair;
|
||||||
|
f[i][2] += delz*fpair;
|
||||||
|
if (newton_pair || j < nlocal) {
|
||||||
|
f[j][0] -= delx*fpair;
|
||||||
|
f[j][1] -= dely*fpair;
|
||||||
|
f[j][2] -= delz*fpair;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (eflag) {
|
||||||
|
if (rsq < cut_coulsq) {
|
||||||
|
ecoul = qqrd2e * qtmp*q[j]*
|
||||||
|
(sqrt(r2inv) + cut_coulinv*cut_coulinv*r - 2.0*cut_coulinv);
|
||||||
|
ecoul *= factor_coul;
|
||||||
|
} else ecoul = 0.0;
|
||||||
|
if (rsq < cut_ljsq) {
|
||||||
|
if (rsq > cut_lj_innersq) {
|
||||||
|
rinv = 1.0/r;
|
||||||
|
r3inv = rinv*rinv*rinv;
|
||||||
|
evdwl12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
|
||||||
|
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
|
||||||
|
evdwl6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
|
||||||
|
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
|
||||||
|
evdwl = evdwl12 + evdwl6;
|
||||||
|
} else {
|
||||||
|
evdwl12 = r6inv*lj3[itype][jtype]*r6inv -
|
||||||
|
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
|
||||||
|
evdwl6 = -lj4[itype][jtype]*r6inv +
|
||||||
|
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
|
||||||
|
evdwl = evdwl12 + evdwl6;
|
||||||
|
}
|
||||||
|
evdwl *= factor_lj;
|
||||||
|
} else evdwl = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (evflag) ev_tally(i,j,nlocal,newton_pair,
|
||||||
|
evdwl,ecoul,fpair,delx,dely,delz);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (vflag_fdotr) virial_fdotr_compute();
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
allocate all arrays
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::allocate()
|
||||||
|
{
|
||||||
|
allocated = 1;
|
||||||
|
int n = atom->ntypes;
|
||||||
|
|
||||||
|
memory->create(setflag,n+1,n+1,"pair:setflag");
|
||||||
|
for (int i = 1; i <= n; i++)
|
||||||
|
for (int j = i; j <= n; j++)
|
||||||
|
setflag[i][j] = 0;
|
||||||
|
|
||||||
|
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
||||||
|
|
||||||
|
memory->create(epsilon,n+1,n+1,"pair:epsilon");
|
||||||
|
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||||
|
memory->create(eps14,n+1,n+1,"pair:eps14");
|
||||||
|
memory->create(sigma14,n+1,n+1,"pair:sigma14");
|
||||||
|
memory->create(lj1,n+1,n+1,"pair:lj1");
|
||||||
|
memory->create(lj2,n+1,n+1,"pair:lj2");
|
||||||
|
memory->create(lj3,n+1,n+1,"pair:lj3");
|
||||||
|
memory->create(lj4,n+1,n+1,"pair:lj4");
|
||||||
|
memory->create(lj14_1,n+1,n+1,"pair:lj14_1");
|
||||||
|
memory->create(lj14_2,n+1,n+1,"pair:lj14_2");
|
||||||
|
memory->create(lj14_3,n+1,n+1,"pair:lj14_3");
|
||||||
|
memory->create(lj14_4,n+1,n+1,"pair:lj14_4");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
global settings
|
||||||
|
unlike other pair styles,
|
||||||
|
there are no individual pair settings that these override
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::settings(int narg, char **arg)
|
||||||
|
{
|
||||||
|
if (narg != 2 && narg != 3)
|
||||||
|
error->all(FLERR,"Illegal pair_style command");
|
||||||
|
|
||||||
|
cut_lj_inner = force->numeric(FLERR,arg[0]);
|
||||||
|
cut_lj = force->numeric(FLERR,arg[1]);
|
||||||
|
if (narg == 2) {
|
||||||
|
cut_coul = cut_lj;
|
||||||
|
} else {
|
||||||
|
cut_coul = force->numeric(FLERR,arg[2]);
|
||||||
|
}
|
||||||
|
|
||||||
|
// indicates pair_style being used for dihedral_charmm
|
||||||
|
|
||||||
|
dihedflag = 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
set coeffs for one or more type pairs
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::coeff(int narg, char **arg)
|
||||||
|
{
|
||||||
|
if (narg != 4 && narg != 6)
|
||||||
|
error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
|
if (!allocated) allocate();
|
||||||
|
|
||||||
|
int ilo,ihi,jlo,jhi;
|
||||||
|
force->bounds(FLERR,arg[0],atom->ntypes,ilo,ihi);
|
||||||
|
force->bounds(FLERR,arg[1],atom->ntypes,jlo,jhi);
|
||||||
|
|
||||||
|
double epsilon_one = force->numeric(FLERR,arg[2]);
|
||||||
|
double sigma_one = force->numeric(FLERR,arg[3]);
|
||||||
|
double eps14_one = epsilon_one;
|
||||||
|
double sigma14_one = sigma_one;
|
||||||
|
if (narg == 6) {
|
||||||
|
eps14_one = force->numeric(FLERR,arg[4]);
|
||||||
|
sigma14_one = force->numeric(FLERR,arg[5]);
|
||||||
|
}
|
||||||
|
|
||||||
|
int count = 0;
|
||||||
|
for (int i = ilo; i <= ihi; i++) {
|
||||||
|
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||||
|
epsilon[i][j] = epsilon_one;
|
||||||
|
sigma[i][j] = sigma_one;
|
||||||
|
eps14[i][j] = eps14_one;
|
||||||
|
sigma14[i][j] = sigma14_one;
|
||||||
|
setflag[i][j] = 1;
|
||||||
|
count++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
init specific to this pair style
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::init_style()
|
||||||
|
{
|
||||||
|
if (!atom->q_flag)
|
||||||
|
error->all(FLERR,"Pair style lj/charmmfsw/coul/charmmfsh "
|
||||||
|
"requires atom attribute q");
|
||||||
|
|
||||||
|
neighbor->request(this,instance_me);
|
||||||
|
|
||||||
|
// require cut_lj_inner < cut_lj
|
||||||
|
|
||||||
|
if (cut_lj_inner >= cut_lj)
|
||||||
|
error->all(FLERR,"Pair inner lj cutoff >= Pair outer lj cutoff");
|
||||||
|
|
||||||
|
cut_lj_innersq = cut_lj_inner * cut_lj_inner;
|
||||||
|
cut_ljsq = cut_lj * cut_lj;
|
||||||
|
cut_ljinv = 1.0/cut_lj;
|
||||||
|
cut_lj_innerinv = 1.0/cut_lj_inner;
|
||||||
|
cut_lj3 = cut_lj * cut_lj * cut_lj;
|
||||||
|
cut_lj3inv = cut_ljinv * cut_ljinv * cut_ljinv;
|
||||||
|
cut_lj_inner3inv = cut_lj_innerinv * cut_lj_innerinv * cut_lj_innerinv;
|
||||||
|
cut_lj_inner3 = cut_lj_inner * cut_lj_inner * cut_lj_inner;
|
||||||
|
cut_lj6 = cut_ljsq * cut_ljsq * cut_ljsq;
|
||||||
|
cut_lj6inv = cut_lj3inv * cut_lj3inv;
|
||||||
|
cut_lj_inner6inv = cut_lj_inner3inv * cut_lj_inner3inv;
|
||||||
|
cut_lj_inner6 = cut_lj_innersq * cut_lj_innersq * cut_lj_innersq;
|
||||||
|
cut_coulsq = cut_coul * cut_coul;
|
||||||
|
cut_coulinv = 1.0/cut_coul;
|
||||||
|
cut_bothsq = MAX(cut_ljsq,cut_coulsq);
|
||||||
|
|
||||||
|
denom_lj = (cut_ljsq-cut_lj_innersq) * (cut_ljsq-cut_lj_innersq) *
|
||||||
|
(cut_ljsq-cut_lj_innersq);
|
||||||
|
denom_lj12 = 1.0/(cut_lj6 - cut_lj_inner6);
|
||||||
|
denom_lj6 = 1.0/(cut_lj3 - cut_lj_inner3);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
init for one type pair i,j and corresponding j,i
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairLJCharmmfswCoulCharmmfsh::init_one(int i, int j)
|
||||||
|
{
|
||||||
|
if (setflag[i][j] == 0) {
|
||||||
|
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
|
||||||
|
sigma[i][i],sigma[j][j]);
|
||||||
|
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
|
||||||
|
eps14[i][j] = mix_energy(eps14[i][i],eps14[j][j],
|
||||||
|
sigma14[i][i],sigma14[j][j]);
|
||||||
|
sigma14[i][j] = mix_distance(sigma14[i][i],sigma14[j][j]);
|
||||||
|
}
|
||||||
|
|
||||||
|
double cut = MAX(cut_lj,cut_coul);
|
||||||
|
|
||||||
|
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||||
|
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||||
|
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
|
||||||
|
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
|
||||||
|
lj14_1[i][j] = 48.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
|
||||||
|
lj14_2[i][j] = 24.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
|
||||||
|
lj14_3[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],12.0);
|
||||||
|
lj14_4[i][j] = 4.0 * eps14[i][j] * pow(sigma14[i][j],6.0);
|
||||||
|
|
||||||
|
lj1[j][i] = lj1[i][j];
|
||||||
|
lj2[j][i] = lj2[i][j];
|
||||||
|
lj3[j][i] = lj3[i][j];
|
||||||
|
lj4[j][i] = lj4[i][j];
|
||||||
|
lj14_1[j][i] = lj14_1[i][j];
|
||||||
|
lj14_2[j][i] = lj14_2[i][j];
|
||||||
|
lj14_3[j][i] = lj14_3[i][j];
|
||||||
|
lj14_4[j][i] = lj14_4[i][j];
|
||||||
|
|
||||||
|
return cut;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes to data file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::write_data(FILE *fp)
|
||||||
|
{
|
||||||
|
for (int i = 1; i <= atom->ntypes; i++)
|
||||||
|
fprintf(fp,"%d %g %g %g %g\n",
|
||||||
|
i,epsilon[i][i],sigma[i][i],eps14[i][i],sigma14[i][i]);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes all pairs to data file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::write_data_all(FILE *fp)
|
||||||
|
{
|
||||||
|
for (int i = 1; i <= atom->ntypes; i++)
|
||||||
|
for (int j = i; j <= atom->ntypes; j++)
|
||||||
|
fprintf(fp,"%d %d %g %g %g %g\n",i,j,
|
||||||
|
epsilon[i][j],sigma[i][j],eps14[i][j],sigma14[i][j]);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes to restart file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::write_restart(FILE *fp)
|
||||||
|
{
|
||||||
|
write_restart_settings(fp);
|
||||||
|
|
||||||
|
int i,j;
|
||||||
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
|
for (j = i; j <= atom->ntypes; j++) {
|
||||||
|
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
||||||
|
if (setflag[i][j]) {
|
||||||
|
fwrite(&epsilon[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&eps14[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&sigma14[i][j],sizeof(double),1,fp);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 reads from restart file, bcasts
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::read_restart(FILE *fp)
|
||||||
|
{
|
||||||
|
read_restart_settings(fp);
|
||||||
|
|
||||||
|
allocate();
|
||||||
|
|
||||||
|
int i,j;
|
||||||
|
int me = comm->me;
|
||||||
|
for (i = 1; i <= atom->ntypes; i++)
|
||||||
|
for (j = i; j <= atom->ntypes; j++) {
|
||||||
|
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
||||||
|
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||||
|
if (setflag[i][j]) {
|
||||||
|
if (me == 0) {
|
||||||
|
fread(&epsilon[i][j],sizeof(double),1,fp);
|
||||||
|
fread(&sigma[i][j],sizeof(double),1,fp);
|
||||||
|
fread(&eps14[i][j],sizeof(double),1,fp);
|
||||||
|
fread(&sigma14[i][j],sizeof(double),1,fp);
|
||||||
|
}
|
||||||
|
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&eps14[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&sigma14[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes to restart file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::write_restart_settings(FILE *fp)
|
||||||
|
{
|
||||||
|
fwrite(&cut_lj_inner,sizeof(double),1,fp);
|
||||||
|
fwrite(&cut_lj,sizeof(double),1,fp);
|
||||||
|
fwrite(&cut_coul,sizeof(double),1,fp);
|
||||||
|
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||||
|
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 reads from restart file, bcasts
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairLJCharmmfswCoulCharmmfsh::read_restart_settings(FILE *fp)
|
||||||
|
{
|
||||||
|
if (comm->me == 0) {
|
||||||
|
fread(&cut_lj_inner,sizeof(double),1,fp);
|
||||||
|
fread(&cut_lj,sizeof(double),1,fp);
|
||||||
|
fread(&cut_coul,sizeof(double),1,fp);
|
||||||
|
fread(&offset_flag,sizeof(int),1,fp);
|
||||||
|
fread(&mix_flag,sizeof(int),1,fp);
|
||||||
|
}
|
||||||
|
MPI_Bcast(&cut_lj_inner,1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&cut_lj,1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||||
|
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairLJCharmmfswCoulCharmmfsh::
|
||||||
|
single(int i, int j, int itype, int jtype,
|
||||||
|
double rsq, double factor_coul, double factor_lj, double &fforce)
|
||||||
|
{
|
||||||
|
double r,rinv,r2inv,r3inv,r6inv,forcecoul,forcelj;
|
||||||
|
double phicoul,philj,philj12,philj6;
|
||||||
|
double switch1;
|
||||||
|
|
||||||
|
r2inv = 1.0/rsq;
|
||||||
|
r = sqrt(rsq);
|
||||||
|
rinv = 1.0/r;
|
||||||
|
if (rsq < cut_coulsq) {
|
||||||
|
forcecoul = force->qqrd2e * atom->q[i]*atom->q[j] *
|
||||||
|
(sqrt(r2inv) - r*cut_coulinv*cut_coulinv);
|
||||||
|
} else forcecoul = 0.0;
|
||||||
|
|
||||||
|
if (rsq < cut_ljsq) {
|
||||||
|
r6inv = r2inv*r2inv*r2inv;
|
||||||
|
r3inv = rinv*rinv*rinv;
|
||||||
|
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
|
||||||
|
if (rsq > cut_lj_innersq) {
|
||||||
|
switch1 = (cut_ljsq-rsq) * (cut_ljsq-rsq) *
|
||||||
|
(cut_ljsq + 2.0*rsq - 3.0*cut_lj_innersq) / denom_lj;
|
||||||
|
forcelj = forcelj*switch1;
|
||||||
|
}
|
||||||
|
} else forcelj = 0.0;
|
||||||
|
|
||||||
|
fforce = (factor_coul*forcecoul + factor_lj*forcelj) * r2inv;
|
||||||
|
|
||||||
|
double eng = 0.0;
|
||||||
|
if (rsq < cut_coulsq) {
|
||||||
|
phicoul = force->qqrd2e * atom->q[i]*atom->q[j] *
|
||||||
|
(sqrt(r2inv) + cut_coulinv*cut_coulinv*r - 2.0*cut_coulinv);
|
||||||
|
eng += factor_coul*phicoul;
|
||||||
|
}
|
||||||
|
if (rsq < cut_ljsq) {
|
||||||
|
if (rsq > cut_lj_innersq) {
|
||||||
|
philj12 = lj3[itype][jtype]*cut_lj6*denom_lj12 *
|
||||||
|
(r6inv - cut_lj6inv)*(r6inv - cut_lj6inv);
|
||||||
|
philj6 = -lj4[itype][jtype]*cut_lj3*denom_lj6 *
|
||||||
|
(r3inv - cut_lj3inv)*(r3inv - cut_lj3inv);;
|
||||||
|
philj = philj12 + philj6;
|
||||||
|
} else {
|
||||||
|
philj12 = r6inv*lj3[itype][jtype]*r6inv -
|
||||||
|
lj3[itype][jtype]*cut_lj_inner6inv*cut_lj6inv;
|
||||||
|
philj6 = -lj4[itype][jtype]*r6inv +
|
||||||
|
lj4[itype][jtype]*cut_lj_inner3inv*cut_lj3inv;
|
||||||
|
philj = philj12 + philj6;
|
||||||
|
}
|
||||||
|
eng += factor_lj*philj;
|
||||||
|
}
|
||||||
|
|
||||||
|
return eng;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void *PairLJCharmmfswCoulCharmmfsh::extract(const char *str, int &dim)
|
||||||
|
{
|
||||||
|
dim = 2;
|
||||||
|
if (strcmp(str,"lj14_1") == 0) return (void *) lj14_1;
|
||||||
|
if (strcmp(str,"lj14_2") == 0) return (void *) lj14_2;
|
||||||
|
if (strcmp(str,"lj14_3") == 0) return (void *) lj14_3;
|
||||||
|
if (strcmp(str,"lj14_4") == 0) return (void *) lj14_4;
|
||||||
|
|
||||||
|
dim = 0;
|
||||||
|
if (strcmp(str,"implicit") == 0) return (void *) &implicit;
|
||||||
|
|
||||||
|
// info extracted by dihedral_charmmf
|
||||||
|
|
||||||
|
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
|
||||||
|
if (strcmp(str,"cut_lj_inner") == 0) return (void *) &cut_lj_inner;
|
||||||
|
if (strcmp(str,"cut_lj") == 0) return (void *) &cut_lj;
|
||||||
|
if (strcmp(str,"dihedflag") == 0) return (void *) &dihedflag;
|
||||||
|
|
||||||
|
return NULL;
|
||||||
|
}
|
||||||
88
src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h
Normal file
88
src/MOLECULE/pair_lj_charmmfsw_coul_charmmfsh.h
Normal file
@ -0,0 +1,88 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
|
certain rights in this software. This software is distributed under
|
||||||
|
the GNU General Public License.
|
||||||
|
|
||||||
|
See the README file in the top-level LAMMPS directory.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef PAIR_CLASS
|
||||||
|
|
||||||
|
PairStyle(lj/charmmfsw/coul/charmmfsh,PairLJCharmmfswCoulCharmmfsh)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_PAIR_LJ_CHARMMFSW_COUL_CHARMMFSH_H
|
||||||
|
#define LMP_PAIR_LJ_CHARMMFSW_COUL_CHARMMFSH_H
|
||||||
|
|
||||||
|
#include "pair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class PairLJCharmmfswCoulCharmmfsh : public Pair {
|
||||||
|
public:
|
||||||
|
PairLJCharmmfswCoulCharmmfsh(class LAMMPS *);
|
||||||
|
virtual ~PairLJCharmmfswCoulCharmmfsh();
|
||||||
|
virtual void compute(int, int);
|
||||||
|
virtual void settings(int, char **);
|
||||||
|
void coeff(int, char **);
|
||||||
|
virtual void init_style();
|
||||||
|
virtual double init_one(int, int);
|
||||||
|
void write_restart(FILE *);
|
||||||
|
void read_restart(FILE *);
|
||||||
|
void write_restart_settings(FILE *);
|
||||||
|
void read_restart_settings(FILE *);
|
||||||
|
void write_data(FILE *);
|
||||||
|
void write_data_all(FILE *);
|
||||||
|
virtual double single(int, int, int, int, double, double, double, double &);
|
||||||
|
virtual void *extract(const char *, int &);
|
||||||
|
|
||||||
|
protected:
|
||||||
|
int implicit;
|
||||||
|
int dihedflag;
|
||||||
|
|
||||||
|
double cut_lj_inner,cut_lj,cut_coul,cut_coulinv,cut_ljinv,cut_lj_innerinv;
|
||||||
|
double cut_lj_innersq,cut_ljsq,cut_coulsq,cut_bothsq;
|
||||||
|
double cut_lj3inv,cut_lj_inner3inv,cut_lj3,cut_lj_inner3;
|
||||||
|
double cut_lj6inv,cut_lj_inner6inv,cut_lj6,cut_lj_inner6;
|
||||||
|
double denom_lj,denom_lj12,denom_lj6;
|
||||||
|
|
||||||
|
double **epsilon,**sigma,**eps14,**sigma14;
|
||||||
|
double **lj1,**lj2,**lj3,**lj4;
|
||||||
|
double **lj14_1,**lj14_2,**lj14_3,**lj14_4;
|
||||||
|
|
||||||
|
virtual void allocate();
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: Incorrect args for pair coefficients
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
|
E: Pair style lj/charmmfsw/coul/charmmfsh requires atom attribute q
|
||||||
|
|
||||||
|
The atom style defined does not have these attributes.
|
||||||
|
|
||||||
|
E: Pair inner cutoff >= Pair outer cutoff
|
||||||
|
|
||||||
|
The specified cutoffs for the pair style are inconsistent.
|
||||||
|
|
||||||
|
*/
|
||||||
|
|
||||||
@ -9,8 +9,11 @@
|
|||||||
the GNU General Public License.
|
the GNU General Public License.
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
-------------------------------------------------------------------------
|
------------------------------------------------------------------------- */
|
||||||
Contributed by Kristen Fichthorn, Tonnam Balankura, Ya Zhou @ Penn State University
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
Contributing authors: Kristen Fichthorn, Tonnam Balankura,
|
||||||
|
Ya Zhou (Penn State University)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include <math.h>
|
#include <math.h>
|
||||||
|
|||||||
Reference in New Issue
Block a user