forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9722 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
ad30952144
commit
45ea5f9795
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@ -8,7 +8,6 @@ if (test $1 = 1) then
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cp angle_cosine_periodic.cpp ..
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cp angle_cosine_squared.cpp ..
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cp angle_harmonic.cpp ..
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cp angle_hybrid.cpp ..
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cp angle_table.cpp ..
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cp atom_vec_angle.cpp ..
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cp atom_vec_bond.cpp ..
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@ -24,12 +23,10 @@ if (test $1 = 1) then
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cp dihedral_charmm.cpp ..
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cp dihedral_harmonic.cpp ..
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cp dihedral_helix.cpp ..
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cp dihedral_hybrid.cpp ..
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cp dihedral_multi_harmonic.cpp ..
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cp dihedral_opls.cpp ..
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cp improper_cvff.cpp ..
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cp improper_harmonic.cpp ..
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cp improper_hybrid.cpp ..
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cp improper_umbrella.cpp ..
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cp pair_hbond_dreiding_lj.cpp ..
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cp pair_hbond_dreiding_morse.cpp ..
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@ -43,7 +40,6 @@ if (test $1 = 1) then
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cp angle_cosine_periodic.h ..
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cp angle_cosine_squared.h ..
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cp angle_harmonic.h ..
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cp angle_hybrid.h ..
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cp angle_table.h ..
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cp atom_vec_angle.h ..
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cp atom_vec_bond.h ..
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@ -59,12 +55,10 @@ if (test $1 = 1) then
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cp dihedral_charmm.h ..
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cp dihedral_harmonic.h ..
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cp dihedral_helix.h ..
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cp dihedral_hybrid.h ..
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cp dihedral_multi_harmonic.h ..
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cp dihedral_opls.h ..
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cp improper_cvff.h ..
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cp improper_harmonic.h ..
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cp improper_hybrid.h ..
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cp improper_umbrella.h ..
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cp pair_hbond_dreiding_lj.h ..
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cp pair_hbond_dreiding_morse.h ..
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@ -80,7 +74,6 @@ elif (test $1 = 0) then
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rm -f ../angle_cosine_periodic.cpp
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rm -f ../angle_cosine_squared.cpp
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rm -f ../angle_harmonic.cpp
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rm -f ../angle_hybrid.cpp
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rm -f ../angle_table.cpp
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rm -f ../atom_vec_angle.cpp
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rm -f ../atom_vec_bond.cpp
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@ -96,12 +89,10 @@ elif (test $1 = 0) then
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rm -f ../dihedral_charmm.cpp
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rm -f ../dihedral_harmonic.cpp
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rm -f ../dihedral_helix.cpp
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rm -f ../dihedral_hybrid.cpp
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rm -f ../dihedral_multi_harmonic.cpp
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rm -f ../dihedral_opls.cpp
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rm -f ../improper_cvff.cpp
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rm -f ../improper_harmonic.cpp
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rm -f ../improper_hybrid.cpp
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rm -f ../improper_umbrella.cpp
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rm -f ../pair_hbond_dreiding_lj.cpp
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rm -f ../pair_hbond_dreiding_morse.cpp
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@ -115,7 +106,6 @@ elif (test $1 = 0) then
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rm -f ../angle_cosine_periodic.h
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rm -f ../angle_cosine_squared.h
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rm -f ../angle_harmonic.h
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rm -f ../angle_hybrid.h
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rm -f ../angle_table.h
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rm -f ../atom_vec_angle.h
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rm -f ../atom_vec_bond.h
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@ -131,12 +121,10 @@ elif (test $1 = 0) then
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rm -f ../dihedral_charmm.h
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rm -f ../dihedral_harmonic.h
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rm -f ../dihedral_helix.h
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rm -f ../dihedral_hybrid.h
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rm -f ../dihedral_multi_harmonic.h
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rm -f ../dihedral_opls.h
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rm -f ../improper_cvff.h
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rm -f ../improper_harmonic.h
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rm -f ../improper_hybrid.h
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rm -f ../improper_umbrella.h
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rm -f ../pair_hbond_dreiding_lj.h
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rm -f ../pair_hbond_dreiding_morse.h
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@ -0,0 +1,368 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "math.h"
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#include "string.h"
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#include "ctype.h"
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#include "angle_hybrid.h"
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#include "atom.h"
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#include "neighbor.h"
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#include "domain.h"
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#include "comm.h"
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#include "force.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define EXTRA 1000
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/* ---------------------------------------------------------------------- */
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AngleHybrid::AngleHybrid(LAMMPS *lmp) : Angle(lmp)
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{
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nstyles = 0;
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}
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/* ---------------------------------------------------------------------- */
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AngleHybrid::~AngleHybrid()
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{
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if (nstyles) {
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for (int i = 0; i < nstyles; i++) delete styles[i];
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delete [] styles;
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for (int i = 0; i < nstyles; i++) delete [] keywords[i];
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delete [] keywords;
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}
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(map);
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delete [] nanglelist;
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delete [] maxangle;
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for (int i = 0; i < nstyles; i++)
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memory->destroy(anglelist[i]);
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delete [] anglelist;
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}
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}
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/* ---------------------------------------------------------------------- */
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void AngleHybrid::compute(int eflag, int vflag)
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{
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int i,j,m,n;
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// save ptrs to original anglelist
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int nanglelist_orig = neighbor->nanglelist;
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int **anglelist_orig = neighbor->anglelist;
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// if this is re-neighbor step, create sub-style anglelists
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// nanglelist[] = length of each sub-style list
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// realloc sub-style anglelist if necessary
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// load sub-style anglelist with 4 values from original anglelist
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if (neighbor->ago == 0) {
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for (m = 0; m < nstyles; m++) nanglelist[m] = 0;
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for (i = 0; i < nanglelist_orig; i++) {
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m = map[anglelist_orig[i][3]];
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if (m >= 0) nanglelist[m]++;
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}
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for (m = 0; m < nstyles; m++) {
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if (nanglelist[m] > maxangle[m]) {
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memory->destroy(anglelist[m]);
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maxangle[m] = nanglelist[m] + EXTRA;
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memory->create(anglelist[m],maxangle[m],4,"angle_hybrid:anglelist");
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}
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nanglelist[m] = 0;
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}
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for (i = 0; i < nanglelist_orig; i++) {
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m = map[anglelist_orig[i][3]];
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if (m < 0) continue;
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n = nanglelist[m];
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anglelist[m][n][0] = anglelist_orig[i][0];
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anglelist[m][n][1] = anglelist_orig[i][1];
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anglelist[m][n][2] = anglelist_orig[i][2];
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anglelist[m][n][3] = anglelist_orig[i][3];
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nanglelist[m]++;
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}
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}
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// call each sub-style's compute function
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// set neighbor->anglelist to sub-style anglelist before call
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// accumulate sub-style global/peratom energy/virial in hybrid
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if (eflag || vflag) ev_setup(eflag,vflag);
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else evflag = 0;
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for (m = 0; m < nstyles; m++) {
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neighbor->nanglelist = nanglelist[m];
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neighbor->anglelist = anglelist[m];
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styles[m]->compute(eflag,vflag);
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if (eflag_global) energy += styles[m]->energy;
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if (vflag_global)
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for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
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if (eflag_atom) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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double *eatom_substyle = styles[m]->eatom;
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for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
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}
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if (vflag_atom) {
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n = atom->nlocal;
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if (force->newton_bond) n += atom->nghost;
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double **vatom_substyle = styles[m]->vatom;
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for (i = 0; i < n; i++)
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for (j = 0; j < 6; j++)
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vatom[i][j] += vatom_substyle[i][j];
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}
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}
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// restore ptrs to original anglelist
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neighbor->nanglelist = nanglelist_orig;
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neighbor->anglelist = anglelist_orig;
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}
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/* ---------------------------------------------------------------------- */
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void AngleHybrid::allocate()
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{
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allocated = 1;
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int n = atom->nangletypes;
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memory->create(map,n+1,"angle:map");
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memory->create(setflag,n+1,"angle:setflag");
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for (int i = 1; i <= n; i++) setflag[i] = 0;
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nanglelist = new int[nstyles];
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maxangle = new int[nstyles];
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anglelist = new int**[nstyles];
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for (int m = 0; m < nstyles; m++) maxangle[m] = 0;
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for (int m = 0; m < nstyles; m++) anglelist[m] = NULL;
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}
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/* ----------------------------------------------------------------------
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create one angle style for each arg in list
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------------------------------------------------------------------------- */
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void AngleHybrid::settings(int narg, char **arg)
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{
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int i,m,istyle;
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if (narg < 1) error->all(FLERR,"Illegal angle_style command");
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// delete old lists, since cannot just change settings
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if (nstyles) {
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for (int i = 0; i < nstyles; i++) delete styles[i];
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delete [] styles;
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for (int i = 0; i < nstyles; i++) delete [] keywords[i];
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delete [] keywords;
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}
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if (allocated) {
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memory->destroy(setflag);
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memory->destroy(map);
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delete [] nanglelist;
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delete [] maxangle;
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for (int i = 0; i < nstyles; i++)
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memory->destroy(anglelist[i]);
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delete [] anglelist;
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}
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allocated = 0;
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// count sub-styles by skipping numeric args
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// one exception is 1st arg of style "table", which is non-numeric word
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// need a better way to skip these exceptions
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nstyles = 0;
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i = 0;
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while (i < narg) {
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if (strcmp(arg[i],"table") == 0) i++;
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i++;
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while (i < narg && !isalpha(arg[i][0])) i++;
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nstyles++;
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}
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// allocate list of sub-styles
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styles = new Angle*[nstyles];
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keywords = new char*[nstyles];
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// allocate each sub-style and call its settings() with subset of args
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// define subset of args for a sub-style by skipping numeric args
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// one exception is 1st arg of style "table", which is non-numeric
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// need a better way to skip these exceptions
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int dummy;
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nstyles = 0;
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i = 0;
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while (i < narg) {
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for (m = 0; m < nstyles; m++)
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if (strcmp(arg[i],keywords[m]) == 0)
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error->all(FLERR,"Angle style hybrid cannot use "
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"same angle style twice");
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if (strcmp(arg[i],"hybrid") == 0)
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error->all(FLERR,"Angle style hybrid cannot have hybrid as an argument");
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if (strcmp(arg[i],"none") == 0)
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error->all(FLERR,"Angle style hybrid cannot have none as an argument");
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styles[nstyles] = force->new_angle(arg[i],lmp->suffix,dummy);
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keywords[nstyles] = new char[strlen(arg[i])+1];
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strcpy(keywords[nstyles],arg[i]);
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istyle = i;
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if (strcmp(arg[i],"table") == 0) i++;
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i++;
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while (i < narg && !isalpha(arg[i][0])) i++;
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styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
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nstyles++;
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}
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}
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/* ----------------------------------------------------------------------
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set coeffs for one type
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---------------------------------------------------------------------- */
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void AngleHybrid::coeff(int narg, char **arg)
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{
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if (!allocated) allocate();
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int ilo,ihi;
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force->bounds(arg[0],atom->nangletypes,ilo,ihi);
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// 2nd arg = angle sub-style name
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// allow for "none" or "skip" as valid sub-style name
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int m;
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for (m = 0; m < nstyles; m++)
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if (strcmp(arg[1],keywords[m]) == 0) break;
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int none = 0;
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int skip = 0;
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if (m == nstyles) {
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if (strcmp(arg[1],"none") == 0) none = 1;
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else if (strcmp(arg[1],"skip") == 0) none = skip = 1;
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else error->all(FLERR,"Angle coeff for hybrid has invalid style");
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}
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// move 1st arg to 2nd arg
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// just copy ptrs, since arg[] points into original input line
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arg[1] = arg[0];
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// invoke sub-style coeff() starting with 1st arg
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if (!none) styles[m]->coeff(narg-1,&arg[1]);
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// set setflag and which type maps to which sub-style
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// if sub-style is skip: auxiliary class2 setting in data file so ignore
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// if sub-style is none: set hybrid setflag, wipe out map
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for (int i = ilo; i <= ihi; i++) {
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if (skip) continue;
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else if (none) {
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setflag[i] = 1;
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map[i] = -1;
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} else {
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setflag[i] = styles[m]->setflag[i];
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map[i] = m;
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}
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}
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}
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/* ----------------------------------------------------------------------
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run angle style specific initialization
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------------------------------------------------------------------------- */
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void AngleHybrid::init_style()
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{
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for (int m = 0; m < nstyles; m++)
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if (styles[m]) styles[m]->init_style();
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}
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/* ----------------------------------------------------------------------
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return an equilbrium angle length
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------------------------------------------------------------------------- */
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double AngleHybrid::equilibrium_angle(int i)
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{
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if (map[i] < 0)
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error->one(FLERR,"Invoked angle equil angle on angle style none");
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return styles[map[i]]->equilibrium_angle(i);
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}
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/* ----------------------------------------------------------------------
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proc 0 writes to restart file
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------------------------------------------------------------------------- */
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void AngleHybrid::write_restart(FILE *fp)
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{
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fwrite(&nstyles,sizeof(int),1,fp);
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int n;
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for (int m = 0; m < nstyles; m++) {
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n = strlen(keywords[m]) + 1;
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fwrite(&n,sizeof(int),1,fp);
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fwrite(keywords[m],sizeof(char),n,fp);
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}
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}
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/* ----------------------------------------------------------------------
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proc 0 reads from restart file, bcasts
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------------------------------------------------------------------------- */
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void AngleHybrid::read_restart(FILE *fp)
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{
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int me = comm->me;
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if (me == 0) fread(&nstyles,sizeof(int),1,fp);
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MPI_Bcast(&nstyles,1,MPI_INT,0,world);
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styles = new Angle*[nstyles];
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keywords = new char*[nstyles];
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allocate();
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int n,dummy;
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for (int m = 0; m < nstyles; m++) {
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if (me == 0) fread(&n,sizeof(int),1,fp);
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MPI_Bcast(&n,1,MPI_INT,0,world);
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keywords[m] = new char[n];
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if (me == 0) fread(keywords[m],sizeof(char),n,fp);
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MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
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styles[m] = force->new_angle(keywords[m],lmp->suffix,dummy);
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}
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}
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/* ---------------------------------------------------------------------- */
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double AngleHybrid::single(int type, int i1, int i2, int i3)
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{
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if (map[type] < 0) error->one(FLERR,"Invoked angle single on angle style none");
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return styles[map[type]]->single(type,i1,i2,i3);
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}
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/* ----------------------------------------------------------------------
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memory usage
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------------------------------------------------------------------------- */
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double AngleHybrid::memory_usage()
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{
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double bytes = maxeatom * sizeof(double);
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bytes += maxvatom*6 * sizeof(double);
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for (int m = 0; m < nstyles; m++) bytes += maxangle[m]*4 * sizeof(int);
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for (int m = 0; m < nstyles; m++)
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if (styles[m]) bytes += styles[m]->memory_usage();
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return bytes;
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}
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@ -0,0 +1,95 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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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 ANGLE_CLASS
|
||||
|
||||
AngleStyle(hybrid,AngleHybrid)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_ANGLE_HYBRID_H
|
||||
#define LMP_ANGLE_HYBRID_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "angle.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AngleHybrid : public Angle {
|
||||
public:
|
||||
int nstyles; // # of different angle styles
|
||||
Angle **styles; // class list for each Angle style
|
||||
char **keywords; // keyword for each Angle style
|
||||
|
||||
AngleHybrid(class LAMMPS *);
|
||||
~AngleHybrid();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
double equilibrium_angle(int);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double single(int, int, int, int);
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int *map; // which style each angle type points to
|
||||
|
||||
int *nanglelist; // # of angles in sub-style anglelists
|
||||
int *maxangle; // max # of angles sub-style lists can store
|
||||
int ***anglelist; // anglelist for each sub-style
|
||||
|
||||
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: Angle style hybrid cannot use same angle style twice
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Angle style hybrid cannot have hybrid as an argument
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Angle style hybrid cannot have none as an argument
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Angle coeff for hybrid has invalid style
|
||||
|
||||
Angle style hybrid uses another angle style as one of its
|
||||
coefficients. The angle style used in the angle_coeff command or read
|
||||
from a restart file is not recognized.
|
||||
|
||||
E: Invoked angle equil angle on angle style none
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Invoked angle single on angle style none
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,350 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "string.h"
|
||||
#include "ctype.h"
|
||||
#include "dihedral_hybrid.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EXTRA 1000
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralHybrid::DihedralHybrid(LAMMPS *lmp) : Dihedral(lmp)
|
||||
{
|
||||
nstyles = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
DihedralHybrid::~DihedralHybrid()
|
||||
{
|
||||
if (nstyles) {
|
||||
for (int i = 0; i < nstyles; i++) delete styles[i];
|
||||
delete [] styles;
|
||||
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
|
||||
delete [] keywords;
|
||||
}
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(map);
|
||||
delete [] ndihedrallist;
|
||||
delete [] maxdihedral;
|
||||
for (int i = 0; i < nstyles; i++)
|
||||
memory->destroy(dihedrallist[i]);
|
||||
delete [] dihedrallist;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralHybrid::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,m,n;
|
||||
|
||||
// save ptrs to original dihedrallist
|
||||
|
||||
int ndihedrallist_orig = neighbor->ndihedrallist;
|
||||
int **dihedrallist_orig = neighbor->dihedrallist;
|
||||
|
||||
// if this is re-neighbor step, create sub-style dihedrallists
|
||||
// ndihedrallist[] = length of each sub-style list
|
||||
// realloc sub-style dihedrallist if necessary
|
||||
// load sub-style dihedrallist with 5 values from original dihedrallist
|
||||
|
||||
if (neighbor->ago == 0) {
|
||||
for (m = 0; m < nstyles; m++) ndihedrallist[m] = 0;
|
||||
for (i = 0; i < ndihedrallist_orig; i++) {
|
||||
m = map[dihedrallist_orig[i][4]];
|
||||
if (m >= 0) ndihedrallist[m]++;
|
||||
}
|
||||
for (m = 0; m < nstyles; m++) {
|
||||
if (ndihedrallist[m] > maxdihedral[m]) {
|
||||
memory->destroy(dihedrallist[m]);
|
||||
maxdihedral[m] = ndihedrallist[m] + EXTRA;
|
||||
memory->create(dihedrallist[m],maxdihedral[m],5,
|
||||
"dihedral_hybrid:dihedrallist");
|
||||
}
|
||||
ndihedrallist[m] = 0;
|
||||
}
|
||||
for (i = 0; i < ndihedrallist_orig; i++) {
|
||||
m = map[dihedrallist_orig[i][4]];
|
||||
if (m < 0) continue;
|
||||
n = ndihedrallist[m];
|
||||
dihedrallist[m][n][0] = dihedrallist_orig[i][0];
|
||||
dihedrallist[m][n][1] = dihedrallist_orig[i][1];
|
||||
dihedrallist[m][n][2] = dihedrallist_orig[i][2];
|
||||
dihedrallist[m][n][3] = dihedrallist_orig[i][3];
|
||||
dihedrallist[m][n][4] = dihedrallist_orig[i][4];
|
||||
ndihedrallist[m]++;
|
||||
}
|
||||
}
|
||||
|
||||
// call each sub-style's compute function
|
||||
// set neighbor->dihedrallist to sub-style dihedrallist before call
|
||||
// accumulate sub-style global/peratom energy/virial in hybrid
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
|
||||
for (m = 0; m < nstyles; m++) {
|
||||
neighbor->ndihedrallist = ndihedrallist[m];
|
||||
neighbor->dihedrallist = dihedrallist[m];
|
||||
|
||||
styles[m]->compute(eflag,vflag);
|
||||
|
||||
if (eflag_global) energy += styles[m]->energy;
|
||||
if (vflag_global)
|
||||
for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
|
||||
if (eflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (force->newton_bond) n += atom->nghost;
|
||||
double *eatom_substyle = styles[m]->eatom;
|
||||
for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
|
||||
}
|
||||
if (vflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (force->newton_bond) n += atom->nghost;
|
||||
double **vatom_substyle = styles[m]->vatom;
|
||||
for (i = 0; i < n; i++)
|
||||
for (j = 0; j < 6; j++)
|
||||
vatom[i][j] += vatom_substyle[i][j];
|
||||
}
|
||||
}
|
||||
|
||||
// restore ptrs to original dihedrallist
|
||||
|
||||
neighbor->ndihedrallist = ndihedrallist_orig;
|
||||
neighbor->dihedrallist = dihedrallist_orig;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralHybrid::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->ndihedraltypes;
|
||||
|
||||
memory->create(map,n+1,"dihedral:map");
|
||||
memory->create(setflag,n+1,"dihedral:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
|
||||
ndihedrallist = new int[nstyles];
|
||||
maxdihedral = new int[nstyles];
|
||||
dihedrallist = new int**[nstyles];
|
||||
for (int m = 0; m < nstyles; m++) maxdihedral[m] = 0;
|
||||
for (int m = 0; m < nstyles; m++) dihedrallist[m] = NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create one dihedral style for each arg in list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralHybrid::settings(int narg, char **arg)
|
||||
{
|
||||
int i,m,istyle;
|
||||
|
||||
if (narg < 1) error->all(FLERR,"Illegal dihedral_style command");
|
||||
|
||||
// delete old lists, since cannot just change settings
|
||||
|
||||
if (nstyles) {
|
||||
for (int i = 0; i < nstyles; i++) delete styles[i];
|
||||
delete [] styles;
|
||||
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
|
||||
delete [] keywords;
|
||||
}
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(map);
|
||||
delete [] ndihedrallist;
|
||||
delete [] maxdihedral;
|
||||
for (int i = 0; i < nstyles; i++)
|
||||
memory->destroy(dihedrallist[i]);
|
||||
delete [] dihedrallist;
|
||||
}
|
||||
allocated = 0;
|
||||
|
||||
// count sub-styles by skipping numeric args
|
||||
// one exception is 1st arg of style "table", which is non-numeric word
|
||||
// need a better way to skip these exceptions
|
||||
|
||||
nstyles = 0;
|
||||
i = 0;
|
||||
while (i < narg) {
|
||||
if (strcmp(arg[i],"table") == 0) i++;
|
||||
i++;
|
||||
while (i < narg && !isalpha(arg[i][0])) i++;
|
||||
nstyles++;
|
||||
}
|
||||
|
||||
// allocate list of sub-styles
|
||||
|
||||
styles = new Dihedral*[nstyles];
|
||||
keywords = new char*[nstyles];
|
||||
|
||||
// allocate each sub-style and call its settings() with subset of args
|
||||
// define subset of args for a sub-style by skipping numeric args
|
||||
// one exception is 1st arg of style "table", which is non-numeric
|
||||
// need a better way to skip these exceptions
|
||||
|
||||
int dummy;
|
||||
nstyles = 0;
|
||||
i = 0;
|
||||
|
||||
while (i < narg) {
|
||||
for (m = 0; m < nstyles; m++)
|
||||
if (strcmp(arg[i],keywords[m]) == 0)
|
||||
error->all(FLERR,"Dihedral style hybrid cannot use "
|
||||
"same dihedral style twice");
|
||||
if (strcmp(arg[i],"hybrid") == 0)
|
||||
error->all(FLERR,
|
||||
"Dihedral style hybrid cannot have hybrid as an argument");
|
||||
if (strcmp(arg[i],"none") == 0)
|
||||
error->all(FLERR,"Dihedral style hybrid cannot have none as an argument");
|
||||
styles[nstyles] = force->new_dihedral(arg[i],lmp->suffix,dummy);
|
||||
keywords[nstyles] = new char[strlen(arg[i])+1];
|
||||
strcpy(keywords[nstyles],arg[i]);
|
||||
istyle = i;
|
||||
if (strcmp(arg[i],"table") == 0) i++;
|
||||
i++;
|
||||
while (i < narg && !isalpha(arg[i][0])) i++;
|
||||
styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
|
||||
nstyles++;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one type
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralHybrid::coeff(int narg, char **arg)
|
||||
{
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->ndihedraltypes,ilo,ihi);
|
||||
|
||||
// 2nd arg = dihedral sub-style name
|
||||
// allow for "none" or "skip" as valid sub-style name
|
||||
|
||||
int m;
|
||||
for (m = 0; m < nstyles; m++)
|
||||
if (strcmp(arg[1],keywords[m]) == 0) break;
|
||||
|
||||
int none = 0;
|
||||
int skip = 0;
|
||||
if (m == nstyles) {
|
||||
if (strcmp(arg[1],"none") == 0) none = 1;
|
||||
else if (strcmp(arg[1],"skip") == 0) none = skip = 1;
|
||||
else error->all(FLERR,"Dihedral coeff for hybrid has invalid style");
|
||||
}
|
||||
|
||||
// move 1st arg to 2nd arg
|
||||
// just copy ptrs, since arg[] points into original input line
|
||||
|
||||
arg[1] = arg[0];
|
||||
|
||||
// invoke sub-style coeff() starting with 1st arg
|
||||
|
||||
if (!none) styles[m]->coeff(narg-1,&arg[1]);
|
||||
|
||||
// set setflag and which type maps to which sub-style
|
||||
// if sub-style is skip: auxiliary class2 setting in data file so ignore
|
||||
// if sub-style is none and not skip: set hybrid setflag, wipe out map
|
||||
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
if (skip) continue;
|
||||
else if (none) {
|
||||
setflag[i] = 1;
|
||||
map[i] = -1;
|
||||
} else {
|
||||
setflag[i] = styles[m]->setflag[i];
|
||||
map[i] = m;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void DihedralHybrid::init_style()
|
||||
{
|
||||
for (int m = 0; m < nstyles; m++)
|
||||
if (styles[m]) styles[m]->init_style();
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralHybrid::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&nstyles,sizeof(int),1,fp);
|
||||
|
||||
int n;
|
||||
for (int m = 0; m < nstyles; m++) {
|
||||
n = strlen(keywords[m]) + 1;
|
||||
fwrite(&n,sizeof(int),1,fp);
|
||||
fwrite(keywords[m],sizeof(char),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void DihedralHybrid::read_restart(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) fread(&nstyles,sizeof(int),1,fp);
|
||||
MPI_Bcast(&nstyles,1,MPI_INT,0,world);
|
||||
styles = new Dihedral*[nstyles];
|
||||
keywords = new char*[nstyles];
|
||||
|
||||
allocate();
|
||||
|
||||
int n,dummy;
|
||||
for (int m = 0; m < nstyles; m++) {
|
||||
if (me == 0) fread(&n,sizeof(int),1,fp);
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
keywords[m] = new char[n];
|
||||
if (me == 0) fread(keywords[m],sizeof(char),n,fp);
|
||||
MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
|
||||
styles[m] = force->new_dihedral(keywords[m],lmp->suffix,dummy);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double DihedralHybrid::memory_usage()
|
||||
{
|
||||
double bytes = maxeatom * sizeof(double);
|
||||
bytes += maxvatom*6 * sizeof(double);
|
||||
for (int m = 0; m < nstyles; m++) bytes += maxdihedral[m]*5 * sizeof(int);
|
||||
for (int m = 0; m < nstyles; m++)
|
||||
if (styles[m]) bytes += styles[m]->memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,85 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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(hybrid,DihedralHybrid)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_DIHEDRAL_HYBRID_H
|
||||
#define LMP_DIHEDRAL_HYBRID_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "dihedral.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class DihedralHybrid : public Dihedral {
|
||||
public:
|
||||
int nstyles; // # of different dihedral styles
|
||||
Dihedral **styles; // class list for each Dihedral style
|
||||
char **keywords; // keyword for each dihedral style
|
||||
|
||||
DihedralHybrid(class LAMMPS *);
|
||||
~DihedralHybrid();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int *map; // which style each dihedral type points to
|
||||
|
||||
int *ndihedrallist; // # of dihedrals in sub-style dihedrallists
|
||||
int *maxdihedral; // max # of dihedrals sub-style lists can store
|
||||
int ***dihedrallist; // dihedrallist for each sub-style
|
||||
|
||||
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: Dihedral style hybrid cannot use same dihedral style twice
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Dihedral style hybrid cannot have hybrid as an argument
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Dihedral style hybrid cannot have none as an argument
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Dihedral coeff for hybrid has invalid style
|
||||
|
||||
Dihedral style hybrid uses another dihedral style as one of its
|
||||
coefficients. The dihedral style used in the dihedral_coeff command
|
||||
or read from a restart file is not recognized.
|
||||
|
||||
*/
|
||||
|
|
@ -0,0 +1,338 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "string.h"
|
||||
#include "ctype.h"
|
||||
#include "improper_hybrid.h"
|
||||
#include "atom.h"
|
||||
#include "neighbor.h"
|
||||
#include "domain.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
#define EXTRA 1000
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ImproperHybrid::ImproperHybrid(LAMMPS *lmp) : Improper(lmp)
|
||||
{
|
||||
nstyles = 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
ImproperHybrid::~ImproperHybrid()
|
||||
{
|
||||
if (nstyles) {
|
||||
for (int i = 0; i < nstyles; i++) delete styles[i];
|
||||
delete [] styles;
|
||||
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
|
||||
delete [] keywords;
|
||||
}
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(map);
|
||||
delete [] nimproperlist;
|
||||
delete [] maximproper;
|
||||
for (int i = 0; i < nstyles; i++)
|
||||
memory->destroy(improperlist[i]);
|
||||
delete [] improperlist;
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ImproperHybrid::compute(int eflag, int vflag)
|
||||
{
|
||||
int i,j,m,n;
|
||||
|
||||
// save ptrs to original improperlist
|
||||
|
||||
int nimproperlist_orig = neighbor->nimproperlist;
|
||||
int **improperlist_orig = neighbor->improperlist;
|
||||
|
||||
// if this is re-neighbor step, create sub-style improperlists
|
||||
// nimproperlist[] = length of each sub-style list
|
||||
// realloc sub-style improperlist if necessary
|
||||
// load sub-style improperlist with 5 values from original improperlist
|
||||
|
||||
if (neighbor->ago == 0) {
|
||||
for (m = 0; m < nstyles; m++) nimproperlist[m] = 0;
|
||||
for (i = 0; i < nimproperlist_orig; i++) {
|
||||
m = map[improperlist_orig[i][4]];
|
||||
nimproperlist[m]++;
|
||||
}
|
||||
for (m = 0; m < nstyles; m++) {
|
||||
if (nimproperlist[m] > maximproper[m]) {
|
||||
memory->destroy(improperlist[m]);
|
||||
maximproper[m] = nimproperlist[m] + EXTRA;
|
||||
memory->create(improperlist[m],maximproper[m],5,
|
||||
"improper_hybrid:improperlist");
|
||||
}
|
||||
nimproperlist[m] = 0;
|
||||
}
|
||||
for (i = 0; i < nimproperlist_orig; i++) {
|
||||
m = map[improperlist_orig[i][4]];
|
||||
if (m < 0) continue;
|
||||
n = nimproperlist[m];
|
||||
improperlist[m][n][0] = improperlist_orig[i][0];
|
||||
improperlist[m][n][1] = improperlist_orig[i][1];
|
||||
improperlist[m][n][2] = improperlist_orig[i][2];
|
||||
improperlist[m][n][3] = improperlist_orig[i][3];
|
||||
improperlist[m][n][4] = improperlist_orig[i][4];
|
||||
nimproperlist[m]++;
|
||||
}
|
||||
}
|
||||
|
||||
// call each sub-style's compute function
|
||||
// set neighbor->improperlist to sub-style improperlist before call
|
||||
// accumulate sub-style global/peratom energy/virial in hybrid
|
||||
|
||||
if (eflag || vflag) ev_setup(eflag,vflag);
|
||||
else evflag = 0;
|
||||
|
||||
for (m = 0; m < nstyles; m++) {
|
||||
neighbor->nimproperlist = nimproperlist[m];
|
||||
neighbor->improperlist = improperlist[m];
|
||||
|
||||
styles[m]->compute(eflag,vflag);
|
||||
|
||||
if (eflag_global) energy += styles[m]->energy;
|
||||
if (vflag_global)
|
||||
for (n = 0; n < 6; n++) virial[n] += styles[m]->virial[n];
|
||||
if (eflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (force->newton_bond) n += atom->nghost;
|
||||
double *eatom_substyle = styles[m]->eatom;
|
||||
for (i = 0; i < n; i++) eatom[i] += eatom_substyle[i];
|
||||
}
|
||||
if (vflag_atom) {
|
||||
n = atom->nlocal;
|
||||
if (force->newton_bond) n += atom->nghost;
|
||||
double **vatom_substyle = styles[m]->vatom;
|
||||
for (i = 0; i < n; i++)
|
||||
for (j = 0; j < 6; j++)
|
||||
vatom[i][j] += vatom_substyle[i][j];
|
||||
}
|
||||
}
|
||||
|
||||
// restore ptrs to original improperlist
|
||||
|
||||
neighbor->nimproperlist = nimproperlist_orig;
|
||||
neighbor->improperlist = improperlist_orig;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void ImproperHybrid::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nimpropertypes;
|
||||
|
||||
memory->create(map,n+1,"improper:map");
|
||||
memory->create(setflag,n+1,"improper:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
|
||||
nimproperlist = new int[nstyles];
|
||||
maximproper = new int[nstyles];
|
||||
improperlist = new int**[nstyles];
|
||||
for (int m = 0; m < nstyles; m++) maximproper[m] = 0;
|
||||
for (int m = 0; m < nstyles; m++) improperlist[m] = NULL;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create one improper style for each arg in list
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ImproperHybrid::settings(int narg, char **arg)
|
||||
{
|
||||
int i,m,istyle;
|
||||
|
||||
if (narg < 1) error->all(FLERR,"Illegal improper_style command");
|
||||
|
||||
// delete old lists, since cannot just change settings
|
||||
|
||||
if (nstyles) {
|
||||
for (int i = 0; i < nstyles; i++) delete styles[i];
|
||||
delete [] styles;
|
||||
for (int i = 0; i < nstyles; i++) delete [] keywords[i];
|
||||
delete [] keywords;
|
||||
}
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(map);
|
||||
delete [] nimproperlist;
|
||||
delete [] maximproper;
|
||||
for (int i = 0; i < nstyles; i++)
|
||||
memory->destroy(improperlist[i]);
|
||||
delete [] improperlist;
|
||||
}
|
||||
allocated = 0;
|
||||
|
||||
// count sub-styles by skipping numeric args
|
||||
// one exception is 1st arg of style "table", which is non-numeric word
|
||||
// need a better way to skip these exceptions
|
||||
|
||||
nstyles = 0;
|
||||
i = 0;
|
||||
while (i < narg) {
|
||||
if (strcmp(arg[i],"table") == 0) i++;
|
||||
i++;
|
||||
while (i < narg && !isalpha(arg[i][0])) i++;
|
||||
nstyles++;
|
||||
}
|
||||
|
||||
// allocate list of sub-styles
|
||||
|
||||
styles = new Improper*[nstyles];
|
||||
keywords = new char*[nstyles];
|
||||
|
||||
// allocate each sub-style and call its settings() with subset of args
|
||||
// define subset of args for a sub-style by skipping numeric args
|
||||
// one exception is 1st arg of style "table", which is non-numeric
|
||||
// need a better way to skip these exceptions
|
||||
|
||||
int dummy;
|
||||
nstyles = 0;
|
||||
i = 0;
|
||||
|
||||
while (i < narg) {
|
||||
for (m = 0; m < nstyles; m++)
|
||||
if (strcmp(arg[i],keywords[m]) == 0)
|
||||
error->all(FLERR,"Improper style hybrid cannot use "
|
||||
"same improper style twice");
|
||||
if (strcmp(arg[i],"hybrid") == 0)
|
||||
error->all(FLERR,
|
||||
"Improper style hybrid cannot have hybrid as an argument");
|
||||
if (strcmp(arg[i],"none") == 0)
|
||||
error->all(FLERR,"Improper style hybrid cannot have none as an argument");
|
||||
styles[nstyles] = force->new_improper(arg[i],lmp->suffix,dummy);
|
||||
keywords[nstyles] = new char[strlen(arg[i])+1];
|
||||
strcpy(keywords[nstyles],arg[i]);
|
||||
istyle = i;
|
||||
if (strcmp(arg[i],"table") == 0) i++;
|
||||
i++;
|
||||
while (i < narg && !isalpha(arg[i][0])) i++;
|
||||
styles[nstyles]->settings(i-istyle-1,&arg[istyle+1]);
|
||||
nstyles++;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one type
|
||||
---------------------------------------------------------------------- */
|
||||
|
||||
void ImproperHybrid::coeff(int narg, char **arg)
|
||||
{
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
force->bounds(arg[0],atom->nimpropertypes,ilo,ihi);
|
||||
|
||||
// 2nd arg = improper sub-style name
|
||||
// allow for "none" as valid sub-style name
|
||||
|
||||
int m;
|
||||
for (m = 0; m < nstyles; m++)
|
||||
if (strcmp(arg[1],keywords[m]) == 0) break;
|
||||
|
||||
int none = 0;
|
||||
if (m == nstyles) {
|
||||
if (strcmp(arg[1],"none") == 0) none = 1;
|
||||
else error->all(FLERR,"Improper coeff for hybrid has invalid style");
|
||||
}
|
||||
|
||||
// move 1st arg to 2nd arg
|
||||
// just copy ptrs, since arg[] points into original input line
|
||||
|
||||
arg[1] = arg[0];
|
||||
|
||||
// invoke sub-style coeff() starting with 1st arg
|
||||
|
||||
if (!none) styles[m]->coeff(narg-1,&arg[1]);
|
||||
|
||||
// set setflag and which type maps to which sub-style
|
||||
// if sub-style is none: set hybrid setflag, wipe out map
|
||||
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
if (none) {
|
||||
setflag[i] = 1;
|
||||
map[i] = -1;
|
||||
} else {
|
||||
setflag[i] = styles[m]->setflag[i];
|
||||
map[i] = m;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ImproperHybrid::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&nstyles,sizeof(int),1,fp);
|
||||
|
||||
int n;
|
||||
for (int m = 0; m < nstyles; m++) {
|
||||
n = strlen(keywords[m]) + 1;
|
||||
fwrite(&n,sizeof(int),1,fp);
|
||||
fwrite(keywords[m],sizeof(char),n,fp);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads from restart file, bcasts
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void ImproperHybrid::read_restart(FILE *fp)
|
||||
{
|
||||
int me = comm->me;
|
||||
if (me == 0) fread(&nstyles,sizeof(int),1,fp);
|
||||
MPI_Bcast(&nstyles,1,MPI_INT,0,world);
|
||||
styles = new Improper*[nstyles];
|
||||
keywords = new char*[nstyles];
|
||||
|
||||
allocate();
|
||||
|
||||
int n,dummy;
|
||||
for (int m = 0; m < nstyles; m++) {
|
||||
if (me == 0) fread(&n,sizeof(int),1,fp);
|
||||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
keywords[m] = new char[n];
|
||||
if (me == 0) fread(keywords[m],sizeof(char),n,fp);
|
||||
MPI_Bcast(keywords[m],n,MPI_CHAR,0,world);
|
||||
styles[m] = force->new_improper(keywords[m],lmp->suffix,dummy);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double ImproperHybrid::memory_usage()
|
||||
{
|
||||
double bytes = maxeatom * sizeof(double);
|
||||
bytes += maxvatom*6 * sizeof(double);
|
||||
for (int m = 0; m < nstyles; m++) bytes += maximproper[m]*5 * sizeof(int);
|
||||
for (int m = 0; m < nstyles; m++)
|
||||
if (styles[m]) bytes += styles[m]->memory_usage();
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,84 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
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 IMPROPER_CLASS
|
||||
|
||||
ImproperStyle(hybrid,ImproperHybrid)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_IMPROPER_HYBRID_H
|
||||
#define LMP_IMPROPER_HYBRID_H
|
||||
|
||||
#include "stdio.h"
|
||||
#include "improper.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ImproperHybrid : public Improper {
|
||||
public:
|
||||
int nstyles; // # of different improper styles
|
||||
Improper **styles; // class list for each Improper style
|
||||
char **keywords; // keyword for each improper style
|
||||
|
||||
ImproperHybrid(class LAMMPS *);
|
||||
~ImproperHybrid();
|
||||
void compute(int, int);
|
||||
void settings(int, char **);
|
||||
void coeff(int, char **);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int *map; // which style each improper type points to
|
||||
|
||||
int *nimproperlist; // # of impropers in sub-style improperlists
|
||||
int *maximproper; // max # of impropers sub-style lists can store
|
||||
int ***improperlist; // improperlist for each sub-style
|
||||
|
||||
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: Improper style hybrid cannot use same improper style twice
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Improper style hybrid cannot have hybrid as an argument
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Improper style hybrid cannot have none as an argument
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Improper coeff for hybrid has invalid style
|
||||
|
||||
Improper style hybrid uses another improper style as one of its
|
||||
coefficients. The improper style used in the improper_coeff command
|
||||
or read from a restart file is not recognized.
|
||||
|
||||
*/
|
||||
Loading…
Reference in New Issue