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lammps/src/modify.cpp
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modify.cpp
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/* ----------------------------------------------------------------------
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 "stdio.h"
#include "string.h"
#include "modify.h"
#include "atom.h"
#include "comm.h"
#include "fix.h"
#include "compute.h"
#include "group.h"
#include "update.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
#define ComputeInclude
#define FixInclude
#include "style.h"
#undef ComputeInclude
#undef FixInclude
using namespace LAMMPS_NS;
#define DELTA 4
// mask settings - same as in fix.cpp
#define INITIAL_INTEGRATE 1
#define PRE_EXCHANGE 2
#define PRE_NEIGHBOR 4
#define POST_FORCE 8
#define FINAL_INTEGRATE 16
#define END_OF_STEP 32
#define THERMO_ENERGY 64
#define INITIAL_INTEGRATE_RESPA 128
#define POST_FORCE_RESPA 256
#define FINAL_INTEGRATE_RESPA 512
#define MIN_POST_FORCE 1024
/* ---------------------------------------------------------------------- */
Modify::Modify(LAMMPS *lmp) : Pointers(lmp)
{
nfix = maxfix = 0;
n_initial_integrate = 0;
n_pre_exchange = n_pre_neighbor = 0;
n_post_force = n_final_integrate = n_end_of_step = n_thermo_energy = 0;
n_initial_integrate_respa = n_post_force_respa = n_final_integrate_respa = 0;
n_min_post_force = 0;
fix = NULL;
fmask = NULL;
list_initial_integrate = NULL;
list_pre_exchange = list_pre_neighbor = NULL;
list_post_force = list_final_integrate = list_end_of_step = NULL;
list_thermo_energy = NULL;
list_initial_integrate_respa = list_post_force_respa = NULL;
list_final_integrate_respa = NULL;
list_min_post_force = NULL;
end_of_step_every = NULL;
nfix_restart_global = 0;
id_restart_global = style_restart_global = state_restart_global = NULL;
nfix_restart_peratom = 0;
id_restart_peratom = style_restart_peratom = NULL;
index_restart_peratom = NULL;
ncompute = maxcompute = 0;
compute = NULL;
}
/* ---------------------------------------------------------------------- */
Modify::~Modify()
{
// delete all fixes
// do it via delete_fix() so callbacks in Atom are also updated correctly
while (nfix) delete_fix(fix[0]->id);
memory->sfree(fix);
memory->sfree(fmask);
delete [] list_initial_integrate;
delete [] list_pre_exchange;
delete [] list_pre_neighbor;
delete [] list_post_force;
delete [] list_final_integrate;
delete [] list_end_of_step;
delete [] list_thermo_energy;
delete [] list_initial_integrate_respa;
delete [] list_post_force_respa;
delete [] list_final_integrate_respa;
delete [] list_min_post_force;
delete [] end_of_step_every;
restart_deallocate();
// delete all computes
for (int i = 0; i < ncompute; i++) delete compute[i];
memory->sfree(compute);
}
/* ----------------------------------------------------------------------
initialize all fixes and computes
------------------------------------------------------------------------- */
void Modify::init()
{
int i;
// delete storage of restart info since it is not valid after 1st run
restart_deallocate();
// init each fix
comm->maxforward_fix = comm->maxreverse_fix = 0;
for (i = 0; i < nfix; i++) fix[i]->init();
// create lists of fixes to call at each stage of run
list_init(INITIAL_INTEGRATE,n_initial_integrate,list_initial_integrate);
list_init(PRE_EXCHANGE,n_pre_exchange,list_pre_exchange);
list_init(PRE_NEIGHBOR,n_pre_neighbor,list_pre_neighbor);
list_init(POST_FORCE,n_post_force,list_post_force);
list_init(FINAL_INTEGRATE,n_final_integrate,list_final_integrate);
list_init_end_of_step(END_OF_STEP,n_end_of_step,list_end_of_step);
list_init_thermo_energy(THERMO_ENERGY,n_thermo_energy,list_thermo_energy);
list_init(INITIAL_INTEGRATE_RESPA,
n_initial_integrate_respa,list_initial_integrate_respa);
list_init(POST_FORCE_RESPA,
n_post_force_respa,list_post_force_respa);
list_init(FINAL_INTEGRATE_RESPA,
n_final_integrate_respa,list_final_integrate_respa);
list_init(MIN_POST_FORCE,n_min_post_force,list_min_post_force);
// init each compute
for (i = 0; i < ncompute; i++) compute[i]->init();
}
/* ----------------------------------------------------------------------
setup for run, calls setup() of all fixes
------------------------------------------------------------------------- */
void Modify::setup()
{
if (update->whichflag == 0)
for (int i = 0; i < nfix; i++) fix[i]->setup();
else
for (int i = 0; i < nfix; i++) fix[i]->min_setup();
}
/* ----------------------------------------------------------------------
1st half of integrate call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::initial_integrate()
{
for (int i = 0; i < n_initial_integrate; i++)
fix[list_initial_integrate[i]]->initial_integrate();
}
/* ----------------------------------------------------------------------
pre_exchange call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::pre_exchange()
{
for (int i = 0; i < n_pre_exchange; i++)
fix[list_pre_exchange[i]]->pre_exchange();
}
/* ----------------------------------------------------------------------
pre_neighbor call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::pre_neighbor()
{
for (int i = 0; i < n_pre_neighbor; i++)
fix[list_pre_neighbor[i]]->pre_neighbor();
}
/* ----------------------------------------------------------------------
force adjustment call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::post_force(int vflag)
{
for (int i = 0; i < n_post_force; i++)
fix[list_post_force[i]]->post_force(vflag);
}
/* ----------------------------------------------------------------------
2nd half of integrate call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::final_integrate()
{
for (int i = 0; i < n_final_integrate; i++)
fix[list_final_integrate[i]]->final_integrate();
}
/* ----------------------------------------------------------------------
end-of-timestep call only for relevant fixes
only call fix->end_of_step() on timesteps that are multiples of nevery
------------------------------------------------------------------------- */
void Modify::end_of_step()
{
for (int i = 0; i < n_end_of_step; i++)
if (update->ntimestep % end_of_step_every[i] == 0)
fix[list_end_of_step[i]]->end_of_step();
}
/* ----------------------------------------------------------------------
thermo energy call only for relevant fixes
called by Thermo clas
arg to Fix thermo() is 0, so fix will return its energy contribution
------------------------------------------------------------------------- */
double Modify::thermo_energy()
{
double energy = 0.0;
for (int i = 0; i < n_thermo_energy; i++)
energy += fix[list_thermo_energy[i]]->thermo(0);
return energy;
}
/* ----------------------------------------------------------------------
1st half of rRESPA integrate call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::initial_integrate_respa(int ilevel, int flag)
{
for (int i = 0; i < n_initial_integrate_respa; i++)
fix[list_initial_integrate_respa[i]]->initial_integrate_respa(ilevel,flag);
}
/* ----------------------------------------------------------------------
rRESPA force adjustment call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::post_force_respa(int vflag, int ilevel, int iloop)
{
for (int i = 0; i < n_post_force_respa; i++)
fix[list_post_force_respa[i]]->post_force_respa(vflag,ilevel,iloop);
}
/* ----------------------------------------------------------------------
2nd half of rRESPA integrate call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::final_integrate_respa(int ilevel)
{
for (int i = 0; i < n_final_integrate_respa; i++)
fix[list_final_integrate_respa[i]]->final_integrate_respa(ilevel);
}
/* ----------------------------------------------------------------------
minimizer force adjustment call only for relevant fixes
------------------------------------------------------------------------- */
void Modify::min_post_force(int vflag)
{
for (int i = 0; i < n_min_post_force; i++)
fix[list_min_post_force[i]]->min_post_force(vflag);
}
/* ----------------------------------------------------------------------
add a new fix or replace one with same ID
------------------------------------------------------------------------- */
void Modify::add_fix(int narg, char **arg)
{
if (domain->box_exist == 0)
error->all("Fix command before simulation box is defined");
if (narg < 3) error->all("Illegal fix command");
// find group ID
int igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find fix group ID");
// if fix ID exists:
// set newflag = 0 so create new fix in same location in fix list
// error if new style does not match old style
// since can't replace it (all when-to-invoke ptrs would be invalid)
// warn if new group != old group
// delete old fix
// set ptr to NULL in case new fix scans list of fixes
// if fix ID does not exist:
// set newflag = 1 so create new fix
// extend fix and fmask lists as necessary
int ifix,newflag;
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(arg[0],fix[ifix]->id) == 0) break;
if (ifix < nfix) {
newflag = 0;
if (strcmp(arg[2],fix[ifix]->style) != 0)
error->all("Replacing a fix, but new style != old style");
if (fix[ifix]->igroup != igroup && comm->me == 0)
error->warning("Replacing a fix, but new group != old group");
delete fix[ifix];
atom->update_callback(ifix);
fix[ifix] = NULL;
} else {
newflag = 1;
if (nfix == maxfix) {
maxfix += DELTA;
fix = (Fix **) memory->srealloc(fix,maxfix*sizeof(Fix *),"modify:fix");
fmask = (int *)
memory->srealloc(fmask,maxfix*sizeof(int),"modify:fmask");
}
}
// create the Fix
if (0) return; // dummy line to enable else-if macro expansion
#define FixClass
#define FixStyle(key,Class) \
else if (strcmp(arg[2],#key) == 0) fix[ifix] = new Class(lmp,narg,arg);
#include "style.h"
#undef FixClass
else error->all("Invalid fix style");
// if fix is new, set it's mask values and increment nfix
if (newflag) {
fmask[ifix] = fix[ifix]->setmask();
nfix++;
}
// check if Fix is in restart_global list
// if yes, pass state info to the Fix so it can reset itself
for (int i = 0; i < nfix_restart_global; i++)
if (strcmp(id_restart_global[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_global[i],fix[ifix]->style) == 0) {
fix[ifix]->restart(state_restart_global[i]);
if (comm->me == 0) {
char *str = "Resetting global state of Fix %s Style %s "
"from restart file info\n";
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
// check if Fix is in restart_peratom list
// if yes, loop over atoms so they can extract info from atom->extra array
for (int i = 0; i < nfix_restart_peratom; i++)
if (strcmp(id_restart_peratom[i],fix[ifix]->id) == 0 &&
strcmp(style_restart_peratom[i],fix[ifix]->style) == 0) {
for (int j = 0; j < atom->nlocal; j++)
fix[ifix]->unpack_restart(j,index_restart_peratom[i]);
if (comm->me == 0) {
char *str = "Resetting per-atom state of Fix %s Style %s "
"from restart file info\n";
if (screen) fprintf(screen,str,fix[ifix]->id,fix[ifix]->style);
if (logfile) fprintf(logfile,str,fix[ifix]->id,fix[ifix]->style);
}
}
}
/* ----------------------------------------------------------------------
modify a Fix's parameters
------------------------------------------------------------------------- */
void Modify::modify_fix(int narg, char **arg)
{
if (narg < 2) error->all("Illegal fix_modify command");
// lookup Fix ID
int ifix;
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(arg[0],fix[ifix]->id) == 0) break;
if (ifix == nfix) error->all("Could not find fix_modify ID");
fix[ifix]->modify_params(narg-1,&arg[1]);
}
/* ----------------------------------------------------------------------
delete a Fix from list of Fixes
Atom class must update indices in its list of callbacks to fixes
------------------------------------------------------------------------- */
void Modify::delete_fix(char *id)
{
int ifix = find_fix(id);
if (ifix < 0) error->all("Could not find fix ID to delete");
delete fix[ifix];
atom->update_callback(ifix);
// move other Fixes and fmask down in list one slot
for (int i = ifix+1; i < nfix; i++) fix[i-1] = fix[i];
for (int i = ifix+1; i < nfix; i++) fmask[i-1] = fmask[i];
nfix--;
}
/* ----------------------------------------------------------------------
find a fix by ID
return index of fix or -1 if not found
------------------------------------------------------------------------- */
int Modify::find_fix(char *id)
{
int ifix;
for (ifix = 0; ifix < nfix; ifix++)
if (strcmp(id,fix[ifix]->id) == 0) break;
if (ifix == nfix) return -1;
return ifix;
}
/* ----------------------------------------------------------------------
add a new compute
------------------------------------------------------------------------- */
void Modify::add_compute(int narg, char **arg)
{
if (narg < 3) error->all("Illegal compute command");
// error checks
for (int icompute = 0; icompute < ncompute; icompute++)
if (strcmp(arg[0],compute[icompute]->id) == 0)
error->all("Reuse of compute ID");
int igroup = group->find(arg[1]);
if (igroup == -1) error->all("Could not find compute group ID");
// extend Compute list if necessary
if (ncompute == maxcompute) {
maxcompute += DELTA;
compute = (Compute **)
memory->srealloc(compute,maxcompute*sizeof(Compute *),"modify:compute");
}
// create the Compute
if (0) return; // dummy line to enable else-if macro expansion
#define ComputeClass
#define ComputeStyle(key,Class) \
else if (strcmp(arg[2],#key) == 0) \
compute[ncompute] = new Class(lmp,narg,arg);
#include "style.h"
else error->all("Invalid compute style");
ncompute++;
}
/* ----------------------------------------------------------------------
modify a Compute's parameters
------------------------------------------------------------------------- */
void Modify::modify_compute(int narg, char **arg)
{
if (narg < 2) error->all("Illegal compute_modify command");
// lookup Compute ID
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(arg[0],compute[icompute]->id) == 0) break;
if (icompute == ncompute) error->all("Could not find compute_modify ID");
compute[icompute]->modify_params(narg-1,&arg[1]);
}
/* ----------------------------------------------------------------------
delete a Compute from list of Computes
------------------------------------------------------------------------- */
void Modify::delete_compute(char *id)
{
int icompute = find_compute(id);
if (icompute < 0) error->all("Could not find compute ID to delete");
delete compute[icompute];
// move other Computes down in list one slot
for (int i = icompute+1; i < ncompute; i++) compute[i-1] = compute[i];
ncompute--;
}
/* ----------------------------------------------------------------------
find a compute by ID
return index of compute or -1 if not found
------------------------------------------------------------------------- */
int Modify::find_compute(char *id)
{
int icompute;
for (icompute = 0; icompute < ncompute; icompute++)
if (strcmp(id,compute[icompute]->id) == 0) break;
if (icompute == ncompute) return -1;
return icompute;
}
/* ----------------------------------------------------------------------
write to restart file for all Fixes with restart info
(1) fixes that have global state
(2) fixes that store per-atom quantities
------------------------------------------------------------------------- */
void Modify::write_restart(FILE *fp)
{
int me = comm->me;
int count = 0;
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
int n;
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_global) {
if (me == 0) {
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
}
fix[i]->write_restart(fp);
}
count = 0;
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) count++;
if (me == 0) fwrite(&count,sizeof(int),1,fp);
for (int i = 0; i < nfix; i++)
if (fix[i]->restart_peratom) {
if (me == 0) {
n = strlen(fix[i]->id) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->id,sizeof(char),n,fp);
n = strlen(fix[i]->style) + 1;
fwrite(&n,sizeof(int),1,fp);
fwrite(fix[i]->style,sizeof(char),n,fp);
n = fix[i]->maxsize_restart();
fwrite(&n,sizeof(int),1,fp);
}
}
}
/* ----------------------------------------------------------------------
read in restart file data on all previously defined Fixes with restart info
(1) fixes that have global state
(2) fixes that store per-atom quantities
return maxsize of extra info that will be stored with any atom
------------------------------------------------------------------------- */
int Modify::read_restart(FILE *fp)
{
// nfix_restart_global = # of restart entries with global state info
int me = comm->me;
if (me == 0) fread(&nfix_restart_global,sizeof(int),1,fp);
MPI_Bcast(&nfix_restart_global,1,MPI_INT,0,world);
// allocate space for each entry
if (nfix_restart_global) {
id_restart_global = new char*[nfix_restart_global];
style_restart_global = new char*[nfix_restart_global];
state_restart_global = new char*[nfix_restart_global];
}
// read each entry and Bcast to all procs
// each entry has id string, style string, chunk of state data
int n;
for (int i = 0; i < nfix_restart_global; i++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
id_restart_global[i] = new char[n];
if (me == 0) fread(id_restart_global[i],sizeof(char),n,fp);
MPI_Bcast(id_restart_global[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style_restart_global[i] = new char[n];
if (me == 0) fread(style_restart_global[i],sizeof(char),n,fp);
MPI_Bcast(style_restart_global[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
state_restart_global[i] = new char[n];
if (me == 0) fread(state_restart_global[i],sizeof(char),n,fp);
MPI_Bcast(state_restart_global[i],n,MPI_CHAR,0,world);
}
// nfix_restart_peratom = # of restart entries with peratom info
int maxsize = 0;
if (me == 0) fread(&nfix_restart_peratom,sizeof(int),1,fp);
MPI_Bcast(&nfix_restart_peratom,1,MPI_INT,0,world);
// allocate space for each entry
if (nfix_restart_peratom) {
id_restart_peratom = new char*[nfix_restart_peratom];
style_restart_peratom = new char*[nfix_restart_peratom];
index_restart_peratom = new int[nfix_restart_peratom];
}
// read each entry and Bcast to all procs
// each entry has id string, style string, maxsize of one atom's data
// set index = which set of extra data this fix represents
for (int i = 0; i < nfix_restart_peratom; i++) {
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
id_restart_peratom[i] = new char[n];
if (me == 0) fread(id_restart_peratom[i],sizeof(char),n,fp);
MPI_Bcast(id_restart_peratom[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
style_restart_peratom[i] = new char[n];
if (me == 0) fread(style_restart_peratom[i],sizeof(char),n,fp);
MPI_Bcast(style_restart_peratom[i],n,MPI_CHAR,0,world);
if (me == 0) fread(&n,sizeof(int),1,fp);
MPI_Bcast(&n,1,MPI_INT,0,world);
maxsize += n;
index_restart_peratom[i] = i;
}
return maxsize;
}
/* ----------------------------------------------------------------------
delete all lists of restart file Fix info
------------------------------------------------------------------------- */
void Modify::restart_deallocate()
{
if (nfix_restart_global) {
for (int i = 0; i < nfix_restart_global; i++) {
delete [] id_restart_global[i];
delete [] style_restart_global[i];
delete [] state_restart_global[i];
}
delete [] id_restart_global;
delete [] style_restart_global;
delete [] state_restart_global;
}
if (nfix_restart_peratom) {
for (int i = 0; i < nfix_restart_peratom; i++) {
delete [] id_restart_peratom[i];
delete [] style_restart_peratom[i];
}
delete [] id_restart_peratom;
delete [] style_restart_peratom;
delete [] index_restart_peratom;
}
nfix_restart_global = nfix_restart_peratom = 0;
}
/* ----------------------------------------------------------------------
create list of fix indices for fixes which match mask
------------------------------------------------------------------------- */
void Modify::list_init(int mask, int &n, int *&list)
{
delete [] list;
n = 0;
for (int i = 0; i < nfix; i++) if (fmask[i] & mask) n++;
list = new int[n];
n = 0;
for (int i = 0; i < nfix; i++) if (fmask[i] & mask) list[n++] = i;
}
/* ----------------------------------------------------------------------
create list of fix indices for end_of_step fixes
also create end_of_step_every[]
------------------------------------------------------------------------- */
void Modify::list_init_end_of_step(int mask, int &n, int *&list)
{
delete [] list;
delete [] end_of_step_every;
n = 0;
for (int i = 0; i < nfix; i++) if (fmask[i] & mask) n++;
list = new int[n];
end_of_step_every = new int[n];
n = 0;
for (int i = 0; i < nfix; i++)
if (fmask[i] & mask) {
list[n] = i;
end_of_step_every[n++] = fix[i]->nevery;
}
}
/* ----------------------------------------------------------------------
create list of fix indices for thermo energy fixes
only added to list if its thermo_energy flag was set via fix_modify
------------------------------------------------------------------------- */
void Modify::list_init_thermo_energy(int mask, int &n, int *&list)
{
delete [] list;
n = 0;
for (int i = 0; i < nfix; i++)
if (fmask[i] & mask && fix[i]->thermo_energy) n++;
list = new int[n];
n = 0;
for (int i = 0; i < nfix; i++)
if (fmask[i] & mask && fix[i]->thermo_energy) list[n++] = i;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory from all fixes
------------------------------------------------------------------------- */
int Modify::memory_usage()
{
int bytes = 0;
for (int i = 0; i < nfix; i++) bytes += fix[i]->memory_usage();
for (int i = 0; i < ncompute; i++) bytes += compute[i]->memory_usage();
return bytes;
}
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