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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1119 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2007-11-02 20:25:11 +00:00
parent f12471d507
commit 6de4e59a38
28 changed files with 610 additions and 280 deletions
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108
src/verlet.cpp
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@ -27,6 +27,7 @@
#include "output.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "fix.h"
#include "timer.h"
#include "memory.h"
@ -34,25 +35,10 @@
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
Verlet::Verlet(LAMMPS *lmp, int narg, char **arg) :
Integrate(lmp, narg, arg)
{
fix_virial_every = NULL;
next_fix_virial = NULL;
}
/* ---------------------------------------------------------------------- */
Verlet::~Verlet()
{
delete [] fix_virial_every;
delete [] next_fix_virial;
}
Integrate(lmp, narg, arg) {}
/* ----------------------------------------------------------------------
initialization before run
@ -65,30 +51,32 @@ void Verlet::init()
if (modify->nfix == 0)
error->warning("No fixes defined, atoms won't move");
// setup virial computations for timestepping
// virial_style = 1 if computed explicitly by pair
// 2 if computed implicitly by pair (sum over ghost atoms)
// virial_every = 1 if computed every timestep (NPT,NPH)
// fix arrays store info on fixes that need virial computed occasionally
// virial_style:
// 1 if computed explicitly by pair->compute via sum over pair interactions
// 2 if computed implicitly by pair->virial_compute via sum over ghost atoms
if (force->newton_pair) virial_style = 2;
else virial_style = 1;
virial_every = 0;
nfix_virial = 0;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->pressure_every == 1) virial_every = 1;
else if (modify->fix[i]->pressure_every > 1) nfix_virial++;
// elist,vlist = list of computes for PE and pressure
if (nfix_virial) {
delete [] fix_virial_every;
delete [] next_fix_virial;
fix_virial_every = new int[nfix_virial];
next_fix_virial = new int[nfix_virial];
nfix_virial = 0;
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->pressure_every > 1)
fix_virial_every[nfix_virial++] = modify->fix[i]->pressure_every;
delete [] elist;
delete [] vlist;
elist = vlist = NULL;
nelist = nvlist = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag) nelist++;
if (modify->compute[i]->pressflag) nvlist++;
}
if (nelist) elist = new Compute*[nelist];
if (nvlist) vlist = new Compute*[nvlist];
nelist = nvlist = 0;
for (int i = 0; i < modify->ncompute; i++) {
if (modify->compute[i]->peflag) elist[nelist++] = modify->compute[i];
if (modify->compute[i]->pressflag) vlist[nvlist++] = modify->compute[i];
}
// set flags for what arrays to clear in force_clear()
@ -127,8 +115,7 @@ void Verlet::setup()
// compute all forces
int eflag = 1;
int vflag = virial_style;
ev_set(update->ntimestep);
force_clear(vflag);
if (force->pair) force->pair->compute(eflag,vflag);
@ -149,21 +136,6 @@ void Verlet::setup()
modify->setup();
output->setup(1);
// setup virial computations for timestepping
int ntimestep = update->ntimestep;
next_virial = 0;
if (virial_every) next_virial = ntimestep + 1;
else {
for (int ivirial = 0; ivirial < nfix_virial; ivirial++) {
next_fix_virial[ivirial] =
(ntimestep/fix_virial_every[ivirial])*fix_virial_every[ivirial] +
fix_virial_every[ivirial];
if (ivirial) next_virial = MIN(next_virial,next_fix_virial[ivirial]);
else next_virial = next_fix_virial[0];
}
}
}
/* ----------------------------------------------------------------------
@ -172,7 +144,7 @@ void Verlet::setup()
void Verlet::iterate(int n)
{
int eflag,vflag,nflag,ntimestep;
int nflag,ntimestep;
for (int i = 0; i < n; i++) {
@ -209,19 +181,10 @@ void Verlet::iterate(int n)
timer->stamp(TIME_NEIGHBOR);
}
// eflag/vflag = 0/1/2 for energy/virial computation
if (ntimestep == output->next_thermo) eflag = 1;
else eflag = 0;
if (ntimestep == output->next_thermo || ntimestep == next_virial) {
vflag = virial_style;
if (virial_every) next_virial++;
else next_virial = fix_virial(ntimestep);
} else vflag = 0;
// force computations
ev_set(ntimestep);
///printf("AAA %d %d %d\n",ntimestep,eflag,vflag);
force_clear(vflag);
timer->stamp();
@ -299,20 +262,3 @@ void Verlet::force_clear(int vflag)
}
}
}
/* ----------------------------------------------------------------------
return next timestep virial should be computed
based on one or more fixes that need virial computed periodically
------------------------------------------------------------------------- */
int Verlet::fix_virial(int ntimestep)
{
int next;
for (int ivirial = 0; ivirial < nfix_virial; ivirial++) {
if (ntimestep == next_fix_virial[ivirial])
next_fix_virial[ivirial] += fix_virial_every[ivirial];
if (ivirial) next = MIN(next,next_fix_virial[ivirial]);
else next = next_fix_virial[0];
}
return next;
}