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fix_smd_setvel.cpp
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Mon, Jul 8, 16:00

fix_smd_setvel.cpp
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/* ----------------------------------------------------------------------
*
* *** Smooth Mach Dynamics ***
*
* This file is part of the USER-SMD package for LAMMPS.
* Copyright (2014) Georg C. Ganzenmueller, georg.ganzenmueller@emi.fhg.de
* Fraunhofer Ernst-Mach Institute for High-Speed Dynamics, EMI,
* Eckerstrasse 4, D-79104 Freiburg i.Br, Germany.
*
* ----------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
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 <string.h>
#include <stdlib.h>
#include "fix_smd_setvel.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "region.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum {
NONE, CONSTANT, EQUAL, ATOM
};
/* ---------------------------------------------------------------------- */
FixSMDSetVel::FixSMDSetVel(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg) {
if (narg < 6)
error->all(FLERR, "Illegal fix setvelocity command");
dynamic_group_allow = 1;
vector_flag = 1;
size_vector = 3;
global_freq = 1;
extvector = 1;
xstr = ystr = zstr = NULL;
if (strstr(arg[3], "v_") == arg[3]) {
int n = strlen(&arg[3][2]) + 1;
xstr = new char[n];
strcpy(xstr, &arg[3][2]);
} else if (strcmp(arg[3], "NULL") == 0) {
xstyle = NONE;
} else {
xvalue = force->numeric(FLERR, arg[3]);
xstyle = CONSTANT;
}
if (strstr(arg[4], "v_") == arg[4]) {
int n = strlen(&arg[4][2]) + 1;
ystr = new char[n];
strcpy(ystr, &arg[4][2]);
} else if (strcmp(arg[4], "NULL") == 0) {
ystyle = NONE;
} else {
yvalue = force->numeric(FLERR, arg[4]);
ystyle = CONSTANT;
}
if (strstr(arg[5], "v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
zstr = new char[n];
strcpy(zstr, &arg[5][2]);
} else if (strcmp(arg[5], "NULL") == 0) {
zstyle = NONE;
} else {
zvalue = force->numeric(FLERR, arg[5]);
zstyle = CONSTANT;
}
// optional args
iregion = -1;
idregion = NULL;
int iarg = 6;
while (iarg < narg) {
if (strcmp(arg[iarg], "region") == 0) {
if (iarg + 2 > narg)
error->all(FLERR, "Illegal fix setvelocity command");
iregion = domain->find_region(arg[iarg + 1]);
if (iregion == -1)
error->all(FLERR, "Region ID for fix setvelocity does not exist");
int n = strlen(arg[iarg + 1]) + 1;
idregion = new char[n];
strcpy(idregion, arg[iarg + 1]);
iarg += 2;
} else
error->all(FLERR, "Illegal fix setvelocity command");
}
force_flag = 0;
foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
maxatom = atom->nmax;
memory->create(sforce, maxatom, 3, "setvelocity:sforce");
}
/* ---------------------------------------------------------------------- */
FixSMDSetVel::~FixSMDSetVel() {
delete[] xstr;
delete[] ystr;
delete[] zstr;
delete[] idregion;
memory->destroy(sforce);
}
/* ---------------------------------------------------------------------- */
int FixSMDSetVel::setmask() {
int mask = 0;
//mask |= INITIAL_INTEGRATE;
mask |= POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixSMDSetVel::init() {
// check variables
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR, "Variable name for fix setvelocity does not exist");
if (input->variable->equalstyle(xvar))
xstyle = EQUAL;
else if (input->variable->atomstyle(xvar))
xstyle = ATOM;
else
error->all(FLERR, "Variable for fix setvelocity is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR, "Variable name for fix setvelocity does not exist");
if (input->variable->equalstyle(yvar))
ystyle = EQUAL;
else if (input->variable->atomstyle(yvar))
ystyle = ATOM;
else
error->all(FLERR, "Variable for fix setvelocity is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR, "Variable name for fix setvelocity does not exist");
if (input->variable->equalstyle(zvar))
zstyle = EQUAL;
else if (input->variable->atomstyle(zvar))
zstyle = ATOM;
else
error->all(FLERR, "Variable for fix setvelocity is invalid style");
}
// set index and check validity of region
if (iregion >= 0) {
iregion = domain->find_region(idregion);
if (iregion == -1)
error->all(FLERR, "Region ID for fix setvelocity does not exist");
}
if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)
varflag = ATOM;
else if (xstyle == EQUAL || ystyle == EQUAL || zstyle == EQUAL)
varflag = EQUAL;
else
varflag = CONSTANT;
// cannot use non-zero forces for a minimization since no energy is integrated
// use fix addforce instead
int flag = 0;
if (update->whichflag == 2) {
if (xstyle == EQUAL || xstyle == ATOM)
flag = 1;
if (ystyle == EQUAL || ystyle == ATOM)
flag = 1;
if (zstyle == EQUAL || zstyle == ATOM)
flag = 1;
if (xstyle == CONSTANT && xvalue != 0.0)
flag = 1;
if (ystyle == CONSTANT && yvalue != 0.0)
flag = 1;
if (zstyle == CONSTANT && zvalue != 0.0)
flag = 1;
}
if (flag)
error->all(FLERR, "Cannot use non-zero forces in an energy minimization");
}
/* ---------------------------------------------------------------------- */
void FixSMDSetVel::setup(int vflag) {
if (strstr(update->integrate_style, "verlet"))
post_force(vflag);
else
error->all(FLERR,"Fix smd/setvel does not support RESPA");
}
/* ---------------------------------------------------------------------- */
void FixSMDSetVel::min_setup(int vflag) {
post_force(vflag);
}
/* ---------------------------------------------------------------------- */
//void FixSMDSetVel::initial_integrate(int vflag) {
void FixSMDSetVel::post_force(int vflag) {
double **x = atom->x;
double **f = atom->f;
double **v = atom->v;
double **vest = atom->vest;
int *mask = atom->mask;
int nlocal = atom->nlocal;
// update region if necessary
Region *region = NULL;
if (iregion >= 0) {
region = domain->regions[iregion];
region->prematch();
}
// reallocate sforce array if necessary
if (varflag == ATOM && atom->nmax > maxatom) {
maxatom = atom->nmax;
memory->destroy(sforce);
memory->create(sforce, maxatom, 3, "setvelocity:sforce");
}
foriginal[0] = foriginal[1] = foriginal[2] = 0.0;
force_flag = 0;
if (varflag == CONSTANT) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0], x[i][1], x[i][2]))
continue;
foriginal[0] += f[i][0];
foriginal[1] += f[i][1];
foriginal[2] += f[i][2];
if (xstyle) {
v[i][0] = xvalue;
vest[i][0] = xvalue;
f[i][0] = 0.0;
}
if (ystyle) {
v[i][1] = yvalue;
vest[i][1] = yvalue;
f[i][1] = 0.0;
}
if (zstyle) {
v[i][2] = zvalue;
vest[i][2] = zvalue;
f[i][2] = 0.0;
}
}
// variable force, wrap with clear/add
} else {
modify->clearstep_compute();
if (xstyle == EQUAL)
xvalue = input->variable->compute_equal(xvar);
else if (xstyle == ATOM)
input->variable->compute_atom(xvar, igroup, &sforce[0][0], 3, 0);
if (ystyle == EQUAL)
yvalue = input->variable->compute_equal(yvar);
else if (ystyle == ATOM)
input->variable->compute_atom(yvar, igroup, &sforce[0][1], 3, 0);
if (zstyle == EQUAL)
zvalue = input->variable->compute_equal(zvar);
else if (zstyle == ATOM)
input->variable->compute_atom(zvar, igroup, &sforce[0][2], 3, 0);
modify->addstep_compute(update->ntimestep + 1);
//printf("setting velocity at timestep %d\n", update->ntimestep);
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (region && !region->match(x[i][0], x[i][1], x[i][2]))
continue;
foriginal[0] += f[i][0];
foriginal[1] += f[i][1];
foriginal[2] += f[i][2];
if (xstyle == ATOM) {
vest[i][0] = v[i][0] = sforce[i][0];
f[i][0] = 0.0;
} else if (xstyle) {
vest[i][0] = v[i][0] = xvalue;
f[i][0] = 0.0;
}
if (ystyle == ATOM) {
vest[i][1] = v[i][1] = sforce[i][1];
f[i][1] = 0.0;
} else if (ystyle) {
vest[i][1] = v[i][1] = yvalue;
f[i][1] = 0.0;
}
if (zstyle == ATOM) {
vest[i][2] = v[i][2] = sforce[i][2];
f[i][2] = 0.0;
} else if (zstyle) {
vest[i][2] = v[i][2] = zvalue;
f[i][2] = 0.0;
}
}
}
}
/* ----------------------------------------------------------------------
return components of total force on fix group before force was changed
------------------------------------------------------------------------- */
double FixSMDSetVel::compute_vector(int n) {
// only sum across procs one time
if (force_flag == 0) {
MPI_Allreduce(foriginal, foriginal_all, 3, MPI_DOUBLE, MPI_SUM, world);
force_flag = 1;
}
return foriginal_all[n];
}
/* ----------------------------------------------------------------------
memory usage of local atom-based array
------------------------------------------------------------------------- */
double FixSMDSetVel::memory_usage() {
double bytes = 0.0;
if (varflag == ATOM)
bytes = atom->nmax * 3 * sizeof(double);
return bytes;
}

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