Page Menu
Home
c4science
Search
Configure Global Search
Log In
Files
F80967568
fix_smd_setvel.cpp
No One
Temporary
Actions
Download File
Edit File
Delete File
View Transforms
Subscribe
Mute Notifications
Award Token
Subscribers
None
File Metadata
Details
File Info
Storage
Attached
Created
Tue, Sep 3, 12:47
Size
9 KB
Mime Type
text/x-c
Expires
Thu, Sep 5, 12:47 (1 d, 23 h)
Engine
blob
Format
Raw Data
Handle
20353317
Attached To
rLAMMPS lammps
fix_smd_setvel.cpp
View Options
/* ----------------------------------------------------------------------
*
* *** 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;
}
Event Timeline
Log In to Comment