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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5023 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2010-10-12 17:58:40 +00:00
parent a7c21670c8
commit 544dde674b
15 changed files with 608 additions and 503 deletions
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220
src/fix_wall.cpp
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@ -16,16 +16,18 @@
#include "string.h"
#include "fix_wall.h"
#include "atom.h"
#include "input.h"
#include "variable.h"
#include "domain.h"
#include "lattice.h"
#include "update.h"
#include "output.h"
#include "respa.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{XLO,XHI,YLO,YHI,ZLO,ZHI};
enum{NONE,EDGE,CONSTANT,VARIABLE};
/* ---------------------------------------------------------------------- */
@ -34,17 +36,13 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
{
scalar_flag = 1;
vector_flag = 1;
size_vector = 6;
global_freq = 1;
extscalar = 1;
extvector = 1;
time_depend = 1;
// parse args
for (int m = 0; m < 6; m++) wallflag[m] = 0;
velflag = 0;
wigflag = 0;
nwall = 0;
int scaleflag = 1;
int iarg = 3;
@ -53,39 +51,42 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
(strcmp(arg[iarg],"ylo") == 0) || (strcmp(arg[iarg],"yhi") == 0) ||
(strcmp(arg[iarg],"zlo") == 0) || (strcmp(arg[iarg],"zhi") == 0)) {
if (iarg+5 > narg) error->all("Illegal fix wall command");
int m;
if (strcmp(arg[iarg],"xlo") == 0) m = XLO;
else if (strcmp(arg[iarg],"xhi") == 0) m = XHI;
else if (strcmp(arg[iarg],"ylo") == 0) m = YLO;
else if (strcmp(arg[iarg],"yhi") == 0) m = YHI;
else if (strcmp(arg[iarg],"zlo") == 0) m = ZLO;
else if (strcmp(arg[iarg],"zhi") == 0) m = ZHI;
wallflag[m] = 1;
coord0[m] = atof(arg[iarg+1]);
epsilon[m] = atof(arg[iarg+2]);
sigma[m] = atof(arg[iarg+3]);
cutoff[m] = atof(arg[iarg+4]);
int newwall;
if (strcmp(arg[iarg],"xlo") == 0) newwall = XLO;
else if (strcmp(arg[iarg],"xhi") == 0) newwall = XHI;
else if (strcmp(arg[iarg],"ylo") == 0) newwall = YLO;
else if (strcmp(arg[iarg],"yhi") == 0) newwall = YHI;
else if (strcmp(arg[iarg],"zlo") == 0) newwall = ZLO;
else if (strcmp(arg[iarg],"zhi") == 0) newwall = ZHI;
for (int m = 0; m < nwall; m++)
if (newwall == wallwhich[m])
error->all("Wall defined twice in fix wall command");
wallwhich[nwall] = newwall;
if (strcmp(arg[iarg+1],"EDGE") == 0) {
wallstyle[nwall] = EDGE;
int dim = wallwhich[nwall] / 2;
int side = wallwhich[nwall] % 2;
if (side == 0) coord0[nwall] = domain->boxlo[dim];
else coord0[nwall] = domain->boxhi[dim];
} else if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
wallstyle[nwall] = VARIABLE;
int n = strlen(&arg[iarg+1][2]) + 1;
varstr[nwall] = new char[n];
strcpy(varstr[nwall],&arg[iarg+1][2]);
} else {
wallstyle[nwall] = CONSTANT;
coord0[nwall] = atof(arg[iarg+1]);
}
epsilon[nwall] = atof(arg[iarg+2]);
sigma[nwall] = atof(arg[iarg+3]);
cutoff[nwall] = atof(arg[iarg+4]);
nwall++;
iarg += 5;
} else if (strcmp(arg[iarg],"vel") == 0) {
if (iarg+2 > narg) error->all("Illegal fix wall command");
velflag = 1;
double vtmp = atof(arg[iarg+1]);
for (int m = 0; m < 6; m++) vel[m] = vtmp;
iarg += 2;
} else if (strcmp(arg[iarg],"wiggle/sin") == 0) {
if (iarg+3 > narg) error->all("Illegal fix wall command");
wigflag = 1;
double atmp = atof(arg[iarg+1]);
period = atof(arg[iarg+2]);
for (int m = 0; m < 6; m++) amplitude[m] = atmp;
iarg += 3;
} else if (strcmp(arg[iarg],"wiggle/cos") == 0) {
if (iarg+3 > narg) error->all("Illegal fix wall command");
wigflag = 2;
double atmp = atof(arg[iarg+1]);
period = atof(arg[iarg+2]);
for (int m = 0; m < 6; m++) amplitude[m] = atmp;
iarg += 3;
} else if (strcmp(arg[iarg],"units") == 0) {
if (iarg+2 > narg) error->all("Illegal fix wall command");
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = 0;
@ -95,66 +96,70 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
} else error->all("Illegal fix wall command");
}
size_vector = nwall;
// error check
int flag = 0;
for (int m = 0; m < 6; m++) if (wallflag[m]) flag = 1;
if (!flag) error->all("Illegal fix wall command");
for (int m = 0; m < 6; m++)
if (wallflag[m] && cutoff[m] <= 0.0)
if (nwall == 0) error->all("Illegal fix wall command");
for (int m = 0; m < nwall; m++)
if (cutoff[m] <= 0.0)
error->all("Fix wall cutoff <= 0.0");
if (velflag && wigflag)
error->all("Cannot set both vel and wiggle in fix wall command");
if ((wallflag[XLO] || wallflag[XHI]) && domain->xperiodic)
error->all("Cannot use fix wall in periodic dimension");
if ((wallflag[YLO] || wallflag[YHI]) && domain->yperiodic)
error->all("Cannot use fix wall in periodic dimension");
if ((wallflag[ZLO] || wallflag[ZHI]) && domain->zperiodic)
error->all("Cannot use fix wall in periodic dimension");
if ((wallflag[ZLO] || wallflag[ZHI]) && domain->dimension == 2)
error->all("Cannot use fix wall zlo/zhi for a 2d simulation");
// setup scaling
if (scaleflag && domain->lattice == NULL)
error->all("Use of fix wall with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
// apply scaling factors to coord0, vel, amplitude
double scale;
for (int m = 0; m < 6; m++) {
if (wallflag[m] == 0) continue;
if (m < 2) scale = xscale;
else if (m < 4) scale = yscale;
else scale = zscale;
coord0[m] *= scale;
if (velflag) vel[m] *= scale;
if (wigflag) amplitude[m] *= scale;
for (int m = 0; m < nwall; m++) {
if ((wallwhich[m] == XLO || wallwhich[m] == XHI) && domain->xperiodic)
error->all("Cannot use fix wall in periodic dimension");
if ((wallwhich[m] == YLO || wallwhich[m] == YHI) && domain->yperiodic)
error->all("Cannot use fix wall in periodic dimension");
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->zperiodic)
error->all("Cannot use fix wall in periodic dimension");
}
// setup oscillations
for (int m = 0; m < nwall; m++)
if ((wallwhich[m] == ZLO || wallwhich[m] == ZHI) && domain->dimension == 2)
error->all("Cannot use fix wall zlo/zhi for a 2d simulation");
// scale coord for CONSTANT walls
if (wigflag) {
double PI = 4.0 * atan(1.0);
omega = 2.0*PI / period;
int flag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == CONSTANT) flag = 1;
if (flag) {
if (scaleflag && domain->lattice == NULL)
error->all("Use of fix wall with undefined lattice");
double xscale,yscale,zscale;
if (scaleflag) {
xscale = domain->lattice->xlattice;
yscale = domain->lattice->ylattice;
zscale = domain->lattice->zlattice;
}
else xscale = yscale = zscale = 1.0;
double scale;
for (int m = 0; m < nwall; m++) {
if (wallwhich[m] < YLO) scale = xscale;
else if (wallwhich[m] < ZLO) scale = yscale;
else scale = zscale;
if (wallstyle[m] == CONSTANT) coord0[m] *= scale;
}
}
// set time_depend if any wall positions are variable
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) time_depend = 1;
eflag = 0;
for (int m = 0; m < 7; m++) ewall[m] = 0.0;
for (int m = 0; m <= nwall; m++) ewall[m] = 0.0;
}
time_origin = update->ntimestep;
/* ---------------------------------------------------------------------- */
FixWall::~FixWall()
{
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) delete [] varstr[m];
}
/* ---------------------------------------------------------------------- */
@ -175,10 +180,18 @@ void FixWall::init()
{
dt = update->dt;
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] != VARIABLE) continue;
varindex[m] = input->variable->find(varstr[m]);
if (varindex[m] < 0)
error->all("Variable name for fix wall does not exist");
if (!input->variable->equalstyle(varindex[m]))
error->all("Variable for fix wall is invalid style");
}
// setup coefficients
for (int m = 0; m < 6; m++)
if (wallflag[m]) precompute(m);
for (int m = 0; m < nwall; m++) precompute(m);
if (strcmp(update->integrate_style,"respa") == 0)
nlevels_respa = ((Respa *) update->integrate)->nlevels;
@ -209,29 +222,18 @@ void FixWall::min_setup(int vflag)
void FixWall::post_force(int vflag)
{
eflag = 0;
for (int m = 0; m < 7; m++) ewall[m] = 0.0;
for (int m = 0; m <= nwall; m++) ewall[m] = 0.0;
// coord0 = initial position of wall
// coord = current position of wall
// evaluate variable if necessary
double delta = (update->ntimestep - time_origin) * dt;
double coord;
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] == VARIABLE)
coord = input->variable->compute_equal(varindex[m]);
else coord = coord0[m];
for (int m = 0; m < 6; m++) {
if (wallflag[m] == 0) continue;
if (velflag) {
if (m % 2 == 0) coord = coord0[m] + delta*vel[m];
else coord = coord0[m] - delta*vel[m];
} else if (wigflag == 1) {
if (m % 2 == 0) coord = coord0[m] + amplitude[m]*sin(omega*delta);
else coord = coord0[m] - amplitude[m]*sin(omega*delta);
} else if (wigflag == 2) {
if (m % 2 == 0) coord = coord0[m] + amplitude[m]*(1.0-cos(omega*delta));
else coord = coord0[m] - amplitude[m]*(1.0-cos(omega*delta));
} else coord = coord0[m];
wall_particle(m,coord);
wall_particle(m,wallwhich[m],coord);
}
}
@ -258,7 +260,7 @@ double FixWall::compute_scalar()
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,7,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(ewall,ewall_all,nwall+1,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[0];
@ -273,7 +275,7 @@ double FixWall::compute_vector(int n)
// only sum across procs one time
if (eflag == 0) {
MPI_Allreduce(ewall,ewall_all,7,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(ewall,ewall_all,nwall+1,MPI_DOUBLE,MPI_SUM,world);
eflag = 1;
}
return ewall_all[n+1];