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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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256
src/fix_indent.cpp
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@ -5,7 +5,7 @@
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
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.
@ -119,35 +119,35 @@ void FixIndent::init()
{
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
if (xvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(xvar))
error->all(FLERR,"Variable for fix indent is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
if (yvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(yvar))
error->all(FLERR,"Variable for fix indent is not equal style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
if (zvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for fix indent is not equal style");
}
if (rstr) {
rvar = input->variable->find(rstr);
if (rvar < 0)
if (rvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(rvar))
error->all(FLERR,"Variable for fix indent is not equal style");
}
if (pstr) {
pvar = input->variable->find(pstr);
if (pvar < 0)
if (pvar < 0)
error->all(FLERR,"Variable name for fix indent does not exist");
if (!input->variable->equalstyle(pvar))
error->all(FLERR,"Variable for fix indent is not equal style");
@ -183,7 +183,7 @@ void FixIndent::post_force(int vflag)
{
// indenter values, 0 = energy, 1-3 = force components
// wrap variable evaluations with clear/add
if (varflag) modify->clearstep_compute();
indenter_flag = 0;
@ -218,29 +218,29 @@ void FixIndent::post_force(int vflag)
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
delx = x[i][0] - ctr[0];
dely = x[i][1] - ctr[1];
delz = x[i][2] - ctr[2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if (side == OUTSIDE) {
dr = r - radius;
fmag = k*dr*dr;
} else {
dr = radius - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
indenter[0] -= k3 * dr*dr*dr;
indenter[1] -= fx;
indenter[2] -= fy;
indenter[3] -= fz;
delx = x[i][0] - ctr[0];
dely = x[i][1] - ctr[1];
delz = x[i][2] - ctr[2];
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if (side == OUTSIDE) {
dr = r - radius;
fmag = k*dr*dr;
} else {
dr = radius - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
indenter[0] -= k3 * dr*dr*dr;
indenter[1] -= fx;
indenter[2] -= fy;
indenter[3] -= fz;
}
// cylindrical indenter
@ -250,7 +250,7 @@ void FixIndent::post_force(int vflag)
// ctr = current indenter axis
// remap into periodic box
// 3rd coord is just near box for remap(), since isn't used
double ctr[3];
if (cdim == 0) {
ctr[0] = domain->boxlo[0];
@ -281,44 +281,44 @@ void FixIndent::post_force(int vflag)
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double delx,dely,delz,r,dr,fmag,fx,fy,fz;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (cdim == 0) {
delx = 0;
dely = x[i][1] - ctr[1];
delz = x[i][2] - ctr[2];
} else if (cdim == 1) {
delx = x[i][0] - ctr[0];
dely = 0;
delz = x[i][2] - ctr[2];
} else {
delx = x[i][0] - ctr[0];
dely = x[i][1] - ctr[1];
delz = 0;
}
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if (side == OUTSIDE) {
dr = r - radius;
fmag = k*dr*dr;
} else {
dr = radius - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
indenter[0] -= k3 * dr*dr*dr;
indenter[1] -= fx;
indenter[2] -= fy;
indenter[3] -= fz;
if (cdim == 0) {
delx = 0;
dely = x[i][1] - ctr[1];
delz = x[i][2] - ctr[2];
} else if (cdim == 1) {
delx = x[i][0] - ctr[0];
dely = 0;
delz = x[i][2] - ctr[2];
} else {
delx = x[i][0] - ctr[0];
dely = x[i][1] - ctr[1];
delz = 0;
}
domain->minimum_image(delx,dely,delz);
r = sqrt(delx*delx + dely*dely + delz*delz);
if (side == OUTSIDE) {
dr = r - radius;
fmag = k*dr*dr;
} else {
dr = radius - r;
fmag = -k*dr*dr;
}
if (dr >= 0.0) continue;
fx = delx*fmag/r;
fy = dely*fmag/r;
fz = delz*fmag/r;
f[i][0] += fx;
f[i][1] += fy;
f[i][2] += fz;
indenter[0] -= k3 * dr*dr*dr;
indenter[1] -= fx;
indenter[2] -= fy;
indenter[3] -= fz;
}
// planar indenter
@ -326,26 +326,26 @@ void FixIndent::post_force(int vflag)
} else {
// plane = current plane position
double plane;
if (pstr) plane = input->variable->compute_equal(pvar);
else plane = pvalue;
double **x = atom->x;
double **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal;
double dr,fatom;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
dr = planeside * (plane - x[i][cdim]);
if (dr >= 0.0) continue;
fatom = -planeside * k*dr*dr;
f[i][cdim] += fatom;
indenter[0] -= k3 * dr*dr*dr;
indenter[cdim+1] -= fatom;
dr = planeside * (plane - x[i][cdim]);
if (dr >= 0.0) continue;
fatom = -planeside * k*dr*dr;
f[i][cdim] += fatom;
indenter[0] -= k3 * dr*dr*dr;
indenter[cdim+1] -= fatom;
}
}
@ -397,7 +397,7 @@ double FixIndent::compute_vector(int n)
}
/* ----------------------------------------------------------------------
parse optional parameters at end of input line
parse optional parameters at end of input line
------------------------------------------------------------------------- */
void FixIndent::options(int narg, char **arg)
@ -416,24 +416,24 @@ void FixIndent::options(int narg, char **arg)
if (iarg+5 > narg) error->all(FLERR,"Illegal fix indent command");
if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) {
int n = strlen(&arg[iarg+1][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[iarg+1][2]);
int n = strlen(&arg[iarg+1][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[iarg+1][2]);
} else xvalue = atof(arg[iarg+1]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[iarg+2][2]);
int n = strlen(&arg[iarg+2][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[iarg+2][2]);
} else yvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[iarg+3][2]);
int n = strlen(&arg[iarg+3][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[iarg+3][2]);
} else zvalue = atof(arg[iarg+3]);
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
int n = strlen(&arg[iarg+4][2]) + 1;
rstr = new char[n];
strcpy(rstr,&arg[iarg+4][2]);
int n = strlen(&arg[iarg+4][2]) + 1;
rstr = new char[n];
strcpy(rstr,&arg[iarg+4][2]);
} else rvalue = atof(arg[iarg+4]);
istyle = SPHERE;
@ -443,47 +443,47 @@ void FixIndent::options(int narg, char **arg)
if (iarg+5 > narg) error->all(FLERR,"Illegal fix indent command");
if (strcmp(arg[iarg+1],"x") == 0) {
cdim = 0;
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[iarg+2][2]);
} else yvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[iarg+3][2]);
} else zvalue = atof(arg[iarg+3]);
cdim = 0;
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[iarg+2][2]);
} else yvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[iarg+3][2]);
} else zvalue = atof(arg[iarg+3]);
} else if (strcmp(arg[iarg+1],"y") == 0) {
cdim = 1;
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[iarg+2][2]);
} else xvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[iarg+3][2]);
} else zvalue = atof(arg[iarg+3]);
cdim = 1;
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[iarg+2][2]);
} else xvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[iarg+3][2]);
} else zvalue = atof(arg[iarg+3]);
} else if (strcmp(arg[iarg+1],"z") == 0) {
cdim = 2;
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[iarg+2][2]);
} else xvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[iarg+3][2]);
} else yvalue = atof(arg[iarg+3]);
cdim = 2;
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[iarg+2][2]);
} else xvalue = atof(arg[iarg+2]);
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[iarg+3][2]);
} else yvalue = atof(arg[iarg+3]);
} else error->all(FLERR,"Illegal fix indent command");
if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
int n = strlen(&arg[iarg+4][2]) + 1;
rstr = new char[n];
strcpy(rstr,&arg[iarg+4][2]);
int n = strlen(&arg[iarg+4][2]) + 1;
rstr = new char[n];
strcpy(rstr,&arg[iarg+4][2]);
} else rvalue = atof(arg[iarg+4]);
istyle = CYLINDER;
@ -497,9 +497,9 @@ void FixIndent::options(int narg, char **arg)
else error->all(FLERR,"Illegal fix indent command");
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
pstr = new char[n];
strcpy(pstr,&arg[iarg+2][2]);
int n = strlen(&arg[iarg+2][2]) + 1;
pstr = new char[n];
strcpy(pstr,&arg[iarg+2][2]);
} else pvalue = atof(arg[iarg+2]);
if (strcmp(arg[iarg+3],"lo") == 0) planeside = -1;