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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8210 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2012-06-01 22:21:46 +00:00
parent cb7dd67f25
commit f8f88f1508
4 changed files with 223 additions and 76 deletions
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261
src/fix_gravity.cpp
View File

@ -20,6 +20,9 @@
#include "update.h"
#include "domain.h"
#include "respa.h"
#include "modify.h"
#include "input.h"
#include "variable.h"
#include "math_const.h"
#include "error.h"
@ -27,7 +30,8 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{CHUTE,SPHERICAL,GRADIENT,VECTOR};
enum{CHUTE,SPHERICAL,VECTOR};
enum{CONSTANT,EQUAL};
/* ---------------------------------------------------------------------- */
@ -36,64 +40,92 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
{
if (narg < 5) error->all(FLERR,"Illegal fix gravity command");
time_depend = 1;
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
magnitude = atof(arg[3]);
mstr = vstr = pstr = tstr = xstr = ystr = zstr = NULL;
mstyle = vstyle = pstyle = tstyle = xstyle = ystyle = zstyle = CONSTANT;
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(&arg[3][2]) + 1;
mstr = new char[n];
strcpy(mstr,&arg[3][2]);
mstyle = EQUAL;
} else {
magnitude = atof(arg[3]);
mstyle = CONSTANT;
}
if (strcmp(arg[4],"chute") == 0) {
if (narg != 6) error->all(FLERR,"Illegal fix gravity command");
style = CHUTE;
phi = 0.0;
theta = 180.0 - atof(arg[5]);
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
vstr = new char[n];
strcpy(vstr,&arg[5][2]);
vstyle = EQUAL;
} else {
vert = atof(arg[5]);
vstyle = CONSTANT;
}
} else if (strcmp(arg[4],"spherical") == 0) {
if (narg != 7) error->all(FLERR,"Illegal fix gravity command");
style = SPHERICAL;
phi = atof(arg[5]);
theta = atof(arg[6]);
} else if (strcmp(arg[4],"gradient") == 0) {
if (narg != 9) error->all(FLERR,"Illegal fix gravity command");
style = GRADIENT;
phi = atof(arg[5]);
theta = atof(arg[6]);
phigrad = atof(arg[7]);
thetagrad = atof(arg[8]);
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
pstr = new char[n];
strcpy(pstr,&arg[5][2]);
pstyle = EQUAL;
} else {
phi = atof(arg[5]);
pstyle = CONSTANT;
}
if (strstr(arg[6],"v_") == arg[6]) {
int n = strlen(&arg[6][2]) + 1;
tstr = new char[n];
strcpy(tstr,&arg[6][2]);
tstyle = EQUAL;
} else {
theta = atof(arg[6]);
tstyle = CONSTANT;
}
} else if (strcmp(arg[4],"vector") == 0) {
if (narg != 8) error->all(FLERR,"Illegal fix gravity command");
style = VECTOR;
xdir = atof(arg[5]);
ydir = atof(arg[6]);
zdir = atof(arg[7]);
if (strstr(arg[5],"v_") == arg[5]) {
int n = strlen(&arg[5][2]) + 1;
xstr = new char[n];
strcpy(xstr,&arg[5][2]);
xstyle = EQUAL;
} else {
xdir = atof(arg[5]);
xstyle = CONSTANT;
}
if (strstr(arg[6],"v_") == arg[6]) {
int n = strlen(&arg[6][2]) + 1;
ystr = new char[n];
strcpy(ystr,&arg[6][2]);
ystyle = EQUAL;
} else {
ydir = atof(arg[6]);
ystyle = CONSTANT;
}
if (strstr(arg[7],"v_") == arg[7]) {
int n = strlen(&arg[7][2]) + 1;
zstr = new char[n];
strcpy(zstr,&arg[7][2]);
zstyle = EQUAL;
} else {
zdir = atof(arg[7]);
zstyle = CONSTANT;
}
} else error->all(FLERR,"Illegal fix gravity command");
degree2rad = MY_PI/180.0;
if (style == CHUTE || style == SPHERICAL || style == GRADIENT) {
if (domain->dimension == 3) {
xgrav = sin(degree2rad * theta) * cos(degree2rad * phi);
ygrav = sin(degree2rad * theta) * sin(degree2rad * phi);
zgrav = cos(degree2rad * theta);
} else {
xgrav = sin(degree2rad * theta);
ygrav = cos(degree2rad * theta);
zgrav = 0.0;
}
} else if (style == VECTOR) {
if (domain->dimension == 3) {
double length = sqrt(xdir*xdir + ydir*ydir + zdir*zdir);
xgrav = xdir/length;
ygrav = ydir/length;
zgrav = zdir/length;
} else {
double length = sqrt(xdir*xdir + ydir*ydir);
xgrav = xdir/length;
ygrav = ydir/length;
zgrav = 0.0;
}
}
time_origin = update->ntimestep;
eflag = 0;
@ -102,6 +134,19 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixGravity::~FixGravity()
{
delete [] mstr;
delete [] vstr;
delete [] pstr;
delete [] tstr;
delete [] xstr;
delete [] ystr;
delete [] zstr;
}
/* ---------------------------------------------------------------------- */
int FixGravity::setmask()
{
int mask = 0;
@ -118,11 +163,66 @@ void FixGravity::init()
if (strstr(update->integrate_style,"respa"))
nlevels_respa = ((Respa *) update->integrate)->nlevels;
dt = update->dt;
// check variables
xacc = magnitude*xgrav;
yacc = magnitude*ygrav;
zacc = magnitude*zgrav;
if (mstr) {
mvar = input->variable->find(mstr);
if (mvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(mvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (vstr) {
vvar = input->variable->find(vstr);
if (vvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(vvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (pstr) {
pvar = input->variable->find(pstr);
if (pvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(pvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (tstr) {
tvar = input->variable->find(tstr);
if (tvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(tvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (xstr) {
xvar = input->variable->find(xstr);
if (xvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(xvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (ystr) {
yvar = input->variable->find(ystr);
if (yvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(yvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
if (zstr) {
zvar = input->variable->find(zstr);
if (zvar < 0)
error->all(FLERR,"Variable name for fix gravity does not exist");
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
varflag = CONSTANT;
if (mstyle != CONSTANT || vstyle != CONSTANT || pstyle != CONSTANT ||
tstyle != CONSTANT || xstyle != CONSTANT || ystyle != CONSTANT ||
zstyle != CONSTANT) varflag = EQUAL;
// set gravity components once and for all
if (varflag == CONSTANT) set_acceleration();
}
/* ---------------------------------------------------------------------- */
@ -142,26 +242,20 @@ void FixGravity::setup(int vflag)
void FixGravity::post_force(int vflag)
{
// update direction of gravity vector if gradient style
// update gravity due to variables
if (style == GRADIENT) {
if (domain->dimension == 3) {
double phi_current = degree2rad *
(phi + (update->ntimestep - time_origin)*dt*phigrad*360.0);
double theta_current = degree2rad *
(theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
xgrav = sin(theta_current) * cos(phi_current);
ygrav = sin(theta_current) * sin(phi_current);
zgrav = cos(theta_current);
} else {
double theta_current = degree2rad *
(theta + (update->ntimestep - time_origin)*dt*thetagrad*360.0);
xgrav = sin(theta_current);
ygrav = cos(theta_current);
}
xacc = magnitude*xgrav;
yacc = magnitude*ygrav;
zacc = magnitude*zgrav;
if (varflag != CONSTANT) {
modify->clearstep_compute();
if (mstyle == EQUAL) magnitude = input->variable->compute_equal(mvar);
if (vstyle == EQUAL) magnitude = input->variable->compute_equal(vvar);
if (pstyle == EQUAL) magnitude = input->variable->compute_equal(pvar);
if (tstyle == EQUAL) magnitude = input->variable->compute_equal(tvar);
if (xstyle == EQUAL) magnitude = input->variable->compute_equal(xvar);
if (ystyle == EQUAL) magnitude = input->variable->compute_equal(yvar);
if (zstyle == EQUAL) magnitude = input->variable->compute_equal(zvar);
modify->addstep_compute(update->ntimestep + 1);
set_acceleration();
}
double **x = atom->x;
@ -204,6 +298,43 @@ void FixGravity::post_force_respa(int vflag, int ilevel, int iloop)
if (ilevel == nlevels_respa-1) post_force(vflag);
}
/* ---------------------------------------------------------------------- */
void FixGravity::set_acceleration()
{
if (style == CHUTE || style == SPHERICAL) {
if (style == CHUTE) {
phi = 0.0;
theta = 180.0 - vert;
}
if (domain->dimension == 3) {
xgrav = sin(degree2rad * theta) * cos(degree2rad * phi);
ygrav = sin(degree2rad * theta) * sin(degree2rad * phi);
zgrav = cos(degree2rad * theta);
} else {
xgrav = sin(degree2rad * theta);
ygrav = cos(degree2rad * theta);
zgrav = 0.0;
}
} else if (style == VECTOR) {
if (domain->dimension == 3) {
double length = sqrt(xdir*xdir + ydir*ydir + zdir*zdir);
xgrav = xdir/length;
ygrav = ydir/length;
zgrav = zdir/length;
} else {
double length = sqrt(xdir*xdir + ydir*ydir);
xgrav = xdir/length;
ygrav = ydir/length;
zgrav = 0.0;
}
}
xacc = magnitude*xgrav;
yacc = magnitude*ygrav;
zacc = magnitude*zgrav;
}
/* ----------------------------------------------------------------------
potential energy in gravity field
------------------------------------------------------------------------- */

12
src/fix_gravity.h
View File

@ -29,6 +29,7 @@ class FixGravity : public Fix {
public:
FixGravity(class LAMMPS *, int, char **);
~FixGravity();
int setmask();
void init();
void setup(int);
@ -38,8 +39,8 @@ class FixGravity : public Fix {
protected:
int style;
double magnitude,dt;
double phi,theta,phigrad,thetagrad;
double magnitude;
double vert,phi,theta;
double xdir,ydir,zdir;
double xgrav,ygrav,zgrav,xacc,yacc,zacc;
double degree2rad;
@ -47,6 +48,13 @@ class FixGravity : public Fix {
int time_origin;
int eflag;
double egrav,egrav_all;
int varflag;
int mstyle,vstyle,pstyle,tstyle,xstyle,ystyle,zstyle;
int mvar,vvar,pvar,tvar,xvar,yvar,zvar;
char *mstr,*vstr,*pstr,*tstr,*xstr,*ystr,*zstr;
void set_acceleration();
};
}

25
src/fix_move.cpp
View File

@ -50,7 +50,6 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
size_peratom_cols = 3;
peratom_freq = 1;
time_integrate = 1;
time_depend = 1;
create_attribute = 1;
// parse args
@ -177,9 +176,11 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
if (mstyle == WIGGLE && azflag && az != 0.0)
error->all(FLERR,"Fix move cannot set wiggle z motion for 2d problem");
if (mstyle == ROTATE && (axis[0] != 0.0 || axis[1] != 0.0))
error->all(FLERR,"Fix move cannot rotate aroung non z-axis for 2d problem");
error->all(FLERR,
"Fix move cannot rotate aroung non z-axis for 2d problem");
if (mstyle == VARIABLE && (zvarstr || vzvarstr))
error->all(FLERR,"Fix move cannot define z or vz variable for 2d problem");
error->all(FLERR,
"Fix move cannot define z or vz variable for 2d problem");
}
if (atom->angmom_flag && comm->me == 0)
@ -310,42 +311,48 @@ void FixMove::init()
if (mstyle == VARIABLE) {
if (xvarstr) {
xvar = input->variable->find(xvarstr);
if (xvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
if (xvar < 0) error->all(FLERR,
"Variable name for fix move does not exist");
if (input->variable->equalstyle(xvar)) xvarstyle = EQUAL;
else if (input->variable->atomstyle(xvar)) xvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
}
if (yvarstr) {
yvar = input->variable->find(yvarstr);
if (yvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
if (yvar < 0) error->all(FLERR,
"Variable name for fix move does not exist");
if (input->variable->equalstyle(yvar)) yvarstyle = EQUAL;
else if (input->variable->atomstyle(yvar)) yvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
}
if (zvarstr) {
zvar = input->variable->find(zvarstr);
if (zvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
if (zvar < 0) error->all(FLERR,
"Variable name for fix move does not exist");
if (input->variable->equalstyle(zvar)) zvarstyle = EQUAL;
else if (input->variable->atomstyle(zvar)) zvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
}
if (vxvarstr) {
vxvar = input->variable->find(vxvarstr);
if (vxvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
if (vxvar < 0) error->all(FLERR,
"Variable name for fix move does not exist");
if (input->variable->equalstyle(vxvar)) vxvarstyle = EQUAL;
else if (input->variable->atomstyle(vxvar)) vxvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
}
if (vyvarstr) {
vyvar = input->variable->find(vyvarstr);
if (vyvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
if (vyvar < 0) error->all(FLERR,
"Variable name for fix move does not exist");
if (input->variable->equalstyle(vyvar)) vyvarstyle = EQUAL;
else if (input->variable->atomstyle(vyvar)) vyvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");
}
if (vzvarstr) {
vzvar = input->variable->find(vzvarstr);
if (vzvar < 0) error->all(FLERR,"Variable name for fix move does not exist");
if (vzvar < 0) error->all(FLERR,
"Variable name for fix move does not exist");
if (input->variable->equalstyle(vzvar)) vzvarstyle = EQUAL;
else if (input->variable->atomstyle(vzvar)) vzvarstyle = ATOM;
else error->all(FLERR,"Variable for fix move is invalid style");

1
src/read_dump.cpp
View File

@ -15,6 +15,7 @@
Contributing author: Timothy Sirk (U Vermont)
------------------------------------------------------------------------- */
#include "lmptype.h"
#include "mpi.h"
#include "string.h"
#include "stdlib.h"