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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9295 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2013-01-18 16:53:13 +00:00
parent 43e422a683
commit 7866cd6a29
8 changed files with 133 additions and 78 deletions
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12
src/FLD/pair_brownian.cpp
View File

@ -115,8 +115,8 @@ void PairBrownian::compute(int eflag, int vflag)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -503,7 +503,7 @@ void PairBrownian::init_style()
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
if (((FixWall *) modify->fix[i])->xflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
@ -523,10 +523,10 @@ void PairBrownian::init_style()
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]);
// Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];

10
src/FLD/pair_brownian_poly.cpp
View File

@ -101,8 +101,8 @@ void PairBrownianPoly::compute(int eflag, int vflag)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -363,10 +363,10 @@ void PairBrownianPoly::init_style()
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]);
// Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];

12
src/FLD/pair_lubricate.cpp
View File

@ -181,8 +181,8 @@ void PairLubricate::compute(int eflag, int vflag)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -597,7 +597,7 @@ void PairLubricate::init_style()
}
if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
if (((FixWall *) modify->fix[i])->xflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
@ -619,10 +619,10 @@ void PairLubricate::init_style()
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];

20
src/FLD/pair_lubricateU.cpp
View File

@ -627,8 +627,8 @@ void PairLubricateU::compute_Fh(double **x)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -866,8 +866,8 @@ void PairLubricateU::compute_RU()
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -1143,8 +1143,8 @@ void PairLubricateU::compute_RU(double **x)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -1879,7 +1879,7 @@ void PairLubricateU::init_style()
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
if (((FixWall *) modify->fix[i])->xflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
@ -1899,10 +1899,10 @@ void PairLubricateU::init_style()
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];

16
src/FLD/pair_lubricateU_poly.cpp
View File

@ -379,8 +379,8 @@ void PairLubricateUPoly::compute_Fh(double **x)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -660,8 +660,8 @@ void PairLubricateUPoly::compute_RU(double **x)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -1212,7 +1212,7 @@ void PairLubricateUPoly::init_style()
flagdeform = 1;
else if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
if (((FixWall *) modify->fix[i])->xflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
@ -1233,10 +1233,10 @@ void PairLubricateUPoly::init_style()
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];

12
src/FLD/pair_lubricate_poly.cpp
View File

@ -165,8 +165,8 @@ void PairLubricatePoly::compute(int eflag, int vflag)
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];
if (side == 0) walllo[dim] = wallcoord;
@ -492,7 +492,7 @@ void PairLubricatePoly::init_style()
}
if (strstr(modify->fix[i]->style,"wall") != NULL){
flagwall = 1; // Walls exist
if (((FixWall *) modify->fix[i])->varflag ) {
if (((FixWall *) modify->fix[i])->xflag ) {
flagwall = 2; // Moving walls exist
wallfix = (FixWall *) modify->fix[i];
}
@ -511,10 +511,10 @@ void PairLubricatePoly::init_style()
for (int m = 0; m < wallfix->nwall; m++){
int dim = wallfix->wallwhich[m] / 2;
int side = wallfix->wallwhich[m] % 2;
if (wallfix->wallstyle[m] == VARIABLE){
wallfix->varindex[m] = input->variable->find(wallfix->varstr[m]);
if (wallfix->xstyle[m] == VARIABLE){
wallfix->xindex[m] = input->variable->find(wallfix->xstr[m]);
//Since fix->wall->init happens after pair->init_style
wallcoord = input->variable->compute_equal(wallfix->varindex[m]);
wallcoord = input->variable->compute_equal(wallfix->xindex[m]);
}
else wallcoord = wallfix->coord0[m];

106
src/fix_wall.cpp
View File

@ -49,6 +49,8 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
fldflag = 0;
int pbcflag = 0;
for (int i = 0; i < 6; i++) xstr[i] = estr[i] = sstr[i] = NULL;
int iarg = 3;
while (iarg < narg) {
if ((strcmp(arg[iarg],"xlo") == 0) || (strcmp(arg[iarg],"xhi") == 0) ||
@ -70,23 +72,41 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
wallwhich[nwall] = newwall;
if (strcmp(arg[iarg+1],"EDGE") == 0) {
wallstyle[nwall] = EDGE;
xstyle[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;
xstyle[nwall] = VARIABLE;
int n = strlen(&arg[iarg+1][2]) + 1;
varstr[nwall] = new char[n];
strcpy(varstr[nwall],&arg[iarg+1][2]);
xstr[nwall] = new char[n];
strcpy(xstr[nwall],&arg[iarg+1][2]);
} else {
wallstyle[nwall] = CONSTANT;
xstyle[nwall] = CONSTANT;
coord0[nwall] = atof(arg[iarg+1]);
}
epsilon[nwall] = atof(arg[iarg+2]);
sigma[nwall] = atof(arg[iarg+3]);
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
estr[nwall] = new char[n];
strcpy(estr[nwall],&arg[iarg+2][2]);
estyle[nwall] = VARIABLE;
} else {
epsilon[nwall] = atof(arg[iarg+2]);
estyle[nwall] = CONSTANT;
}
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
sstr[nwall] = new char[n];
strcpy(sstr[nwall],&arg[iarg+3][2]);
sstyle[nwall] = VARIABLE;
} else {
sigma[nwall] = atof(arg[iarg+3]);
sstyle[nwall] = CONSTANT;
}
cutoff[nwall] = atof(arg[iarg+4]);
nwall++;
iarg += 5;
@ -136,11 +156,11 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
}
}
// scale factors for CONSTANT and VARIABLE walls
// scale factors for wall position for CONSTANT and VARIABLE walls
int flag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] != EDGE) flag = 1;
if (xstyle[m] != EDGE) flag = 1;
if (flag) {
if (scaleflag && domain->lattice == NULL)
@ -154,18 +174,24 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
else xscale = yscale = zscale = 1.0;
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] != CONSTANT) continue;
if (xstyle[m] != CONSTANT) continue;
if (wallwhich[m] < YLO) coord0[m] *= xscale;
else if (wallwhich[m] < ZLO) coord0[m] *= yscale;
else coord0[m] *= zscale;
}
}
// set varflag if any wall positions are variable
// set xflag if any wall positions are variable
// set vflag if any wall positions are variable
// set wstyle to VARIABLE if either epsilon or sigma is a variable
varflag = 0;
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) varflag = 1;
vflag = xflag = 0;
for (int m = 0; m < nwall; m++) {
if (xstyle[m] == VARIABLE) xflag = 1;
if (xflag || estyle[m] == VARIABLE || sstyle[m] == VARIABLE) vflag = 1;
if (estyle[m] == VARIABLE || sstyle[m] == VARIABLE) wstyle[m] = VARIABLE;
else wstyle[m] = CONSTANT;
}
eflag = 0;
for (int m = 0; m <= nwall; m++) ewall[m] = 0.0;
@ -175,8 +201,11 @@ FixWall::FixWall(LAMMPS *lmp, int narg, char **arg) :
FixWall::~FixWall()
{
for (int m = 0; m < nwall; m++)
if (wallstyle[m] == VARIABLE) delete [] varstr[m];
for (int m = 0; m < nwall; m++) {
delete [] xstr[m];
delete [] estr[m];
delete [] sstr[m];
}
}
/* ---------------------------------------------------------------------- */
@ -203,12 +232,27 @@ 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(FLERR,"Variable name for fix wall does not exist");
if (!input->variable->equalstyle(varindex[m]))
error->all(FLERR,"Variable for fix wall is invalid style");
if (xstyle[m] == VARIABLE) {
xindex[m] = input->variable->find(xstr[m]);
if (xindex[m] < 0)
error->all(FLERR,"Variable name for fix wall does not exist");
if (!input->variable->equalstyle(xindex[m]))
error->all(FLERR,"Variable for fix wall is invalid style");
}
if (estyle[m] == VARIABLE) {
eindex[m] = input->variable->find(estr[m]);
if (eindex[m] < 0)
error->all(FLERR,"Variable name for fix wall does not exist");
if (!input->variable->equalstyle(eindex[m]))
error->all(FLERR,"Variable for fix wall is invalid style");
}
if (sstyle[m] == VARIABLE) {
sindex[m] = input->variable->find(sstr[m]);
if (sindex[m] < 0)
error->all(FLERR,"Variable name for fix wall does not exist");
if (!input->variable->equalstyle(sindex[m]))
error->all(FLERR,"Variable for fix wall is invalid style");
}
}
// setup coefficients
@ -256,23 +300,31 @@ void FixWall::post_force(int vflag)
for (int m = 0; m <= nwall; m++) ewall[m] = 0.0;
// coord = current position of wall
// evaluate variable if necessary, wrap with clear/add
// evaluate variables if necessary, wrap with clear/add
// for epsilon/sigma variables need to re-invoke precompute()
if (varflag) modify->clearstep_compute();
if (vflag) modify->clearstep_compute();
double coord;
for (int m = 0; m < nwall; m++) {
if (wallstyle[m] == VARIABLE) {
coord = input->variable->compute_equal(varindex[m]);
if (xstyle[m] == VARIABLE) {
coord = input->variable->compute_equal(xindex[m]);
if (wallwhich[m] < YLO) coord *= xscale;
else if (wallwhich[m] < ZLO) coord *= yscale;
else coord *= zscale;
} else coord = coord0[m];
if (wstyle[m] == VARIABLE) {
if (estyle[m] == VARIABLE)
epsilon[m] = input->variable->compute_equal(eindex[m]);
if (sstyle[m] == VARIABLE)
sigma[m] = input->variable->compute_equal(sindex[m]);
precompute(m);
}
wall_particle(m,wallwhich[m],coord);
}
if (varflag) modify->addstep_compute(update->ntimestep + 1);
if (vflag) modify->addstep_compute(update->ntimestep + 1);
}
/* ---------------------------------------------------------------------- */

23
src/fix_wall.h
View File

@ -20,6 +20,14 @@ namespace LAMMPS_NS {
class FixWall : public Fix {
public:
int nwall;
int wallwhich[6];
double coord0[6];
int xflag; // 1 if any wall position is a variable
int xstyle[6];
int xindex[6];
char *xstr[6];
FixWall(class LAMMPS *, int, char **);
virtual ~FixWall();
int setmask();
@ -36,20 +44,15 @@ class FixWall : public Fix {
virtual void precompute(int) = 0;
virtual void wall_particle(int, int, double) = 0;
int nwall;
int wallwhich[6];
double coord0[6];
int varflag;
int wallstyle[6];
int varindex[6];
char *varstr[6];
protected:
double epsilon[6],sigma[6],cutoff[6];
double ewall[7],ewall_all[7];
double xscale,yscale,zscale;
int eflag;
int estyle[6],sstyle[6],wstyle[6];
int eindex[6],sindex[6];
char *estr[6],*sstr[6];
int vflag; // 1 if any wall position,epsilon,sigma is a var
int eflag; // per-wall flag for energy summation
int nlevels_respa;
double dt;
int fldflag;