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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15118 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-06-07 15:20:19 +00:00
parent 97ae23af75
commit 2927a9aee1
4 changed files with 81 additions and 10 deletions
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74
src/USER-DPD/atom_vec_dpd.cpp
View File

@ -35,9 +35,9 @@ AtomVecDPD::AtomVecDPD(LAMMPS *lmp) : AtomVec(lmp)
mass_type = 1; mass_type = 1;
comm_x_only = comm_f_only = 0; // we communicate not only x forward but also dpdTheta comm_x_only = comm_f_only = 0; // we communicate not only x forward but also dpdTheta
size_forward = 6; // 3 + dpdTheta + uCond + uMech size_forward = 7; // 3 + dpdTheta + uCond + uMech + uChem
size_reverse = 3; // 3 size_reverse = 3; // 3
size_border = 9; // 6 + dpdTheta + uCond + uMech size_border = 12; // 6 + dpdTheta + uCond + uMech + uChem + uCG + uCGnew
size_velocity = 3; size_velocity = 3;
size_data_atom = 6; // we read id + type + dpdTheta + x + y + z size_data_atom = 6; // we read id + type + dpdTheta + x + y + z
size_data_vel = 4; size_data_vel = 4;
@ -73,8 +73,12 @@ void AtomVecDPD::grow(int n)
dpdTheta = memory->grow(atom->dpdTheta, nmax, "atom:dpdTheta"); dpdTheta = memory->grow(atom->dpdTheta, nmax, "atom:dpdTheta");
uCond = memory->grow(atom->uCond,nmax,"atom:uCond"); uCond = memory->grow(atom->uCond,nmax,"atom:uCond");
uMech = memory->grow(atom->uMech,nmax,"atom:uMech"); uMech = memory->grow(atom->uMech,nmax,"atom:uMech");
uChem = memory->grow(atom->uChem,nmax,"atom:uChem");
uCG = memory->grow(atom->uCG,nmax,"atom:uCG");
uCGnew = memory->grow(atom->uCGnew,nmax,"atom:uCGnew");
duCond = memory->grow(atom->duCond,nmax,"atom:duCond"); duCond = memory->grow(atom->duCond,nmax,"atom:duCond");
duMech = memory->grow(atom->duMech,nmax,"atom:duMech"); duMech = memory->grow(atom->duMech,nmax,"atom:duMech");
duChem = memory->grow(atom->duChem,nmax,"atom:duChem");
if (atom->nextra_grow) if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++) for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@ -94,8 +98,12 @@ void AtomVecDPD::grow_reset()
dpdTheta = atom->dpdTheta; dpdTheta = atom->dpdTheta;
uCond = atom->uCond; uCond = atom->uCond;
uMech = atom->uMech; uMech = atom->uMech;
uChem = atom->uChem;
uCG = atom->uCG;
uCGnew = atom->uCGnew;
duCond = atom->duCond; duCond = atom->duCond;
duMech = atom->duMech; duMech = atom->duMech;
duChem = atom->duChem;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -117,6 +125,9 @@ void AtomVecDPD::copy(int i, int j, int delflag)
dpdTheta[j] = dpdTheta[i]; dpdTheta[j] = dpdTheta[i];
uCond[j] = uCond[i]; uCond[j] = uCond[i];
uMech[j] = uMech[i]; uMech[j] = uMech[i];
uChem[j] = uChem[i];
uCG[j] = uCG[i];
uCGnew[j] = uCGnew[i];
if (atom->nextra_grow) if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++) for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@ -141,6 +152,7 @@ int AtomVecDPD::pack_comm(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
} }
} else { } else {
if (domain->triclinic == 0) { if (domain->triclinic == 0) {
@ -160,6 +172,7 @@ int AtomVecDPD::pack_comm(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
} }
} }
return m; return m;
@ -186,6 +199,7 @@ int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
} }
} else { } else {
if (domain->triclinic == 0) { if (domain->triclinic == 0) {
@ -209,6 +223,7 @@ int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
} }
} else { } else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
@ -231,6 +246,7 @@ int AtomVecDPD::pack_comm_vel(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
} }
} }
} }
@ -252,6 +268,7 @@ void AtomVecDPD::unpack_comm(int n, int first, double *buf)
dpdTheta[i] = buf[m++]; dpdTheta[i] = buf[m++];
uCond[i] = buf[m++]; uCond[i] = buf[m++];
uMech[i] = buf[m++]; uMech[i] = buf[m++];
uChem[i] = buf[m++];
} }
} }
@ -273,6 +290,7 @@ void AtomVecDPD::unpack_comm_vel(int n, int first, double *buf)
dpdTheta[i] = buf[m++]; dpdTheta[i] = buf[m++];
uCond[i] = buf[m++]; uCond[i] = buf[m++];
uMech[i] = buf[m++]; uMech[i] = buf[m++];
uChem[i] = buf[m++];
} }
} }
@ -328,6 +346,9 @@ int AtomVecDPD::pack_border(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
buf[m++] = uCG[j];
buf[m++] = uCGnew[j];
} }
} else { } else {
if (domain->triclinic == 0) { if (domain->triclinic == 0) {
@ -350,6 +371,9 @@ int AtomVecDPD::pack_border(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
buf[m++] = uCG[j];
buf[m++] = uCGnew[j];
} }
} }
@ -384,6 +408,9 @@ int AtomVecDPD::pack_border_vel(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
buf[m++] = uCG[j];
buf[m++] = uCGnew[j];
} }
} else { } else {
if (domain->triclinic == 0) { if (domain->triclinic == 0) {
@ -410,6 +437,9 @@ int AtomVecDPD::pack_border_vel(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
buf[m++] = uCG[j];
buf[m++] = uCGnew[j];
} }
} else { } else {
dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4]; dvx = pbc[0]*h_rate[0] + pbc[5]*h_rate[5] + pbc[4]*h_rate[4];
@ -435,6 +465,9 @@ int AtomVecDPD::pack_border_vel(int n, int *list, double *buf,
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
buf[m++] = uCG[j];
buf[m++] = uCGnew[j];
} }
} }
} }
@ -458,6 +491,9 @@ int AtomVecDPD::pack_comm_hybrid(int n, int *list, double *buf)
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
buf[m++] = uCG[j];
buf[m++] = uCGnew[j];
} }
return m; return m;
} }
@ -474,6 +510,9 @@ int AtomVecDPD::pack_border_hybrid(int n, int *list, double *buf)
buf[m++] = dpdTheta[j]; buf[m++] = dpdTheta[j];
buf[m++] = uCond[j]; buf[m++] = uCond[j];
buf[m++] = uMech[j]; buf[m++] = uMech[j];
buf[m++] = uChem[j];
buf[m++] = uCG[j];
buf[m++] = uCGnew[j];
} }
return m; return m;
} }
@ -497,6 +536,9 @@ void AtomVecDPD::unpack_border(int n, int first, double *buf)
dpdTheta[i] = buf[m++]; dpdTheta[i] = buf[m++];
uCond[i] = buf[m++]; uCond[i] = buf[m++];
uMech[i] = buf[m++]; uMech[i] = buf[m++];
uChem[i] = buf[m++];
uCG[i] = buf[m++];
uCGnew[i] = buf[m++];
} }
if (atom->nextra_border) if (atom->nextra_border)
@ -527,6 +569,9 @@ void AtomVecDPD::unpack_border_vel(int n, int first, double *buf)
dpdTheta[i] = buf[m++]; dpdTheta[i] = buf[m++];
uCond[i] = buf[m++]; uCond[i] = buf[m++];
uMech[i] = buf[m++]; uMech[i] = buf[m++];
uChem[i] = buf[m++];
uCG[i] = buf[m++];
uCGnew[i] = buf[m++];
} }
if (atom->nextra_border) if (atom->nextra_border)
@ -547,6 +592,7 @@ int AtomVecDPD::unpack_comm_hybrid(int n, int first, double *buf)
dpdTheta[i] = buf[m++]; dpdTheta[i] = buf[m++];
uCond[i] = buf[m++]; uCond[i] = buf[m++];
uMech[i] = buf[m++]; uMech[i] = buf[m++];
uChem[i] = buf[m++];
} }
return m; return m;
} }
@ -563,6 +609,9 @@ int AtomVecDPD::unpack_border_hybrid(int n, int first, double *buf)
dpdTheta[i] = buf[m++]; dpdTheta[i] = buf[m++];
uCond[i] = buf[m++]; uCond[i] = buf[m++];
uMech[i] = buf[m++]; uMech[i] = buf[m++];
uChem[i] = buf[m++];
uCG[i] = buf[m++];
uCGnew[i] = buf[m++];
} }
return m; return m;
} }
@ -588,6 +637,9 @@ int AtomVecDPD::pack_exchange(int i, double *buf)
buf[m++] = dpdTheta[i]; buf[m++] = dpdTheta[i];
buf[m++] = uCond[i]; buf[m++] = uCond[i];
buf[m++] = uMech[i]; buf[m++] = uMech[i];
buf[m++] = uChem[i];
buf[m++] = uCG[i];
buf[m++] = uCGnew[i];
if (atom->nextra_grow) if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++) for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@ -618,6 +670,9 @@ int AtomVecDPD::unpack_exchange(double *buf)
dpdTheta[nlocal] = buf[m++]; dpdTheta[nlocal] = buf[m++];
uCond[nlocal] = buf[m++]; uCond[nlocal] = buf[m++];
uMech[nlocal] = buf[m++]; uMech[nlocal] = buf[m++];
uChem[nlocal] = buf[m++];
uCG[nlocal] = buf[m++];
uCGnew[nlocal] = buf[m++];
if (atom->nextra_grow) if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++) for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
@ -638,7 +693,7 @@ int AtomVecDPD::size_restart()
int i; int i;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
int n = 14 * nlocal; // 11 + dpdTheta + uCond + uMech int n = 15 * nlocal; // 11 + dpdTheta + uCond + uMech + uChem
if (atom->nextra_restart) if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++) for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
@ -670,6 +725,7 @@ int AtomVecDPD::pack_restart(int i, double *buf)
buf[m++] = dpdTheta[i]; buf[m++] = dpdTheta[i];
buf[m++] = uCond[i]; buf[m++] = uCond[i];
buf[m++] = uMech[i]; buf[m++] = uMech[i];
buf[m++] = uChem[i];
if (atom->nextra_restart) if (atom->nextra_restart)
for (int iextra = 0; iextra < atom->nextra_restart; iextra++) for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
@ -706,6 +762,7 @@ int AtomVecDPD::unpack_restart(double *buf)
dpdTheta[nlocal] = buf[m++]; dpdTheta[nlocal] = buf[m++];
uCond[nlocal] = buf[m++]; uCond[nlocal] = buf[m++];
uMech[nlocal] = buf[m++]; uMech[nlocal] = buf[m++];
uChem[nlocal] = buf[m++];
double **extra = atom->extra; double **extra = atom->extra;
if (atom->nextra_store) { if (atom->nextra_store) {
@ -742,8 +799,12 @@ void AtomVecDPD::create_atom(int itype, double *coord)
dpdTheta[nlocal] = 0.0; dpdTheta[nlocal] = 0.0;
uCond[nlocal] = 0.0; uCond[nlocal] = 0.0;
uMech[nlocal] = 0.0; uMech[nlocal] = 0.0;
uChem[nlocal] = 0.0;
uCG[nlocal] = 0.0;
uCGnew[nlocal] = 0.0;
duCond[nlocal] = 0.0; duCond[nlocal] = 0.0;
duMech[nlocal] = 0.0; duMech[nlocal] = 0.0;
duChem[nlocal] = 0.0;
atom->nlocal++; atom->nlocal++;
} }
@ -781,6 +842,9 @@ void AtomVecDPD::data_atom(double *coord, tagint imagetmp, char **values)
rho[nlocal] = 0.0; rho[nlocal] = 0.0;
uCond[nlocal] = 0.0; uCond[nlocal] = 0.0;
uMech[nlocal] = 0.0; uMech[nlocal] = 0.0;
uChem[nlocal] = 0.0;
uCG[nlocal] = 0.0;
uCGnew[nlocal] = 0.0;
atom->nlocal++; atom->nlocal++;
} }
@ -870,8 +934,12 @@ bigint AtomVecDPD::memory_usage()
if (atom->memcheck("dpdTheta")) bytes += memory->usage(dpdTheta,nmax); if (atom->memcheck("dpdTheta")) bytes += memory->usage(dpdTheta,nmax);
if (atom->memcheck("uCond")) bytes += memory->usage(uCond,nmax); if (atom->memcheck("uCond")) bytes += memory->usage(uCond,nmax);
if (atom->memcheck("uMech")) bytes += memory->usage(uMech,nmax); if (atom->memcheck("uMech")) bytes += memory->usage(uMech,nmax);
if (atom->memcheck("uChem")) bytes += memory->usage(uChem,nmax);
if (atom->memcheck("uCG")) bytes += memory->usage(uCG,nmax);
if (atom->memcheck("uCGnew")) bytes += memory->usage(uCGnew,nmax);
if (atom->memcheck("duCond")) bytes += memory->usage(duCond,nmax); if (atom->memcheck("duCond")) bytes += memory->usage(duCond,nmax);
if (atom->memcheck("duMech")) bytes += memory->usage(duMech,nmax); if (atom->memcheck("duMech")) bytes += memory->usage(duMech,nmax);
if (atom->memcheck("duChem")) bytes += memory->usage(duChem,nmax);
return bytes; return bytes;
} }

4
src/USER-DPD/atom_vec_dpd.h
View File

@ -58,8 +58,8 @@ class AtomVecDPD : public AtomVec {
void write_data(FILE *, int, double **); void write_data(FILE *, int, double **);
int write_data_hybrid(FILE *, double *); int write_data_hybrid(FILE *, double *);
bigint memory_usage(); bigint memory_usage();
double *uCond,*uMech,*dpdTheta,*rho; double *uCond,*uMech,*uChem,*uCG,*uCGnew,*rho,*dpdTheta;
double *duCond,*duMech; double *duCond,*duMech,*duChem;
protected: protected:
tagint *tag; tagint *tag;

3
src/USER-DPD/compute_dpd.cpp
View File

@ -59,6 +59,7 @@ void ComputeDpd::compute_vector()
double *uCond = atom->uCond; double *uCond = atom->uCond;
double *uMech = atom->uMech; double *uMech = atom->uMech;
double *uChem = atom->uChem;
double *dpdTheta = atom->dpdTheta; double *dpdTheta = atom->dpdTheta;
int nlocal = atom->nlocal; int nlocal = atom->nlocal;
int *mask = atom->mask; int *mask = atom->mask;
@ -72,7 +73,7 @@ void ComputeDpd::compute_vector()
if (mask[i] & groupbit){ if (mask[i] & groupbit){
dpdU[0] += uCond[i]; dpdU[0] += uCond[i];
dpdU[1] += uMech[i]; dpdU[1] += uMech[i];
dpdU[2] += uCond[i] + uMech[i]; dpdU[2] += uChem[i];
dpdU[3] += 1.0 / dpdTheta[i]; dpdU[3] += 1.0 / dpdTheta[i];
dpdU[4]++; dpdU[4]++;
} }

10
src/USER-DPD/compute_dpd_atom.cpp
View File

@ -40,7 +40,7 @@ ComputeDpdAtom::ComputeDpdAtom(LAMMPS *lmp, int narg, char **arg) :
if (narg != 3) error->all(FLERR,"Illegal compute dpd/atom command"); if (narg != 3) error->all(FLERR,"Illegal compute dpd/atom command");
peratom_flag = 1; peratom_flag = 1;
size_peratom_cols = 3; size_peratom_cols = 4;
nmax = 0; nmax = 0;
dpdAtom = NULL; dpdAtom = NULL;
@ -77,21 +77,23 @@ void ComputeDpdAtom::compute_peratom()
double *uCond = atom->uCond; double *uCond = atom->uCond;
double *uMech = atom->uMech; double *uMech = atom->uMech;
double *uChem = atom->uChem;
double *dpdTheta = atom->dpdTheta; double *dpdTheta = atom->dpdTheta;
int nlocal = atom->nlocal;
int *mask = atom->mask; int *mask = atom->mask;
if (atom->nmax > nmax) { if (nlocal > nmax) {
memory->destroy(dpdAtom); memory->destroy(dpdAtom);
nmax = atom->nmax; nmax = atom->nmax;
memory->create(dpdAtom,nmax,size_peratom_cols,"dpd/atom:dpdAtom"); memory->create(dpdAtom,nmax,size_peratom_cols,"dpd/atom:dpdAtom");
array_atom = dpdAtom; array_atom = dpdAtom;
} }
const int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++){ for (int i = 0; i < nlocal; i++){
if (mask[i] & groupbit){ if (mask[i] & groupbit){
dpdAtom[i][0] = uCond[i]; dpdAtom[i][0] = uCond[i];
dpdAtom[i][1] = uMech[i]; dpdAtom[i][1] = uMech[i];
dpdAtom[i][2] = dpdTheta[i]; dpdAtom[i][2] = uChem[i];
dpdAtom[i][3] = dpdTheta[i];
} }
} }
} }