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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10114 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2013-06-27 21:44:07 +00:00
parent 8d699db7a8
commit 71a19e3883
3 changed files with 124 additions and 31 deletions
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64
src/KSPACE/pair_lj_long_tip4p_long.cpp
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@ -484,6 +484,7 @@ void PairLJLongTIP4PLong::compute_inner()
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
// atom->nmax > nmax will occur during setup
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(hneigh);
@ -999,6 +1000,19 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
// initialize hneigh[2] to 0 every step
int nlocal = atom->nlocal;
int nall = nlocal + atom->nghost;
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(hneigh);
memory->create(hneigh,nmax,3,"pair:hneigh");
memory->destroy(newsite);
memory->create(newsite,nmax,3,"pair:newsite");
}
if (neighbor->ago == 0) {
for (i = 0; i < nall; i++) hneigh[i][0] = -1;
for (i = 0; i < nall; i++) hneigh[i][2] = 0;
}
double **f = atom->f;
double **x = atom->x;
@ -1236,7 +1250,6 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
cforce = forcecoul * r2inv;
fvirial = (forcecoul + respa_coul) * r2inv;
double fvcf = fvirial/cforce;
// if i,j are not O atoms, force is applied directly
// if i or j are O atoms, force is on fictitious atom & partitioned
@ -1291,15 +1304,27 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
f[iH2][2] += fH[2];
if (vflag) {
fd[0] = delx*fvirial;
fd[1] = dely*fvirial;
fd[2] = delz*fvirial;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
domain->closest_image(x[i],x[iH1],xH1);
domain->closest_image(x[i],x[iH2],xH2);
v[0] = (x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0])*fvcf;
v[1] = (x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1])*fvcf;
v[2] = (x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2])*fvcf;
v[3] = (x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1])*fvcf;
v[4] = (x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2])*fvcf;
v[5] = (x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2])*fvcf;
v[0] = x[i][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] = x[i][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] = x[i][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] = x[i][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] = x[i][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] = x[i][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
}
vlist[n++] = i;
vlist[n++] = iH1;
@ -1349,15 +1374,28 @@ void PairLJLongTIP4PLong::compute_outer(int eflag, int vflag)
f[jH2][2] += fH[2];
if (vflag) {
fd[0] = -delx*fvirial;
fd[1] = -dely*fvirial;
fd[2] = -delz*fvirial;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
domain->closest_image(x[j],x[jH1],xH1);
domain->closest_image(x[j],x[jH2],xH2);
v[0] += (x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0])*fvcf;
v[1] += (x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1])*fvcf;
v[2] += (x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2])*fvcf;
v[3] += (x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1])*fvcf;
v[4] += (x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2])*fvcf;
v[5] += (x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2])*fvcf;
v[0] += x[j][0]*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] += x[j][1]*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] += x[j][2]*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] += x[j][0]*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] += x[j][0]*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] += x[j][1]*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
}
vlist[n++] = j;
vlist[n++] = jH1;

16
src/KSPACE/pppm_disp.cpp
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@ -70,7 +70,7 @@ PPPMDisp::PPPMDisp(LAMMPS *lmp, int narg, char **arg) : KSpace(lmp, narg, arg)
triclinic_support = 0;
pppmflag = dispersionflag = 1;
accuracy_relative = atof(arg[0]);
accuracy_relative = fabs(force->numeric(FLERR,arg[0]));
nfactors = 3;
factors = new int[nfactors];
@ -1137,7 +1137,7 @@ void PPPMDisp::compute(int eflag, int vflag)
if (slabflag) slabcorr(eflag);
if (function[0]) energy += energy_1;
if (function[1]) energy += energy_6;
if (function[1] + function[2]) energy += energy_6;
// convert atoms back from lamda to box coords
@ -2838,12 +2838,15 @@ void PPPMDisp::calc_csum()
MPI_Allreduce(neach,neach_all,ntypes+1,MPI_INT,MPI_SUM,world);
// copmute csumij and csumi
double d1, d2;
if (function[1]){
for (i=1; i<=ntypes; i++) {
for (j=1; j<=ntypes; j++) {
csumi[i] += neach_all[j]*B[i]*B[j];
csumij += neach_all[i]*neach_all[j]*B[i]*B[j];
d1 = neach_all[i]*B[i];
d2 = neach_all[j]*B[j];
csumij += d1*d2;
//csumij += neach_all[i]*neach_all[j]*B[i]*B[j];
}
}
} else {
@ -2851,7 +2854,10 @@ void PPPMDisp::calc_csum()
for (j=1; j<=ntypes; j++) {
for (k=0; k<=6; k++) {
csumi[i] += neach_all[j]*B[7*i + k]*B[7*(j+1)-k-1];
csumij += neach_all[i]*neach_all[j]*B[7*i + k]*B[7*(j+1)-k-1];
d1 = neach_all[i]*B[7*i + k];
d2 = neach_all[j]*B[7*(j+1)-k-1];
csumij += d1*d2;
//csumij += neach_all[i]*neach_all[j]*B[7*i + k]*B[7*(j+1)-k-1];
}
}
}

75
src/USER-OMP/pair_lj_long_tip4p_long_omp.cpp
View File

@ -425,6 +425,30 @@ void PairLJLongTIP4PLongOMP::compute_outer(int eflag, int vflag)
const int order6 = ewald_order&(1<<6);
const int nall = atom->nlocal + atom->nghost;
// reallocate hneigh_thr & newsite_thr if necessary
// initialize hneigh_thr[0] to -1 on steps when reneighboring occured
// initialize hneigh_thr[2] to 0 every step
if (atom->nmax > nmax) {
nmax = atom->nmax;
memory->destroy(hneigh_thr);
memory->create(hneigh_thr,nmax,"pair:hneigh_thr");
memory->destroy(newsite_thr);
memory->create(newsite_thr,nmax,"pair:newsite_thr");
}
int i;
// tag entire list as completely invalid after a neighbor
// list update, since that can change the order of atoms.
if (neighbor->ago == 0) {
for (i = 0; i < nall; i++) hneigh_thr[i].a = -1;
// indicate that the coordinates for the M point need to
// be updated. this needs to be done only if neighbor list
// has been updated in compute_outer
for (i = 0; i < nall; i++) hneigh_thr[i].t = 0;
}
const int nthreads = comm->nthreads;
const int inum = listouter->inum;
@ -1798,7 +1822,6 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
cforce = forcecoul * r2inv;
fvirial = (forcecoul + respa_coul) * r2inv;
double fvcf = fvirial/cforce;
// if i,j are not O atoms, force is applied directly
// if i or j are O atoms, force is on fictitious atom & partitioned
@ -1853,15 +1876,28 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
f[iH2][2] += fH[2];
if (EVFLAG) {
fd[0] = delx*fvirial;
fd[1] = dely*fvirial;
fd[2] = delz*fvirial;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
domain->closest_image(&x[i].x,&x[iH1].x,xH1);
domain->closest_image(&x[i].x,&x[iH2].x,xH2);
v[0] = (x[i].x*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0])*fvcf;
v[1] = (x[i].y*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1])*fvcf;
v[2] = (x[i].z*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2])*fvcf;
v[3] = (x[i].x*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1])*fvcf;
v[4] = (x[i].x*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2])*fvcf;
v[5] = (x[i].y*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2])*fvcf;
v[0] = x[i].x*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] = x[i].y*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] = x[i].z*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] = x[i].x*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] = x[i].x*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] = x[i].y*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
}
vlist[n++] = i;
vlist[n++] = iH1;
@ -1911,15 +1947,28 @@ void PairLJLongTIP4PLongOMP::eval_outer(int iifrom, int iito, ThrData * const th
f[jH2][2] += fH[2];
if (EVFLAG) {
fd[0] = -delx*fvirial;
fd[1] = -dely*fvirial;
fd[2] = -delz*fvirial;
fO[0] = fd[0]*(1 - alpha);
fO[1] = fd[1]*(1 - alpha);
fO[2] = fd[2]*(1 - alpha);
fH[0] = 0.5 * alpha * fd[0];
fH[1] = 0.5 * alpha * fd[1];
fH[2] = 0.5 * alpha * fd[2];
domain->closest_image(&x[j].x,&x[jH1].x,xH1);
domain->closest_image(&x[j].x,&x[jH2].x,xH2);
v[0] += (x[j].x*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0])*fvcf;
v[1] += (x[j].y*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1])*fvcf;
v[2] += (x[j].z*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2])*fvcf;
v[3] += (x[j].x*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1])*fvcf;
v[4] += (x[j].x*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2])*fvcf;
v[5] += (x[j].y*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2])*fvcf;
v[0] += x[j].x*fO[0] + xH1[0]*fH[0] + xH2[0]*fH[0];
v[1] += x[j].y*fO[1] + xH1[1]*fH[1] + xH2[1]*fH[1];
v[2] += x[j].z*fO[2] + xH1[2]*fH[2] + xH2[2]*fH[2];
v[3] += x[j].x*fO[1] + xH1[0]*fH[1] + xH2[0]*fH[1];
v[4] += x[j].x*fO[2] + xH1[0]*fH[2] + xH2[0]*fH[2];
v[5] += x[j].y*fO[2] + xH1[1]*fH[2] + xH2[1]*fH[2];
}
vlist[n++] = j;
vlist[n++] = jH1;