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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5124 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-10-25 20:26:25 +00:00
parent e6b8cca30c
commit 5b5aedb034
3 changed files with 117 additions and 67 deletions
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41
src/compute_pair.cpp
View File

@ -21,34 +21,42 @@
using namespace LAMMPS_NS;
enum{EPAIR,EVDWL,ECOUL};
/* ---------------------------------------------------------------------- */
ComputePair::ComputePair(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 4) error->all("Illegal compute pair command");
if (narg < 4 || narg > 5) error->all("Illegal compute pair command");
if (igroup) error->all("Compute pair must use group all");
scalar_flag = 1;
extscalar = 1;
peflag = 1;
timeflag = 1;
int n = strlen(arg[3]) + 1;
pstyle = new char[n];
strcpy(pstyle,arg[3]);
if (narg == 5) {
if (strcmp(arg[4],"epair") == 0) evalue = EPAIR;
if (strcmp(arg[4],"evdwl") == 0) evalue = EVDWL;
if (strcmp(arg[4],"ecoul") == 0) evalue = ECOUL;
} else evalue = EPAIR;
pair = force->pair_match(pstyle,1);
if (!pair) error->all("Unrecognized pair style in compute pair command");
npair = pair->nextra;
if (!npair)
error->all("Pair style in compute pair command stores no values");
// settings
if (npair) {
vector_flag = 1;
size_vector = npair;
extvector = 1;
peflag = 1;
timeflag = 1;
one = new double[npair];
vector = new double[npair];
} else one = vector = NULL;
}
/* ---------------------------------------------------------------------- */
@ -72,6 +80,23 @@ void ComputePair::init()
/* ---------------------------------------------------------------------- */
double ComputePair::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (update->eflag_global != invoked_scalar)
error->all("Energy was not tallied on needed timestep");
double eng;
if (evalue == EPAIR) eng = pair->eng_vdwl + pair->eng_coul;
else if (evalue == EVDWL) eng = pair->eng_vdwl;
else if (evalue == ECOUL) eng = pair->eng_coul;
MPI_Allreduce(&eng,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
return scalar;
}
/* ---------------------------------------------------------------------- */
void ComputePair::compute_vector()
{
invoked_vector = update->ntimestep;

3
src/compute_pair.h
View File

@ -29,10 +29,11 @@ class ComputePair : public Compute {
ComputePair(class LAMMPS *, int, char **);
~ComputePair();
void init();
double compute_scalar();
void compute_vector();
private:
int npair;
int evalue,npair;
char *pstyle;
class Pair *pair;
double *one;

116
src/pair.cpp
View File

@ -426,6 +426,7 @@ void Pair::ev_tally(int i, int j, int nlocal, int newton_pair,
void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair,
double delx, double dely, double delz)
{
double v[6];
if (eflag_either) {
if (eflag_global) {
@ -436,23 +437,30 @@ void Pair::ev_tally_full(int i, double evdwl, double ecoul, double fpair,
}
if (vflag_either) {
v[0] = 0.5*delx*delx*fpair;
v[1] = 0.5*dely*dely*fpair;
v[2] = 0.5*delz*delz*fpair;
v[3] = 0.5*delx*dely*fpair;
v[4] = 0.5*delx*delz*fpair;
v[5] = 0.5*dely*delz*fpair;
if (vflag_global) {
virial[0] += 0.5*delx*delx*fpair;
virial[1] += 0.5*dely*dely*fpair;
virial[2] += 0.5*delz*delz*fpair;
virial[3] += 0.5*delx*dely*fpair;
virial[4] += 0.5*delx*delz*fpair;
virial[5] += 0.5*dely*delz*fpair;
}
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
}
if (vflag_atom) {
vatom[i][0] += 0.5*delx*delx*fpair;
vatom[i][1] += 0.5*dely*dely*fpair;
vatom[i][2] += 0.5*delz*delz*fpair;
vatom[i][3] += 0.5*delx*dely*fpair;
vatom[i][4] += 0.5*delx*delz*fpair;
vatom[i][5] += 0.5*dely*delz*fpair;
vatom[i][0] += v[0];
vatom[i][1] += v[1];
vatom[i][2] += v[2];
vatom[i][3] += v[3];
vatom[i][4] += v[4];
vatom[i][5] += v[5];
}
}
}
@ -576,36 +584,36 @@ void Pair::ev_tally_xyz_full(int i, double evdwl, double ecoul,
}
if (vflag_either) {
v[0] = delx*fx;
v[1] = dely*fy;
v[2] = delz*fz;
v[3] = delx*fy;
v[4] = delx*fz;
v[5] = dely*fz;
}
v[0] = 0.5*delx*fx;
v[1] = 0.5*dely*fy;
v[2] = 0.5*delz*fz;
v[3] = 0.5*delx*fy;
v[4] = 0.5*delx*fz;
v[5] = 0.5*dely*fz;
if (vflag_global) {
virial[0] += 0.5*v[0];
virial[1] += 0.5*v[1];
virial[2] += 0.5*v[2];
virial[3] += 0.5*v[3];
virial[4] += 0.5*v[4];
virial[5] += 0.5*v[5];
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
}
if (vflag_atom) {
vatom[i][0] += 0.5*v[0];
vatom[i][1] += 0.5*v[1];
vatom[i][2] += 0.5*v[2];
vatom[i][3] += 0.5*v[3];
vatom[i][4] += 0.5*v[4];
vatom[i][5] += 0.5*v[5];
vatom[i][0] += v[0];
vatom[i][1] += v[1];
vatom[i][2] += v[2];
vatom[i][3] += v[3];
vatom[i][4] += v[4];
vatom[i][5] += v[5];
}
}
}
/* ----------------------------------------------------------------------
tally eng_vdwl and virial into global and per-atom accumulators
called by SW potential, newton_pair is always on
called by SW and hbond potentials, newton_pair is always on
virial = riFi + rjFj + rkFk = (rj-ri) Fj + (rk-ri) Fk = drji*fj + drki*fk
------------------------------------------------------------------------- */
@ -627,20 +635,36 @@ void Pair::ev_tally3(int i, int j, int k, double evdwl, double ecoul,
}
}
if (vflag_atom) {
v[0] = THIRD * (drji[0]*fj[0] + drki[0]*fk[0]);
v[1] = THIRD * (drji[1]*fj[1] + drki[1]*fk[1]);
v[2] = THIRD * (drji[2]*fj[2] + drki[2]*fk[2]);
v[3] = THIRD * (drji[0]*fj[1] + drki[0]*fk[1]);
v[4] = THIRD * (drji[0]*fj[2] + drki[0]*fk[2]);
v[5] = THIRD * (drji[1]*fj[2] + drki[1]*fk[2]);
if (vflag_either) {
v[0] = drji[0]*fj[0] + drki[0]*fk[0];
v[1] = drji[1]*fj[1] + drki[1]*fk[1];
v[2] = drji[2]*fj[2] + drki[2]*fk[2];
v[3] = drji[0]*fj[1] + drki[0]*fk[1];
v[4] = drji[0]*fj[2] + drki[0]*fk[2];
v[5] = drji[1]*fj[2] + drki[1]*fk[2];
vatom[i][0] += v[0]; vatom[i][1] += v[1]; vatom[i][2] += v[2];
vatom[i][3] += v[3]; vatom[i][4] += v[4]; vatom[i][5] += v[5];
vatom[j][0] += v[0]; vatom[j][1] += v[1]; vatom[j][2] += v[2];
vatom[j][3] += v[3]; vatom[j][4] += v[4]; vatom[j][5] += v[5];
vatom[k][0] += v[0]; vatom[k][1] += v[1]; vatom[k][2] += v[2];
vatom[k][3] += v[3]; vatom[k][4] += v[4]; vatom[k][5] += v[5];
if (vflag_global) {
virial[0] += v[0];
virial[1] += v[1];
virial[2] += v[2];
virial[3] += v[3];
virial[4] += v[4];
virial[5] += v[5];
}
if (vflag_atom) {
vatom[i][0] += THIRD*v[0]; vatom[i][1] += THIRD*v[1];
vatom[i][2] += THIRD*v[2]; vatom[i][3] += THIRD*v[3];
vatom[i][4] += THIRD*v[4]; vatom[i][5] += THIRD*v[5];
vatom[j][0] += THIRD*v[0]; vatom[j][1] += THIRD*v[1];
vatom[j][2] += THIRD*v[2]; vatom[j][3] += THIRD*v[3];
vatom[j][4] += THIRD*v[4]; vatom[j][5] += THIRD*v[5];
vatom[k][0] += THIRD*v[0]; vatom[k][1] += THIRD*v[1];
vatom[k][2] += THIRD*v[2]; vatom[k][3] += THIRD*v[3];
vatom[k][4] += THIRD*v[4]; vatom[k][5] += THIRD*v[5];
}
}
}