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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5718 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2011-02-22 22:41:12 +00:00
parent a21e59fa7e
commit 2bd4074d8c
8 changed files with 24 additions and 18 deletions
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3
src/USER-EFF/compute_ke_atom_eff.cpp
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@ -15,6 +15,7 @@
Contributing author: Andres Jaramillo-Botero Contributing author: Andres Jaramillo-Botero
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "math.h"
#include "string.h" #include "string.h"
#include "compute_ke_atom_eff.h" #include "compute_ke_atom_eff.h"
#include "atom.h" #include "atom.h"
@ -96,7 +97,7 @@ void ComputeKEAtomEff::compute_peratom()
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
ke[i] = 0.5 * mvv2e * mass[type[i]] * ke[i] = 0.5 * mvv2e * mass[type[i]] *
(v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]); (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]);
if (abs(spin[i])==1) if (fabs(spin[i])==1)
ke[i] += 0.5 * mvv2e * mass[type[i]] * ervel[i]*ervel[i] * 0.75; ke[i] += 0.5 * mvv2e * mass[type[i]] * ervel[i]*ervel[i] * 0.75;
} else ke[i] = 0.0; } else ke[i] = 0.0;
} }

3
src/USER-EFF/compute_ke_eff.cpp
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@ -16,6 +16,7 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "mpi.h" #include "mpi.h"
#include "math.h"
#include "compute_ke_eff.h" #include "compute_ke_eff.h"
#include "atom.h" #include "atom.h"
#include "update.h" #include "update.h"
@ -70,7 +71,7 @@ double ComputeKEEff::compute_scalar()
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
ke += mass[type[i]]*(v[i][0]*v[i][0] + v[i][1]*v[i][1] + ke += mass[type[i]]*(v[i][0]*v[i][0] + v[i][1]*v[i][1] +
v[i][2]*v[i][2]); v[i][2]*v[i][2]);
if (abs(spin[i])==1) ke += 0.75*mass[type[i]]*ervel[i]*ervel[i]; if (fabs(spin[i])==1) ke += 0.75*mass[type[i]]*ervel[i]*ervel[i];
} }
} }

9
src/USER-EFF/compute_temp_deform_eff.cpp
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@ -16,8 +16,9 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "mpi.h" #include "mpi.h"
#include "compute_temp_deform_eff.h" #include "math.h"
#include "string.h" #include "string.h"
#include "compute_temp_deform_eff.h"
#include "domain.h" #include "domain.h"
#include "atom.h" #include "atom.h"
#include "update.h" #include "update.h"
@ -107,7 +108,7 @@ void ComputeTempDeformEff::dof_compute()
int one = 0; int one = 0;
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (abs(spin[i])==1) one++; if (fabs(spin[i]) == 1) one++;
} }
int nelectrons; int nelectrons;
MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world); MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
@ -158,7 +159,7 @@ double ComputeTempDeformEff::compute_scalar()
if (mass) { if (mass) {
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] + t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2])* mass[type[i]]; vthermal[2]*vthermal[2])* mass[type[i]];
if (abs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i]; if (fabs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i];
} }
} }
@ -209,7 +210,7 @@ void ComputeTempDeformEff::compute_vector()
t[3] += massone * vthermal[0]*vthermal[1]; t[3] += massone * vthermal[0]*vthermal[1];
t[4] += massone * vthermal[0]*vthermal[2]; t[4] += massone * vthermal[0]*vthermal[2];
t[5] += massone * vthermal[1]*vthermal[2]; t[5] += massone * vthermal[1]*vthermal[2];
if (abs(spin[i])==1) { if (fabs(spin[i])==1) {
t[0] += 0.75 * massone * ervel[i]*ervel[i]; t[0] += 0.75 * massone * ervel[i]*ervel[i];
t[1] += 0.75 * massone * ervel[i]*ervel[i]; t[1] += 0.75 * massone * ervel[i]*ervel[i];
t[2] += 0.75 * massone * ervel[i]*ervel[i]; t[2] += 0.75 * massone * ervel[i]*ervel[i];

7
src/USER-EFF/compute_temp_eff.cpp
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@ -16,6 +16,7 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "mpi.h" #include "mpi.h"
#include "math.h"
#include "string.h" #include "string.h"
#include "compute_temp_eff.h" #include "compute_temp_eff.h"
#include "atom.h" #include "atom.h"
@ -80,7 +81,7 @@ void ComputeTempEff::dof_compute()
int one = 0; int one = 0;
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (abs(spin[i])==1) one++; if (fabs(spin[i])==1) one++;
} }
int nelectrons; int nelectrons;
MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world); MPI_Allreduce(&one,&nelectrons,1,MPI_INT,MPI_SUM,world);
@ -114,7 +115,7 @@ double ComputeTempEff::compute_scalar()
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]]; mass[type[i]];
if (abs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i]; if (fabs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i];
} }
} }
} }
@ -153,7 +154,7 @@ void ComputeTempEff::compute_vector()
t[3] += massone * v[i][0]*v[i][1]; t[3] += massone * v[i][0]*v[i][1];
t[4] += massone * v[i][0]*v[i][2]; t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2]; t[5] += massone * v[i][1]*v[i][2];
if (abs(spin[i])==1) { if (fabs(spin[i])==1) {
t[0] += 0.75*massone*ervel[i]*ervel[i]; t[0] += 0.75*massone*ervel[i]*ervel[i];
t[1] += 0.75*massone*ervel[i]*ervel[i]; t[1] += 0.75*massone*ervel[i]*ervel[i];
t[2] += 0.75*massone*ervel[i]*ervel[i]; t[2] += 0.75*massone*ervel[i]*ervel[i];

7
src/USER-EFF/compute_temp_region_eff.cpp
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@ -16,6 +16,7 @@
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "mpi.h" #include "mpi.h"
#include "math.h"
#include "string.h" #include "string.h"
#include "compute_temp_region_eff.h" #include "compute_temp_region_eff.h"
#include "atom.h" #include "atom.h"
@ -114,7 +115,7 @@ double ComputeTempRegionEff::compute_scalar()
count++; count++;
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) *
mass[type[i]]; mass[type[i]];
if (abs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i]; if (fabs(spin[i])==1) t += 0.75*mass[type[i]]*ervel[i]*ervel[i];
} }
} }
@ -127,7 +128,7 @@ double ComputeTempRegionEff::compute_scalar()
int one = 0; int one = 0;
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) { if (mask[i] & groupbit && region->match(x[i][0],x[i][1],x[i][2])) {
if (abs(spin[i])==1) one++; if (fabs(spin[i])==1) one++;
} }
int nelectrons_region; int nelectrons_region;
MPI_Allreduce(&one,&nelectrons_region,1,MPI_INT,MPI_SUM,world); MPI_Allreduce(&one,&nelectrons_region,1,MPI_INT,MPI_SUM,world);
@ -173,7 +174,7 @@ void ComputeTempRegionEff::compute_vector()
t[4] += massone * v[i][0]*v[i][2]; t[4] += massone * v[i][0]*v[i][2];
t[5] += massone * v[i][1]*v[i][2]; t[5] += massone * v[i][1]*v[i][2];
if (abs(spin[i])==1) { if (fabs(spin[i])==1) {
t[0] += 0.75 * massone * ervel[i]*ervel[i]; t[0] += 0.75 * massone * ervel[i]*ervel[i];
t[1] += 0.75 * massone * ervel[i]*ervel[i]; t[1] += 0.75 * massone * ervel[i]*ervel[i];
t[2] += 0.75 * massone * ervel[i]*ervel[i]; t[2] += 0.75 * massone * ervel[i]*ervel[i];

6
src/USER-EFF/fix_nh_eff.cpp
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@ -60,7 +60,7 @@ void FixNHEff::nve_v()
for (int i = 0; i < nlocal; i++) { for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { if (mask[i] & groupbit) {
if (abs(spin[i])==1) { if (fabs(spin[i])==1) {
dtfm = dtf / mass[type[i]]; dtfm = dtf / mass[type[i]];
ervel[i] = dtfm * erforce[i] / 0.75; ervel[i] = dtfm * erforce[i] / 0.75;
} }
@ -87,7 +87,7 @@ void FixNHEff::nve_x()
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) if (mask[i] & groupbit)
if (abs(spin[i])==1) eradius[i] += dtv * ervel[i]; if (fabs(spin[i])==1) eradius[i] += dtv * ervel[i];
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -108,5 +108,5 @@ void FixNHEff::nh_v_temp()
for (int i = 0; i < nlocal; i++) for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) if (mask[i] & groupbit)
if (abs(spin[i])==1) ervel[i] *= factor_eta; if (fabs(spin[i])==1) ervel[i] *= factor_eta;
} }

5
src/USER-EFF/fix_nve_eff.cpp
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@ -15,6 +15,7 @@
Contributing author: Andres Jaramillo-Botero (Caltech) Contributing author: Andres Jaramillo-Botero (Caltech)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h" #include "stdio.h"
#include "string.h" #include "string.h"
#include "fix_nve_eff.h" #include "fix_nve_eff.h"
@ -98,7 +99,7 @@ void FixNVEEff::initial_integrate(int vflag)
x[i][0] += dtv * v[i][0]; x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1]; x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2]; x[i][2] += dtv * v[i][2];
if (abs(spin[i])==1) { if (fabs(spin[i])==1) {
ervel[i] += dtfm * erforce[i] / 0.75; ervel[i] += dtfm * erforce[i] / 0.75;
eradius[i] += dtv * ervel[i]; eradius[i] += dtv * ervel[i];
} }
@ -133,7 +134,7 @@ void FixNVEEff::final_integrate()
v[i][0] += dtfm * f[i][0]; v[i][0] += dtfm * f[i][0];
v[i][1] += dtfm * f[i][1]; v[i][1] += dtfm * f[i][1];
v[i][2] += dtfm * f[i][2]; v[i][2] += dtfm * f[i][2];
if (abs(spin[i])==1) if (fabs(spin[i])==1)
ervel[i] += dtfm * erforce[i] / 0.75; ervel[i] += dtfm * erforce[i] / 0.75;
} }
} }

2
src/USER-EFF/fix_nvt_sllod_eff.cpp
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@ -121,7 +121,7 @@ void FixNVTSllodEff::nh_v_temp()
v[i][1] = v[i][1]*factor_eta - dthalf*vdelu[1]; v[i][1] = v[i][1]*factor_eta - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor_eta - dthalf*vdelu[2]; v[i][2] = v[i][2]*factor_eta - dthalf*vdelu[2];
temperature->restore_bias(i,v[i]); temperature->restore_bias(i,v[i]);
if (abs(spin[i])==1) if (fabs(spin[i])==1)
ervel[i] = ervel[i]*factor_eta - ervel[i] = ervel[i]*factor_eta -
dthalf*sqrt(pow(vdelu[0],2)+pow(vdelu[1],2)+pow(vdelu[2],2)); dthalf*sqrt(pow(vdelu[0],2)+pow(vdelu[1],2)+pow(vdelu[2],2));
} }