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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1653 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-03-20 15:32:33 +00:00
parent 08e197abc7
commit 4b237db3de
26 changed files with 122 additions and 100 deletions
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5
src/ASPHERE/compute_temp_asphere.cpp
View File

@ -293,9 +293,9 @@ void ComputeTempAsphere::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempAsphere::restore_bias(double *v)
void ComputeTempAsphere::restore_bias(int i, double *v)
{
if (tbias) tbias->restore_bias(v);
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------
@ -307,4 +307,3 @@ void ComputeTempAsphere::restore_bias_all()
{
if (tbias) tbias->restore_bias_all();
}

2
src/ASPHERE/compute_temp_asphere.h
View File

@ -28,7 +28,7 @@ class ComputeTempAsphere : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
private:

4
src/ASPHERE/fix_npt_asphere.cpp
View File

@ -122,7 +122,7 @@ void FixNPTAsphere::initial_integrate(int vflag)
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}
@ -205,7 +205,7 @@ void FixNPTAsphere::final_integrate()
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
angmom[i][0] = (angmom[i][0] + dtf * torque[i][0]) * factor_rotate;
angmom[i][1] = (angmom[i][1] + dtf * torque[i][1]) * factor_rotate;
angmom[i][2] = (angmom[i][2] + dtf * torque[i][2]) * factor_rotate;

4
src/ASPHERE/fix_nvt_asphere.cpp
View File

@ -118,7 +118,7 @@ void FixNVTAsphere::initial_integrate(int vflag)
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
@ -178,7 +178,7 @@ void FixNVTAsphere::final_integrate()
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
angmom[i][0] = (angmom[i][0] + dtf*torque[i][0]) * factor;
angmom[i][1] = (angmom[i][1] + dtf*torque[i][1]) * factor;
angmom[i][2] = (angmom[i][2] + dtf*torque[i][2]) * factor;

8
src/compute.cpp
View File

@ -15,9 +15,10 @@
#include "stdlib.h"
#include "string.h"
#include "ctype.h"
#include "comm.h"
#include "compute.h"
#include "group.h"
#include "domain.h"
#include "modify.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
@ -124,6 +125,11 @@ void Compute::modify_params(int narg, char **arg)
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
int icompute = modify->find_compute(id_bias);
if (icompute < 0) error->all("Could not find compute_modify bias ID");
Compute *temperature = modify->compute[icompute];
if (temperature->igroup != igroup && comm->me == 0)
error->warning("Group for compute_modify bias != compute group");
}
iarg += 2;
} else error->all("Illegal compute_modify command");

2
src/compute.h
View File

@ -79,7 +79,7 @@ class Compute : protected Pointers {
virtual void remove_bias(int, double *) {}
virtual void remove_bias_all() {}
virtual void restore_bias(double *) {}
virtual void restore_bias(int, double *) {}
virtual void restore_bias_all() {}
void addstep(int);

4
src/compute_temp.cpp
View File

@ -183,9 +183,9 @@ void ComputeTemp::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTemp::restore_bias(double *v)
void ComputeTemp::restore_bias(int i, double *v)
{
if (tbias) tbias->restore_bias(v);
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------

2
src/compute_temp.h
View File

@ -28,7 +28,7 @@ class ComputeTemp : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
private:

20
src/compute_temp_com.cpp
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@ -188,9 +188,11 @@ void ComputeTempCOM::compute_vector()
void ComputeTempCOM::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
if (atom->mask[i] & groupbit) {
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
}
}
/* ----------------------------------------------------------------------
@ -218,12 +220,14 @@ void ComputeTempCOM::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempCOM::restore_bias(double *v)
void ComputeTempCOM::restore_bias(int i, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
if (atom->mask[i] & groupbit) {
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------

2
src/compute_temp_com.h
View File

@ -28,7 +28,7 @@ class ComputeTempCOM : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
private:

38
src/compute_temp_deform.cpp
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@ -222,18 +222,20 @@ void ComputeTempDeform::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
domain->x2lamda(atom->x[i],lamda);
vbias[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vbias[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbias[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
if (atom->mask[i] & groupbit) {
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
domain->x2lamda(atom->x[i],lamda);
vbias[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vbias[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbias[2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
}
}
/* ----------------------------------------------------------------------
@ -277,12 +279,14 @@ void ComputeTempDeform::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempDeform::restore_bias(double *v)
void ComputeTempDeform::restore_bias(int i, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
if (atom->mask[i] & groupbit) {
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------

2
src/compute_temp_deform.h
View File

@ -28,7 +28,7 @@ class ComputeTempDeform : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
double memory_usage();

36
src/compute_temp_partial.cpp
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@ -176,17 +176,19 @@ void ComputeTempPartial::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
if (!xflag) {
vbias[0] = v[0];
v[0] = 0.0;
}
if (!yflag) {
vbias[1] = v[1];
v[1] = 0.0;
}
if (!zflag) {
vbias[2] = v[2];
v[2] = 0.0;
if (atom->mask[i] & groupbit) {
if (!xflag) {
vbias[0] = v[0];
v[0] = 0.0;
}
if (!yflag) {
vbias[1] = v[1];
v[1] = 0.0;
}
if (!zflag) {
vbias[2] = v[2];
v[2] = 0.0;
}
}
}
@ -231,12 +233,14 @@ void ComputeTempPartial::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempPartial::restore_bias(double *v)
void ComputeTempPartial::restore_bias(int i, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
if (atom->mask[i] & groupbit) {
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------

2
src/compute_temp_partial.h
View File

@ -28,7 +28,7 @@ class ComputeTempPartial : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
double memory_usage();

19
src/compute_temp_ramp.cpp
View File

@ -260,11 +260,14 @@ void ComputeTempRamp::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
double fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vbias[v_dim] = v_lo + fraction*(v_hi - v_lo);
v[v_dim] -= vbias[v_dim];
if (atom->mask[i] & groupbit) {
double fraction =
(atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vbias[v_dim] = v_lo + fraction*(v_hi - v_lo);
v[v_dim] -= vbias[v_dim];
}
}
/* ----------------------------------------------------------------------
@ -302,10 +305,10 @@ void ComputeTempRamp::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRamp::restore_bias(double *v)
void ComputeTempRamp::restore_bias(int i, double *v)
{
v[v_dim] += vbias[v_dim];
if (tbias) tbias->restore_bias(v);
if (atom->mask[i] & groupbit) v[v_dim] += vbias[v_dim];
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------

2
src/compute_temp_ramp.h
View File

@ -28,7 +28,7 @@ class ComputeTempRamp : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
double memory_usage();

34
src/compute_temp_region.cpp
View File

@ -174,15 +174,16 @@ void ComputeTempRegion::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
double *x = atom->x[i];
if (atom->mask[i] & groupbit &&
domain->regions[iregion]->match(x[0],x[1],x[2]))
vbias[0] = vbias[1] = vbias[2] = 0.0;
else {
vbias[0] = v[0];
vbias[1] = v[1];
vbias[2] = v[2];
v[0] = v[1] = v[2] = 0.0;
if (atom->mask[i] & groupbit) {
double *x = atom->x[i];
if (domain->regions[iregion]->match(x[0],x[1],x[2]))
vbias[0] = vbias[1] = vbias[2] = 0.0;
else {
vbias[0] = v[0];
vbias[1] = v[1];
vbias[2] = v[2];
v[0] = v[1] = v[2] = 0.0;
}
}
}
@ -208,8 +209,7 @@ void ComputeTempRegion::remove_bias_all()
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (atom->mask[i] & groupbit &&
domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2]))
vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
else {
vbiasall[i][0] = v[i][0];
@ -225,12 +225,14 @@ void ComputeTempRegion::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRegion::restore_bias(double *v)
void ComputeTempRegion::restore_bias(int i, double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
if (atom->mask[i] & groupbit) {
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------

2
src/compute_temp_region.h
View File

@ -28,7 +28,7 @@ class ComputeTempRegion : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
double memory_usage();

4
src/compute_temp_sphere.cpp
View File

@ -237,9 +237,9 @@ void ComputeTempSphere::remove_bias_all()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempSphere::restore_bias(double *v)
void ComputeTempSphere::restore_bias(int i, double *v)
{
if (tbias) tbias->restore_bias(v);
if (tbias) tbias->restore_bias(i,v);
}
/* ----------------------------------------------------------------------

2
src/compute_temp_sphere.h
View File

@ -28,7 +28,7 @@ class ComputeTempSphere : public Compute {
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias(int, double *);
void restore_bias_all();
private:

4
src/fix_langevin.cpp
View File

@ -191,7 +191,7 @@ void FixLangevin::post_force(int vflag)
f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (v[i][2] != 0.0)
f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}
@ -235,7 +235,7 @@ void FixLangevin::post_force(int vflag)
f[i][1] += gamma1*v[i][1] + gamma2*(random->uniform()-0.5);
if (v[i][2] != 0.0)
f[i][2] += gamma1*v[i][2] + gamma2*(random->uniform()-0.5);
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}

8
src/fix_npt.cpp
View File

@ -401,7 +401,7 @@ void FixNPT::initial_integrate(int vflag)
v[i][0] = v[i][0]*factor[0] + dtfm*f[i][0];
v[i][1] = v[i][1]*factor[1] + dtfm*f[i][1];
v[i][2] = v[i][2]*factor[2] + dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}
@ -464,7 +464,7 @@ void FixNPT::final_integrate()
v[i][0] = (v[i][0] + dtfm*f[i][0]) * factor[0];
v[i][1] = (v[i][1] + dtfm*f[i][1]) * factor[1];
v[i][2] = (v[i][2] + dtfm*f[i][2]) * factor[2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}
@ -608,7 +608,7 @@ void FixNPT::initial_integrate_respa(int vflag, int ilevel, int flag)
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}
@ -673,7 +673,7 @@ void FixNPT::final_integrate_respa(int ilevel)
v[i][0] += dtfm*f[i][0];
v[i][1] += dtfm*f[i][1];
v[i][2] += dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}

6
src/fix_nvt.cpp
View File

@ -196,7 +196,7 @@ void FixNVT::initial_integrate(int vflag)
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
x[i][2] += dtv * v[i][2];
@ -239,7 +239,7 @@ void FixNVT::final_integrate()
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}
@ -315,7 +315,7 @@ void FixNVT::initial_integrate_respa(int vflag, int ilevel, int flag)
v[i][0] = v[i][0]*factor + dtfm*f[i][0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}

6
src/fix_nvt_sllod.cpp
View File

@ -109,7 +109,7 @@ void FixNVTSlodd::initial_integrate(int vflag)
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
x[i][0] += dtv * v[i][0];
x[i][1] += dtv * v[i][1];
@ -152,7 +152,7 @@ void FixNVTSlodd::final_integrate()
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
@ -223,7 +223,7 @@ void FixNVTSlodd::initial_integrate_respa(int vflag, int ilevel, int flag)
v[i][0] = v[i][0]*factor + dtfm*f[i][0] - dthalf*vdelu[0];
v[i][1] = v[i][1]*factor + dtfm*f[i][1] - dthalf*vdelu[1];
v[i][2] = v[i][2]*factor + dtfm*f[i][2] - dthalf*vdelu[2];
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}

2
src/fix_temp_berendsen.cpp
View File

@ -135,7 +135,7 @@ void FixTempBerendsen::end_of_step()
v[i][0] *= lamda;
v[i][1] *= lamda;
v[i][2] *= lamda;
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}

2
src/fix_temp_rescale.cpp
View File

@ -144,7 +144,7 @@ void FixTempRescale::end_of_step()
v[i][0] *= factor;
v[i][1] *= factor;
v[i][2] *= factor;
temperature->restore_bias(v[i]);
temperature->restore_bias(i,v[i]);
}
}
}