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lammps
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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1655 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2008-03-20 17:35:20 +00:00
parent 4b237db3de
commit a49e234a37
18 changed files with 70 additions and 30 deletions
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7
src/ASPHERE/compute_temp_asphere.cpp
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@ -68,7 +68,7 @@ void ComputeTempAsphere::init()
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
dof_compute();
tempbias = 0;
tbias = NULL;
@ -84,11 +84,12 @@ void ComputeTempAsphere::init()
/* ---------------------------------------------------------------------- */
void ComputeTempAsphere::recount()
void ComputeTempAsphere::dof_compute()
{
double natoms = group->count(igroup);
int dimension = domain->dimension;
dof = dimension * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
// add rotational degrees of freedom
@ -181,7 +182,7 @@ double ComputeTempAsphere::compute_scalar()
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
if (dynamic || tbias) dof_compute();
scalar *= tfactor;
return scalar;
}

2
src/ASPHERE/compute_temp_asphere.h
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@ -38,7 +38,7 @@ class ComputeTempAsphere : public Compute {
Compute *tbias; // ptr to additional bias compute
void recount();
void dof_compute();
void calculate_inertia();
};

3
src/compute.cpp
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@ -17,6 +17,7 @@
#include "ctype.h"
#include "comm.h"
#include "compute.h"
#include "domain.h"
#include "group.h"
#include "modify.h"
#include "lattice.h"
@ -71,7 +72,9 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
comm_forward = comm_reverse = 0;
// set modify defaults
// should change 3 to dimension
//extra_dof = domain->dimension;
extra_dof = 3;
dynamic = 0;

1
src/compute.h
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@ -77,6 +77,7 @@ class Compute : protected Pointers {
virtual int pack_reverse_comm(int, int, double *) {return 0;}
virtual void unpack_reverse_comm(int, int *, double *) {}
virtual double dof_remove(double &) {return 0.0;}
virtual void remove_bias(int, double *) {}
virtual void remove_bias_all() {}
virtual void restore_bias(int, double *) {}

11
src/compute_temp.cpp
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@ -56,7 +56,7 @@ void ComputeTemp::init()
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
dof_compute();
tempbias = 0;
tbias = NULL;
@ -70,12 +70,13 @@ void ComputeTemp::init()
/* ---------------------------------------------------------------------- */
void ComputeTemp::recount()
void ComputeTemp::dof_compute()
{
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
if (dof > 0.0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
}
@ -89,7 +90,7 @@ double ComputeTemp::compute_scalar()
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
} else tempbias = 0;
}
double **v = atom->v;
double *mass = atom->mass;
@ -114,7 +115,7 @@ double ComputeTemp::compute_scalar()
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
if (dynamic || tbias) dof_compute();
scalar *= tfactor;
return scalar;
}

2
src/compute_temp.h
View File

@ -37,7 +37,7 @@ class ComputeTemp : public Compute {
Compute *tbias; // ptr to additional bias compute
void recount();
void dof_compute();
};
}

7
src/compute_temp_com.cpp
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@ -63,7 +63,7 @@ void ComputeTempCOM::init()
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
dof_compute();
masstotal = group->mass(igroup);
tbias = NULL;
@ -76,10 +76,11 @@ void ComputeTempCOM::init()
/* ---------------------------------------------------------------------- */
void ComputeTempCOM::recount()
void ComputeTempCOM::dof_compute()
{
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -126,7 +127,7 @@ double ComputeTempCOM::compute_scalar()
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
if (dynamic || tbias) dof_compute();
scalar *= tfactor;
return scalar;
}

2
src/compute_temp_com.h
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@ -38,7 +38,7 @@ class ComputeTempCOM : public Compute {
double vbias[3]; // stored velocity bias for one atom
Compute *tbias; // ptr to additional bias compute
void recount();
void dof_compute();
};
}

6
src/compute_temp_deform.cpp
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@ -71,7 +71,7 @@ void ComputeTempDeform::init()
fix_dof = 0;
for (i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
dof_compute();
tbias = NULL;
if (id_bias) {
@ -95,10 +95,11 @@ void ComputeTempDeform::init()
/* ---------------------------------------------------------------------- */
void ComputeTempDeform::recount()
void ComputeTempDeform::dof_compute()
{
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -156,6 +157,7 @@ double ComputeTempDeform::compute_scalar()
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic || tbias) dof_compute();
scalar *= tfactor;
return scalar;
}

2
src/compute_temp_deform.h
View File

@ -41,7 +41,7 @@ class ComputeTempDeform : public Compute {
int maxbias; // size of vbiasall array
Compute *tbias; // ptr to additional bias compute
void recount();
void dof_compute();
};
}

20
src/compute_temp_partial.cpp
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@ -16,6 +16,7 @@
#include "compute_temp_partial.h"
#include "atom.h"
#include "force.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "group.h"
@ -65,7 +66,7 @@ void ComputeTempPartial::init()
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
dof_compute();
tbias = NULL;
if (id_bias) {
@ -77,10 +78,11 @@ void ComputeTempPartial::init()
/* ---------------------------------------------------------------------- */
void ComputeTempPartial::recount()
void ComputeTempPartial::dof_compute()
{
double natoms = group->count(igroup);
dof = (xflag+yflag+zflag) * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -88,6 +90,18 @@ void ComputeTempPartial::recount()
/* ---------------------------------------------------------------------- */
double ComputeTempPartial::dof_remove(double &natoms)
{
double rmdof = 0.0;
if (tbias) rmdof = tbias->dof_remove(natoms);
int activedim = xflag+yflag+zflag;
if (domain->dimension == 2) activedim = xflag+yflag;
rmdof += (domain->dimension - activedim) * natoms;
return rmdof;
}
/* ---------------------------------------------------------------------- */
double ComputeTempPartial::compute_scalar()
{
invoked |= INVOKED_SCALAR;
@ -122,7 +136,7 @@ double ComputeTempPartial::compute_scalar()
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
if (dynamic || tbias) dof_compute();
scalar *= tfactor;
return scalar;
}

3
src/compute_temp_partial.h
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@ -26,6 +26,7 @@ class ComputeTempPartial : public Compute {
double compute_scalar();
void compute_vector();
double dof_remove(double &);
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(int, double *);
@ -42,7 +43,7 @@ class ComputeTempPartial : public Compute {
int maxbias; // size of vbiasall array
Compute *tbias; // ptr to additional bias compute
void recount();
void dof_compute();
};
}

7
src/compute_temp_ramp.cpp
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@ -130,7 +130,7 @@ void ComputeTempRamp::init()
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
dof_compute();
tbias = NULL;
if (id_bias) {
@ -142,10 +142,11 @@ void ComputeTempRamp::init()
/* ---------------------------------------------------------------------- */
void ComputeTempRamp::recount()
void ComputeTempRamp::dof_compute()
{
double natoms = group->count(igroup);
dof = domain->dimension * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -195,7 +196,7 @@ double ComputeTempRamp::compute_scalar()
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
if (dynamic || tbias) dof_compute();
scalar *= tfactor;
return scalar;
}

2
src/compute_temp_ramp.h
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@ -45,7 +45,7 @@ class ComputeTempRamp : public Compute {
int maxbias; // size of vbiasall array
Compute *tbias; // ptr to additional bias compute
void recount();
void dof_compute();
};
}

14
src/compute_temp_region.cpp
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@ -73,6 +73,17 @@ void ComputeTempRegion::init()
/* ---------------------------------------------------------------------- */
double ComputeTempRegion::dof_remove(double &natoms)
{
double rmdof = 0.0;
if (tbias) rmdof = tbias->dof_remove(natoms);
natoms -= natoms_region;
rmdof += domain->dimension * natoms;
return rmdof;
}
/* ---------------------------------------------------------------------- */
double ComputeTempRegion::compute_scalar()
{
invoked |= INVOKED_SCALAR;
@ -117,7 +128,8 @@ double ComputeTempRegion::compute_scalar()
tarray[0] = count;
tarray[1] = t;
MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world);
dof = domain->dimension * tarray_all[0] - extra_dof;
natoms_region = tarray_all[0];
dof = domain->dimension * natoms_region - extra_dof;
if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz);
else scalar = 0.0;
return scalar;

2
src/compute_temp_region.h
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@ -26,6 +26,7 @@ class ComputeTempRegion : public Compute {
double compute_scalar();
void compute_vector();
double dof_remove(double &);
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(int, double *);
@ -34,6 +35,7 @@ class ComputeTempRegion : public Compute {
private:
int iregion;
double natoms_region;
double vbias[3]; // stored velocity bias for one atom
double **vbiasall; // stored velocity bias for all atoms

7
src/compute_temp_sphere.cpp
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@ -60,7 +60,7 @@ void ComputeTempSphere::init()
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
dof_compute();
tempbias = 0;
tbias = NULL;
@ -85,11 +85,12 @@ void ComputeTempSphere::init()
/* ---------------------------------------------------------------------- */
void ComputeTempSphere::recount()
void ComputeTempSphere::dof_compute()
{
double natoms = group->count(igroup);
if (domain->dimension == 3) dof = 6.0 * natoms;
else dof = 3.0 * natoms;
if (tbias) dof -= tbias->dof_remove(natoms);
dof -= extra_dof + fix_dof;
if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz);
else tfactor = 0.0;
@ -138,7 +139,7 @@ double ComputeTempSphere::compute_scalar()
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
if (dynamic || tbias) dof_compute();
scalar *= tfactor;
return scalar;
}

2
src/compute_temp_sphere.h
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@ -38,7 +38,7 @@ class ComputeTempSphere : public Compute {
Compute *tbias; // ptr to additional bias compute
void recount();
void dof_compute();
};
}