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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1651 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2008-03-20 14:53:21 +00:00
parent 848aece2b4
commit ebe2ee9bac
28 changed files with 833 additions and 99 deletions
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10
src/ASPHERE/compute_erotate_asphere.cpp
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@ -25,7 +25,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeERotateASphere::ComputeERotateASphere(LAMMPS *lmp, int narg, char **arg) :
ComputeERotateAsphere::ComputeERotateAsphere(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all("Illegal compute erotate/asphere command");
@ -42,14 +42,14 @@ ComputeERotateASphere::ComputeERotateASphere(LAMMPS *lmp, int narg, char **arg)
/* ---------------------------------------------------------------------- */
ComputeERotateASphere::~ComputeERotateASphere()
ComputeERotateAsphere::~ComputeERotateAsphere()
{
memory->destroy_2d_double_array(inertia);
}
/* ---------------------------------------------------------------------- */
void ComputeERotateASphere::init()
void ComputeERotateAsphere::init()
{
pfactor = 0.5 * force->mvv2e;
@ -61,7 +61,7 @@ void ComputeERotateASphere::init()
/* ---------------------------------------------------------------------- */
double ComputeERotateASphere::compute_scalar()
double ComputeERotateAsphere::compute_scalar()
{
invoked |= INVOKED_SCALAR;
@ -102,7 +102,7 @@ double ComputeERotateASphere::compute_scalar()
principal moments of inertia for ellipsoids
------------------------------------------------------------------------- */
void ComputeERotateASphere::calculate_inertia()
void ComputeERotateAsphere::calculate_inertia()
{
double *mass = atom->mass;
double **shape = atom->shape;

6
src/ASPHERE/compute_erotate_asphere.h
View File

@ -18,10 +18,10 @@
namespace LAMMPS_NS {
class ComputeERotateASphere : public Compute {
class ComputeERotateAsphere : public Compute {
public:
ComputeERotateASphere(class LAMMPS *, int, char **);
~ComputeERotateASphere();
ComputeERotateAsphere(class LAMMPS *, int, char **);
~ComputeERotateAsphere();
void init();
double compute_scalar();

61
src/ASPHERE/compute_temp_asphere.cpp
View File

@ -70,6 +70,13 @@ void ComputeTempAsphere::init()
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
tempbias = 1;
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
} else tempbias = 0;
calculate_inertia();
}
@ -122,6 +129,12 @@ double ComputeTempAsphere::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double **quat = atom->quat;
double **angmom = atom->angmom;
@ -163,6 +176,8 @@ double ComputeTempAsphere::compute_scalar()
}
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
scalar *= tfactor;
@ -177,6 +192,11 @@ void ComputeTempAsphere::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double **quat = atom->quat;
double **angmom = atom->angmom;
@ -223,6 +243,8 @@ void ComputeTempAsphere::compute_vector()
t[5] += inertia[itype][2]*wbody[1]*wbody[2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
@ -245,3 +267,42 @@ void ComputeTempAsphere::calculate_inertia()
(shape[i][0]*shape[i][0]+shape[i][1]*shape[i][1]) / 5.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempAsphere::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempAsphere::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempAsphere::restore_bias(double *v)
{
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempAsphere::restore_bias_all()
{
if (tbias) tbias->restore_bias_all();
}

7
src/ASPHERE/compute_temp_asphere.h
View File

@ -26,11 +26,18 @@ class ComputeTempAsphere : public Compute {
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
private:
int fix_dof;
double tfactor;
double **inertia;
Compute *tbias; // ptr to additional bias compute
void recount();
void calculate_inertia();
};

16
src/ASPHERE/fix_npt_asphere.cpp
View File

@ -35,7 +35,7 @@ enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNPTASphere::FixNPTASphere(LAMMPS *lmp, int narg, char **arg) :
FixNPTAsphere::FixNPTAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNPT(lmp, narg, arg)
{
if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
@ -46,7 +46,7 @@ FixNPTASphere::FixNPTASphere(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
void FixNPTASphere::init()
void FixNPTAsphere::init()
{
FixNPT::init();
dtq = 0.5 * update->dt;
@ -56,7 +56,7 @@ void FixNPTASphere::init()
1st half of Verlet update
------------------------------------------------------------------------- */
void FixNPTASphere::initial_integrate(int vflag)
void FixNPTAsphere::initial_integrate(int vflag)
{
int i;
double dtfm;
@ -168,7 +168,7 @@ void FixNPTASphere::initial_integrate(int vflag)
2nd half of Verlet update
------------------------------------------------------------------------- */
void FixNPTASphere::final_integrate()
void FixNPTAsphere::final_integrate()
{
int i;
double dtfm;
@ -251,7 +251,7 @@ void FixNPTASphere::final_integrate()
/* ---------------------------------------------------------------------- */
void FixNPTASphere::reset_dt()
void FixNPTAsphere::reset_dt()
{
FixNPT::reset_dt();
dtq = 0.5 * update->dt;
@ -261,7 +261,7 @@ void FixNPTASphere::reset_dt()
Richardson iteration to update quaternion accurately
------------------------------------------------------------------------- */
void FixNPTASphere::richardson(double *q, double *m, double *moments)
void FixNPTAsphere::richardson(double *q, double *m, double *moments)
{
// compute omega at 1/2 step from m at 1/2 step and q at 0
@ -320,7 +320,7 @@ void FixNPTASphere::richardson(double *q, double *m, double *moments)
and divide by principal moments
------------------------------------------------------------------------- */
void FixNPTASphere::omega_from_mq(double *q, double *m, double *inertia,
void FixNPTAsphere::omega_from_mq(double *q, double *m, double *inertia,
double *w)
{
double rot[3][3];
@ -339,7 +339,7 @@ void FixNPTASphere::omega_from_mq(double *q, double *m, double *inertia,
shape = x,y,z radii in body frame
------------------------------------------------------------------------- */
void FixNPTASphere::calculate_inertia(double mass, double *shape,
void FixNPTAsphere::calculate_inertia(double mass, double *shape,
double *inertia)
{
inertia[0] = mass*(shape[1]*shape[1]+shape[2]*shape[2])/5.0;

4
src/ASPHERE/fix_npt_asphere.h
View File

@ -18,9 +18,9 @@
namespace LAMMPS_NS {
class FixNPTASphere : public FixNPT {
class FixNPTAsphere : public FixNPT {
public:
FixNPTASphere(class LAMMPS *, int, char **);
FixNPTAsphere(class LAMMPS *, int, char **);
void init();
void initial_integrate(int);
void final_integrate();

16
src/ASPHERE/fix_nve_asphere.cpp
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@ -34,7 +34,7 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
FixNVEASphere::FixNVEASphere(LAMMPS *lmp, int narg, char **arg) :
FixNVEAsphere::FixNVEAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNVE(lmp, narg, arg)
{
if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
@ -47,14 +47,14 @@ FixNVEASphere::FixNVEASphere(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
FixNVEASphere::~FixNVEASphere()
FixNVEAsphere::~FixNVEAsphere()
{
memory->destroy_2d_double_array(inertia);
}
/* ---------------------------------------------------------------------- */
void FixNVEASphere::init()
void FixNVEAsphere::init()
{
FixNVE::init();
calculate_inertia();
@ -62,7 +62,7 @@ void FixNVEASphere::init()
/* ---------------------------------------------------------------------- */
void FixNVEASphere::initial_integrate(int vflag)
void FixNVEAsphere::initial_integrate(int vflag)
{
double dtfm;
@ -102,7 +102,7 @@ void FixNVEASphere::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
void FixNVEASphere::final_integrate()
void FixNVEAsphere::final_integrate()
{
double dtfm;
@ -133,7 +133,7 @@ void FixNVEASphere::final_integrate()
Richardson iteration to update quaternion accurately
------------------------------------------------------------------------- */
void FixNVEASphere::richardson(double *q, double *m, double *moments)
void FixNVEAsphere::richardson(double *q, double *m, double *moments)
{
// compute omega at 1/2 step from m at 1/2 step and q at 0
@ -192,7 +192,7 @@ void FixNVEASphere::richardson(double *q, double *m, double *moments)
and divide by principal moments
------------------------------------------------------------------------- */
void FixNVEASphere::omega_from_mq(double *q, double *m, double *moments,
void FixNVEAsphere::omega_from_mq(double *q, double *m, double *moments,
double *w)
{
double rot[3][3];
@ -210,7 +210,7 @@ void FixNVEASphere::omega_from_mq(double *q, double *m, double *moments,
principal moments of inertia for ellipsoids
------------------------------------------------------------------------- */
void FixNVEASphere::calculate_inertia()
void FixNVEAsphere::calculate_inertia()
{
double *mass = atom->mass;
double **shape = atom->shape;

6
src/ASPHERE/fix_nve_asphere.h
View File

@ -18,10 +18,10 @@
namespace LAMMPS_NS {
class FixNVEASphere : public FixNVE {
class FixNVEAsphere : public FixNVE {
public:
FixNVEASphere(class LAMMPS *, int, char **);
~FixNVEASphere();
FixNVEAsphere(class LAMMPS *, int, char **);
~FixNVEAsphere();
void init();
void initial_integrate(int);
void final_integrate();

16
src/ASPHERE/fix_nvt_asphere.cpp
View File

@ -36,7 +36,7 @@ enum{NOBIAS,BIAS};
/* ---------------------------------------------------------------------- */
FixNVTASphere::FixNVTASphere(LAMMPS *lmp, int narg, char **arg) :
FixNVTAsphere::FixNVTAsphere(LAMMPS *lmp, int narg, char **arg) :
FixNVT(lmp, narg, arg)
{
if (!atom->quat_flag || !atom->angmom_flag || !atom->torque_flag ||
@ -47,7 +47,7 @@ FixNVTASphere::FixNVTASphere(LAMMPS *lmp, int narg, char **arg) :
/* ---------------------------------------------------------------------- */
void FixNVTASphere::init()
void FixNVTAsphere::init()
{
FixNVT::init();
dtq = 0.5 * update->dt;
@ -55,7 +55,7 @@ void FixNVTASphere::init()
/* ---------------------------------------------------------------------- */
void FixNVTASphere::initial_integrate(int vflag)
void FixNVTAsphere::initial_integrate(int vflag)
{
double dtfm;
@ -141,7 +141,7 @@ void FixNVTASphere::initial_integrate(int vflag)
/* ---------------------------------------------------------------------- */
void FixNVTASphere::final_integrate()
void FixNVTAsphere::final_integrate()
{
double dtfm;
@ -199,7 +199,7 @@ void FixNVTASphere::final_integrate()
/* ---------------------------------------------------------------------- */
void FixNVTASphere::reset_dt()
void FixNVTAsphere::reset_dt()
{
FixNVT::reset_dt();
dtq = 0.5 * update->dt;
@ -209,7 +209,7 @@ void FixNVTASphere::reset_dt()
Richardson iteration to update quaternion accurately
------------------------------------------------------------------------- */
void FixNVTASphere::richardson(double *q, double *m, double *moments)
void FixNVTAsphere::richardson(double *q, double *m, double *moments)
{
// compute omega at 1/2 step from m at 1/2 step and q at 0
@ -268,7 +268,7 @@ void FixNVTASphere::richardson(double *q, double *m, double *moments)
and divide by principal moments
------------------------------------------------------------------------- */
void FixNVTASphere::omega_from_mq(double *q, double *m, double *inertia,
void FixNVTAsphere::omega_from_mq(double *q, double *m, double *inertia,
double *w)
{
double rot[3][3];
@ -287,7 +287,7 @@ void FixNVTASphere::omega_from_mq(double *q, double *m, double *inertia,
shape = x,y,z radii in body frame
------------------------------------------------------------------------- */
void FixNVTASphere::calculate_inertia(double mass, double *shape,
void FixNVTAsphere::calculate_inertia(double mass, double *shape,
double *inertia)
{
inertia[0] = mass*(shape[1]*shape[1]+shape[2]*shape[2])/5.0;

4
src/ASPHERE/fix_nvt_asphere.h
View File

@ -18,9 +18,9 @@
namespace LAMMPS_NS {
class FixNVTASphere : public FixNVT {
class FixNVTAsphere : public FixNVT {
public:
FixNVTASphere(class LAMMPS *, int, char **);
FixNVTAsphere(class LAMMPS *, int, char **);
void init();
void initial_integrate(int);
void final_integrate();

8
src/ASPHERE/style_asphere.h
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@ -25,7 +25,7 @@ AtomStyle(ellipsoid,AtomVecEllipsoid)
#endif
#ifdef ComputeClass
ComputeStyle(erotate/asphere,ComputeERotateASphere)
ComputeStyle(erotate/asphere,ComputeERotateAsphere)
ComputeStyle(temp/asphere,ComputeTempAsphere)
#endif
@ -36,9 +36,9 @@ ComputeStyle(temp/asphere,ComputeTempAsphere)
#endif
#ifdef FixClass
FixStyle(nve/asphere,FixNVEASphere)
FixStyle(nvt/asphere,FixNVTASphere)
FixStyle(npt/asphere,FixNPTASphere)
FixStyle(nve/asphere,FixNVEAsphere)
FixStyle(nvt/asphere,FixNVTAsphere)
FixStyle(npt/asphere,FixNPTAsphere)
#endif
#ifdef PairInclude

26
src/compute.cpp
View File

@ -60,7 +60,10 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
scalar_flag = vector_flag = peratom_flag = 0;
tempflag = pressflag = peflag = 0;
pressatomflag = peatomflag = 0;
tempbias = 0;
id_bias = NULL;
id_pre = NULL;
timeflag = 0;
invoked = 0;
@ -83,6 +86,7 @@ Compute::~Compute()
{
delete [] id;
delete [] style;
delete [] id_bias;
delete [] id_pre;
memory->sfree(tlist);
@ -112,6 +116,16 @@ void Compute::modify_params(int narg, char **arg)
else if (strcmp(arg[iarg+1],"yes") == 0) thermoflag = 1;
else error->all("Illegal compute_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"bias") == 0) {
if (iarg+2 > narg) error->all("Illegal compute_modify command");
delete [] id_bias;
if (strcmp(arg[iarg+1],"NULL") == 0) id_bias = NULL;
else {
int n = strlen(arg[iarg+1]) + 1;
id_bias = new char[n];
strcpy(id_bias,arg[iarg+1]);
}
iarg += 2;
} else error->all("Illegal compute_modify command");
}
}
@ -163,15 +177,3 @@ int Compute::matchstep(int ntimestep)
}
return 0;
}
/* ----------------------------------------------------------------------
add back in velocity bias removed by remove_bias() to leave thermal temp
assume remove_bias() was previously called for this atom
------------------------------------------------------------------------- */
void Compute::restore_bias(double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
}

9
src/compute.h
View File

@ -45,8 +45,9 @@ class Compute : protected Pointers {
int peflag; // 1 if Compute calculates PE (uses Force energies)
int peatomflag; // 1 if Compute calculates per-atom PE
int tempbias; // 0/1 if has bias routines for isolating thermal temp
double vbias[3]; // stored velocity bias for one atom
int tempbias; // 0/1 if Compute temp includes
// self or extra bias via compute_modify
char *id_bias; // ID of extra Compute temp that adds bias
char *id_pre; // ID of pre-compute the Compute may store
@ -77,7 +78,9 @@ class Compute : protected Pointers {
virtual void unpack_reverse_comm(int, int *, double *) {}
virtual void remove_bias(int, double *) {}
void restore_bias(double *);
virtual void remove_bias_all() {}
virtual void restore_bias(double *) {}
virtual void restore_bias_all() {}
void addstep(int);
int matchstep(int);

60
src/compute_temp.cpp
View File

@ -57,6 +57,13 @@ void ComputeTemp::init()
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
tempbias = 1;
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
@ -76,6 +83,12 @@ double ComputeTemp::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
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;
double *rmass = atom->rmass;
@ -96,6 +109,8 @@ double ComputeTemp::compute_scalar()
t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * rmass[i];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
scalar *= tfactor;
@ -110,6 +125,11 @@ void ComputeTemp::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -132,6 +152,46 @@ void ComputeTemp::compute_vector()
t[5] += massone * v[i][1]*v[i][2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTemp::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTemp::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTemp::restore_bias(double *v)
{
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTemp::restore_bias_all()
{
if (tbias) tbias->restore_bias_all();
}

7
src/compute_temp.h
View File

@ -26,10 +26,17 @@ class ComputeTemp : public Compute {
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
private:
int fix_dof;
double tfactor;
Compute *tbias; // ptr to additional bias compute
void recount();
};

87
src/compute_temp_com.cpp
View File

@ -45,7 +45,6 @@ ComputeTempCOM::ComputeTempCOM(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
tempflag = 1;
tempbias = 1;
vbias[0] = vbias[1] = vbias[2] = 0.0;
vector = new double[6];
}
@ -66,6 +65,12 @@ void ComputeTempCOM::init()
fix_dof += modify->fix[i]->dof(igroup);
recount();
masstotal = group->mass(igroup);
if (id_bias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
@ -87,6 +92,12 @@ double ComputeTempCOM::compute_scalar()
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
if (dynamic) masstotal = group->mass(igroup);
group->vcm(igroup,masstotal,vbias);
@ -111,6 +122,8 @@ double ComputeTempCOM::compute_scalar()
vthermal[2]*vthermal[2]) * rmass[i];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
scalar *= tfactor;
@ -126,6 +139,11 @@ void ComputeTempCOM::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
if (dynamic) masstotal = group->mass(igroup);
group->vcm(igroup,masstotal,vbias);
@ -156,15 +174,74 @@ void ComputeTempCOM::compute_vector()
t[5] += massone * vthermal[1]*vthermal[2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempCOM::remove_bias(int i, double *v)
{
v[0] = v[0] - vbias[0];
v[1] = v[1] - vbias[1];
v[2] = v[2] - vbias[2];
if (tbias) tbias->remove_bias(i,v);
v[0] -= vbias[0];
v[1] -= vbias[1];
v[2] -= vbias[2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempCOM::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] -= vbias[0];
v[i][1] -= vbias[1];
v[i][2] -= vbias[2];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempCOM::restore_bias(double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempCOM::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbias[0];
v[i][1] += vbias[1];
v[i][2] += vbias[2];
}
if (tbias) tbias->restore_bias_all();
}

7
src/compute_temp_com.h
View File

@ -25,12 +25,19 @@ class ComputeTempCOM : public Compute {
void init();
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
private:
int fix_dof;
double tfactor,masstotal;
double vbias[3]; // stored velocity bias for one atom
Compute *tbias; // ptr to additional bias compute
void recount();
};

147
src/compute_temp_deform.cpp
View File

@ -26,6 +26,7 @@
#include "fix_deform.h"
#include "group.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -48,6 +49,8 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
tempflag = 1;
tempbias = 1;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
@ -55,6 +58,7 @@ ComputeTempDeform::ComputeTempDeform(LAMMPS *lmp, int narg, char **arg) :
ComputeTempDeform::~ComputeTempDeform()
{
memory->destroy_2d_double_array(vbiasall);
delete [] vector;
}
@ -69,6 +73,12 @@ void ComputeTempDeform::init()
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
// check fix deform remap settings
for (i = 0; i < modify->nfix; i++)
@ -101,6 +111,12 @@ double ComputeTempDeform::compute_scalar()
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -118,35 +134,25 @@ double ComputeTempDeform::compute_scalar()
double t = 0.0;
if (mass) {
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
if (mass)
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * mass[type[i]];
}
}
else
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(x[i],lamda);
vstream[0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vstream[1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vstream[2] = h_rate[2]*lamda[2] + h_ratelo[2];
vthermal[0] = v[i][0] - vstream[0];
vthermal[1] = v[i][1] - vstream[1];
vthermal[2] = v[i][2] - vstream[2];
else
t += (vthermal[0]*vthermal[0] + vthermal[1]*vthermal[1] +
vthermal[2]*vthermal[2]) * rmass[i];
}
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
scalar *= tfactor;
@ -161,6 +167,11 @@ void ComputeTempDeform::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -196,14 +207,20 @@ void ComputeTempDeform::compute_vector()
t[5] += massone * vthermal[1]*vthermal[2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (int i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
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;
@ -217,3 +234,81 @@ void ComputeTempDeform::remove_bias(int i, double *v)
v[1] -= vbias[1];
v[2] -= vbias[2];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempDeform::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxbias) {
memory->destroy_2d_double_array(vbiasall);
maxbias = atom->nmax;
vbiasall = memory->create_2d_double_array(maxbias,3,
"compute/temp:vbiasall");
}
double lamda[3];
double *h_rate = domain->h_rate;
double *h_ratelo = domain->h_ratelo;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
domain->x2lamda(atom->x[i],lamda);
vbiasall[i][0] = h_rate[0]*lamda[0] + h_rate[5]*lamda[1] +
h_rate[4]*lamda[2] + h_ratelo[0];
vbiasall[i][1] = h_rate[1]*lamda[1] + h_rate[3]*lamda[2] + h_ratelo[1];
vbiasall[i][2] = h_rate[2]*lamda[2] + h_ratelo[2];
v[i][0] -= vbiasall[i][0];
v[i][1] -= vbiasall[i][1];
v[i][2] -= vbiasall[i][2];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempDeform::restore_bias(double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempDeform::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbiasall[i][0];
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
}
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */
double ComputeTempDeform::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}

10
src/compute_temp_deform.h
View File

@ -25,12 +25,22 @@ class ComputeTempDeform : public Compute {
void init();
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
double memory_usage();
private:
int fix_dof;
double tfactor;
double vbias[3]; // stored velocity bias for one atom
double **vbiasall; // stored velocity bias for all atoms
int maxbias; // size of vbiasall array
Compute *tbias; // ptr to additional bias compute
void recount();
};

110
src/compute_temp_partial.cpp
View File

@ -19,6 +19,7 @@
#include "modify.h"
#include "fix.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -43,8 +44,9 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
tempflag = 1;
tempbias = 1;
vbias[0] = vbias[1] = vbias[2] = 0.0;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
@ -52,6 +54,7 @@ ComputeTempPartial::ComputeTempPartial(LAMMPS *lmp, int narg, char **arg) :
ComputeTempPartial::~ComputeTempPartial()
{
memory->destroy_2d_double_array(vbiasall);
delete [] vector;
}
@ -63,6 +66,12 @@ void ComputeTempPartial::init()
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
@ -82,6 +91,12 @@ double ComputeTempPartial::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -103,6 +118,8 @@ double ComputeTempPartial::compute_scalar()
zflag*v[i][2]*v[i][2]) * rmass[i];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
scalar *= tfactor;
@ -117,6 +134,11 @@ void ComputeTempPartial::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double *mass = atom->mass;
double *rmass = atom->rmass;
@ -139,14 +161,20 @@ void ComputeTempPartial::compute_vector()
t[5] += massone * yflag*zflag*v[i][1]*v[i][2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
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;
@ -160,3 +188,81 @@ void ComputeTempPartial::remove_bias(int i, double *v)
v[2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempPartial::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxbias) {
memory->destroy_2d_double_array(vbiasall);
maxbias = atom->nmax;
vbiasall = memory->create_2d_double_array(maxbias,3,
"compute/temp:vbiasall");
}
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
if (!xflag) {
vbiasall[i][0] = v[i][0];
v[i][0] = 0.0;
}
if (!yflag) {
vbiasall[i][1] = v[i][1];
v[i][1] = 0.0;
}
if (!zflag) {
vbiasall[i][2] = v[i][2];
v[i][2] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempPartial::restore_bias(double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempPartial::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbiasall[i][0];
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
}
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */
double ComputeTempPartial::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}

10
src/compute_temp_partial.h
View File

@ -25,13 +25,23 @@ class ComputeTempPartial : public Compute {
void init();
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
double memory_usage();
private:
int xflag,yflag,zflag;
int fix_dof;
double tfactor;
double vbias[3]; // stored velocity bias for one atom
double **vbiasall; // stored velocity bias for all atoms
int maxbias; // size of vbiasall array
Compute *tbias; // ptr to additional bias compute
void recount();
};

99
src/compute_temp_ramp.cpp
View File

@ -22,6 +22,7 @@
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -108,8 +109,9 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
extvector = 1;
tempflag = 1;
tempbias = 1;
vbias[0] = vbias[1] = vbias[2] = 0.0;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
@ -117,6 +119,7 @@ ComputeTempRamp::ComputeTempRamp(LAMMPS *lmp, int narg, char **arg) :
ComputeTempRamp::~ComputeTempRamp()
{
memory->destroy_2d_double_array(vbiasall);
delete [] vector;
}
@ -128,6 +131,12 @@ void ComputeTempRamp::init()
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
@ -149,6 +158,12 @@ double ComputeTempRamp::compute_scalar()
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -176,6 +191,8 @@ double ComputeTempRamp::compute_scalar()
vthermal[2]*vthermal[2]) * rmass[i];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
scalar *= tfactor;
@ -191,6 +208,11 @@ void ComputeTempRamp::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -223,17 +245,90 @@ void ComputeTempRamp::compute_vector()
t[5] += massone * vthermal[1]*vthermal[2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
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];
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRamp::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxbias) {
memory->destroy_2d_double_array(vbiasall);
maxbias = atom->nmax;
vbiasall = memory->create_2d_double_array(maxbias,3,
"compute/temp:vbiasall");
}
double fraction;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
fraction = (atom->x[i][coord_dim] - coord_lo) / (coord_hi - coord_lo);
fraction = MAX(fraction,0.0);
fraction = MIN(fraction,1.0);
vbiasall[i][v_dim] = v_lo + fraction*(v_hi - v_lo);
v[i][v_dim] -= vbiasall[i][v_dim];
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRamp::restore_bias(double *v)
{
v[v_dim] += vbias[v_dim];
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempRamp::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit)
v[i][v_dim] += vbiasall[i][v_dim];
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */
double ComputeTempRamp::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}

10
src/compute_temp_ramp.h
View File

@ -25,7 +25,12 @@ class ComputeTempRamp : public Compute {
void init();
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
double memory_usage();
private:
int coord_dim;
@ -35,6 +40,11 @@ class ComputeTempRamp : public Compute {
int scaleflag,fix_dof;
double tfactor,xscale,yscale,zscale;
double vbias[3]; // stored velocity bias for one atom
double **vbiasall; // stored velocity bias for all atoms
int maxbias; // size of vbiasall array
Compute *tbias; // ptr to additional bias compute
void recount();
};

108
src/compute_temp_region.cpp
View File

@ -16,8 +16,10 @@
#include "compute_temp_region.h"
#include "atom.h"
#include "force.h"
#include "modify.h"
#include "domain.h"
#include "region.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
@ -42,6 +44,8 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
tempflag = 1;
tempbias = 1;
maxbias = 0;
vbiasall = NULL;
vector = new double[6];
}
@ -49,6 +53,7 @@ ComputeTempRegion::ComputeTempRegion(LAMMPS *lmp, int narg, char **arg) :
ComputeTempRegion::~ComputeTempRegion()
{
memory->destroy_2d_double_array(vbiasall);
delete [] vector;
}
@ -57,6 +62,12 @@ ComputeTempRegion::~ComputeTempRegion()
void ComputeTempRegion::init()
{
dof = 0;
if (id_bias) {
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
}
}
/* ---------------------------------------------------------------------- */
@ -65,6 +76,12 @@ double ComputeTempRegion::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -93,6 +110,8 @@ double ComputeTempRegion::compute_scalar()
}
}
if (tbias) tbias->restore_bias_all();
double tarray[2],tarray_all[2];
tarray[0] = count;
tarray[1] = t;
@ -111,6 +130,11 @@ void ComputeTempRegion::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **x = atom->x;
double **v = atom->v;
double *mass = atom->mass;
@ -135,14 +159,20 @@ void ComputeTempRegion::compute_vector()
t[5] += massone * v[i][1]*v[i][2];
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ---------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
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]))
@ -154,3 +184,79 @@ void ComputeTempRegion::remove_bias(int i, double *v)
v[0] = v[1] = v[2] = 0.0;
}
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempRegion::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
if (nlocal > maxbias) {
memory->destroy_2d_double_array(vbiasall);
maxbias = atom->nmax;
vbiasall = memory->create_2d_double_array(maxbias,3,
"compute/temp:vbiasall");
}
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]))
vbiasall[i][0] = vbiasall[i][1] = vbiasall[i][2] = 0.0;
else {
vbiasall[i][0] = v[i][0];
vbiasall[i][1] = v[i][1];
vbiasall[i][2] = v[i][2];
v[i][0] = v[i][1] = v[i][2] = 0.0;
}
}
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempRegion::restore_bias(double *v)
{
v[0] += vbias[0];
v[1] += vbias[1];
v[2] += vbias[2];
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempRegion::restore_bias_all()
{
double **v = atom->v;
int *mask = atom->mask;
int nlocal = atom->nlocal;
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) {
v[i][0] += vbiasall[i][0];
v[i][1] += vbiasall[i][1];
v[i][2] += vbiasall[i][2];
}
if (tbias) tbias->restore_bias_all();
}
/* ---------------------------------------------------------------------- */
double ComputeTempRegion::memory_usage()
{
double bytes = maxbias * sizeof(double);
return bytes;
}

10
src/compute_temp_region.h
View File

@ -25,10 +25,20 @@ class ComputeTempRegion : public Compute {
void init();
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
double memory_usage();
private:
int iregion;
double vbias[3]; // stored velocity bias for one atom
double **vbiasall; // stored velocity bias for all atoms
int maxbias; // size of vbiasall array
Compute *tbias; // ptr to additional bias compute
};
}

61
src/compute_temp_sphere.cpp
View File

@ -62,6 +62,13 @@ void ComputeTempSphere::init()
fix_dof += modify->fix[i]->dof(igroup);
recount();
if (id_bias) {
tempbias = 1;
int i = modify->find_compute(id_bias);
if (i < 0) error->all("Could not find compute ID for temperature bias");
tbias = modify->compute[i];
} else tempbias = 0;
if (atom->mass) {
double *mass = atom->mass;
double **shape = atom->shape;
@ -92,6 +99,12 @@ double ComputeTempSphere::compute_scalar()
{
invoked |= INVOKED_SCALAR;
if (tbias) {
if (!(tbias->invoked & INVOKED_SCALAR))
double tmp = tbias->compute_scalar();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *mass = atom->mass;
@ -120,6 +133,8 @@ double ComputeTempSphere::compute_scalar()
}
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
if (dynamic) recount();
scalar *= tfactor;
@ -134,6 +149,11 @@ void ComputeTempSphere::compute_vector()
invoked |= INVOKED_VECTOR;
if (tbias) {
if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector();
tbias->remove_bias_all();
}
double **v = atom->v;
double **omega = atom->omega;
double *mass = atom->mass;
@ -186,6 +206,47 @@ void ComputeTempSphere::compute_vector()
}
}
if (tbias) tbias->restore_bias_all();
MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world);
for (i = 0; i < 6; i++) vector[i] *= force->mvv2e;
}
/* ----------------------------------------------------------------------
remove velocity bias from atom I to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempSphere::remove_bias(int i, double *v)
{
if (tbias) tbias->remove_bias(i,v);
}
/* ----------------------------------------------------------------------
remove velocity bias from all atoms to leave thermal velocity
------------------------------------------------------------------------- */
void ComputeTempSphere::remove_bias_all()
{
if (tbias) tbias->remove_bias_all();
}
/* ----------------------------------------------------------------------
add back in velocity bias to atom I removed by remove_bias()
assume remove_bias() was previously called
------------------------------------------------------------------------- */
void ComputeTempSphere::restore_bias(double *v)
{
if (tbias) tbias->restore_bias(v);
}
/* ----------------------------------------------------------------------
add back in velocity bias to all atoms removed by remove_bias_all()
assume remove_bias_all() was previously called
------------------------------------------------------------------------- */
void ComputeTempSphere::restore_bias_all()
{
if (tbias) tbias->restore_bias_all();
}

7
src/compute_temp_sphere.h
View File

@ -26,11 +26,18 @@ class ComputeTempSphere : public Compute {
double compute_scalar();
void compute_vector();
void remove_bias(int, double *);
void remove_bias_all();
void restore_bias(double *);
void restore_bias_all();
private:
int fix_dof;
double tfactor;
double *inertia;
Compute *tbias; // ptr to additional bias compute
void recount();
};

8
src/style_asphere.h
View File

@ -25,7 +25,7 @@ AtomStyle(ellipsoid,AtomVecEllipsoid)
#endif
#ifdef ComputeClass
ComputeStyle(erotate/asphere,ComputeERotateASphere)
ComputeStyle(erotate/asphere,ComputeERotateAsphere)
ComputeStyle(temp/asphere,ComputeTempAsphere)
#endif
@ -36,9 +36,9 @@ ComputeStyle(temp/asphere,ComputeTempAsphere)
#endif
#ifdef FixClass
FixStyle(nve/asphere,FixNVEASphere)
FixStyle(nvt/asphere,FixNVTASphere)
FixStyle(npt/asphere,FixNPTASphere)
FixStyle(nve/asphere,FixNVEAsphere)
FixStyle(nvt/asphere,FixNVTAsphere)
FixStyle(npt/asphere,FixNPTAsphere)
#endif
#ifdef PairInclude