From 2e8b9cf4b48e44fce11d3d2d6836cbde3f2ee61d Mon Sep 17 00:00:00 2001 From: sjplimp Date: Fri, 21 Mar 2008 00:14:38 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1656 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- src/ASPHERE/compute_temp_asphere.cpp | 88 +++++++++++++------------- src/ASPHERE/compute_temp_asphere.h | 4 +- src/compute.cpp | 18 ------ src/compute.h | 6 +- src/compute_temp.cpp | 66 +------------------- src/compute_temp.h | 7 --- src/compute_temp_com.cpp | 51 +++------------ src/compute_temp_com.h | 3 +- src/compute_temp_deform.cpp | 64 +++++-------------- src/compute_temp_deform.h | 2 - src/compute_temp_partial.cpp | 83 +++++++------------------ src/compute_temp_partial.h | 4 +- src/compute_temp_ramp.cpp | 50 +++------------ src/compute_temp_ramp.h | 2 - src/compute_temp_region.cpp | 85 ++++++++----------------- src/compute_temp_region.h | 5 +- src/compute_temp_sphere.cpp | 93 ++++++++++++++++------------ src/compute_temp_sphere.h | 4 +- 18 files changed, 188 insertions(+), 447 deletions(-) diff --git a/src/ASPHERE/compute_temp_asphere.cpp b/src/ASPHERE/compute_temp_asphere.cpp index 5006b489d6..35c08ec50c 100755 --- a/src/ASPHERE/compute_temp_asphere.cpp +++ b/src/ASPHERE/compute_temp_asphere.cpp @@ -37,7 +37,8 @@ using namespace LAMMPS_NS; ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg != 3) error->all("Illegal compute temp command"); + if (narg != 3 || narg != 4) + error->all("Illegal compute temp/asphere command"); if (!atom->quat_flag || !atom->angmom_flag) error->all("Compute temp/asphere requires atom attributes quat, angmom"); @@ -48,6 +49,15 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) : extvector = 1; tempflag = 1; + tempbias = 0; + id_bias = NULL; + if (narg == 4) { + tempbias = 1; + int n = strlen(arg[3]) + 1; + id_bias = new char[n]; + strcpy(id_bias,arg[3]); + } + vector = new double[6]; inertia = memory->create_2d_double_array(atom->ntypes+1,3,"fix_temp_sphere:inertia"); @@ -57,6 +67,7 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) : ComputeTempAsphere::~ComputeTempAsphere() { + delete [] id_bias; delete [] vector; memory->destroy_2d_double_array(inertia); } @@ -65,20 +76,25 @@ ComputeTempAsphere::~ComputeTempAsphere() void ComputeTempAsphere::init() { + if (tempbias) { + int i = modify->find_compute(id_bias); + if (i < 0) error->all("Could not find compute ID for temperature bias"); + tbias = modify->compute[i]; + if (tbias->tempflag == 0) + error->all("Bias compute does not calculate temperature"); + if (tbias->tempbias == 0) + error->all("Bias compute does not calculate a velocity bias"); + if (tbias->igroup != igroup) + error->all("Bias compute group does not match compute group"); + tbias->init(); + if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2; + } + fix_dof = 0; for (int i = 0; i < modify->nfix; i++) fix_dof += modify->fix[i]->dof(igroup); dof_compute(); - tempbias = 0; - tbias = NULL; - 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]; - } - calculate_inertia(); } @@ -89,10 +105,10 @@ 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 + if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms; + + // rotational degrees of freedom // 0 for sphere, 2 for uniaxial, 3 for biaxial double **shape = atom->shape; @@ -101,27 +117,30 @@ void ComputeTempAsphere::dof_compute() int nlocal = atom->nlocal; int itype; - int rot_dof = 0; + int count = 0; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { + if (tempbias == 2 && tbias->dof_remove(i)) continue; itype = type[i]; if (dimension == 2) { if (shape[itype][0] == shape[itype][1]) continue; - else rot_dof += 1; + else count++; } else { if (shape[itype][0] == shape[itype][1] && shape[itype][1] == shape[itype][2]) continue; else if (shape[itype][0] == shape[itype][1] || shape[itype][1] == shape[itype][2] || - shape[itype][0] == shape[itype][2]) rot_dof += 2; - else rot_dof += 3; + shape[itype][0] == shape[itype][2]) count += 2; + else count += 3; } } - int rot_total; - MPI_Allreduce(&rot_dof,&rot_total,1,MPI_INT,MPI_SUM,world); - dof += rot_total; + int count_all; + MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world); + dof += count_all; + dof -= extra_dof + fix_dof; if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; } @@ -132,7 +151,7 @@ double ComputeTempAsphere::compute_scalar() { invoked |= INVOKED_SCALAR; - if (tbias) { + if (tempbias) { if (!(tbias->invoked & INVOKED_SCALAR)) double tmp = tbias->compute_scalar(); tbias->remove_bias_all(); @@ -179,10 +198,10 @@ double ComputeTempAsphere::compute_scalar() } } - if (tbias) tbias->restore_bias_all(); + if (tempbias) tbias->restore_bias_all(); MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world); - if (dynamic || tbias) dof_compute(); + if (dynamic || tempbias == 2) dof_compute(); scalar *= tfactor; return scalar; } @@ -195,7 +214,7 @@ void ComputeTempAsphere::compute_vector() invoked |= INVOKED_VECTOR; - if (tbias) { + if (tempbias) { if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector(); tbias->remove_bias_all(); } @@ -246,7 +265,7 @@ void ComputeTempAsphere::compute_vector() t[5] += inertia[itype][2]*wbody[1]*wbody[2]; } - if (tbias) tbias->restore_bias_all(); + if (tempbias) tbias->restore_bias_all(); MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world); for (i = 0; i < 6; i++) vector[i] *= force->mvv2e; @@ -280,15 +299,6 @@ 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 @@ -298,13 +308,3 @@ void ComputeTempAsphere::restore_bias(int i, double *v) { if (tbias) tbias->restore_bias(i,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(); -} diff --git a/src/ASPHERE/compute_temp_asphere.h b/src/ASPHERE/compute_temp_asphere.h index c8dbe84249..dc1c52107c 100755 --- a/src/ASPHERE/compute_temp_asphere.h +++ b/src/ASPHERE/compute_temp_asphere.h @@ -27,15 +27,13 @@ class ComputeTempAsphere : public Compute { void compute_vector(); void remove_bias(int, double *); - void remove_bias_all(); void restore_bias(int, double *); - void restore_bias_all(); private: int fix_dof; double tfactor; double **inertia; - + char *id_bias; Compute *tbias; // ptr to additional bias compute void dof_compute(); diff --git a/src/compute.cpp b/src/compute.cpp index 6a5c20e37a..3ba2a56a2f 100644 --- a/src/compute.cpp +++ b/src/compute.cpp @@ -62,9 +62,7 @@ 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; @@ -90,7 +88,6 @@ Compute::~Compute() { delete [] id; delete [] style; - delete [] id_bias; delete [] id_pre; memory->sfree(tlist); @@ -120,21 +117,6 @@ 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]); - 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"); } } diff --git a/src/compute.h b/src/compute.h index 63e042a50e..8eadb4a4e7 100644 --- a/src/compute.h +++ b/src/compute.h @@ -45,9 +45,7 @@ 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 Compute temp includes - // self or extra bias via compute_modify - char *id_bias; // ID of extra Compute temp that adds bias + int tempbias; // 0/1 if Compute temp includes self/extra bias char *id_pre; // ID of pre-compute the Compute may store @@ -77,7 +75,7 @@ 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 int dof_remove(int) {return 0;} virtual void remove_bias(int, double *) {} virtual void remove_bias_all() {} virtual void restore_bias(int, double *) {} diff --git a/src/compute_temp.cpp b/src/compute_temp.cpp index 0c898cc2fb..263eb39fa0 100644 --- a/src/compute_temp.cpp +++ b/src/compute_temp.cpp @@ -38,6 +38,7 @@ ComputeTemp::ComputeTemp(LAMMPS *lmp, int narg, char **arg) : extscalar = 0; extvector = 1; tempflag = 1; + tempbias = 0; vector = new double[6]; } @@ -57,15 +58,6 @@ void ComputeTemp::init() for (int i = 0; i < modify->nfix; i++) fix_dof += modify->fix[i]->dof(igroup); dof_compute(); - - tempbias = 0; - tbias = NULL; - 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]; - } } /* ---------------------------------------------------------------------- */ @@ -74,7 +66,6 @@ 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 > 0.0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; @@ -86,12 +77,6 @@ double ComputeTemp::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; @@ -112,10 +97,8 @@ 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 || tbias) dof_compute(); + if (dynamic) dof_compute(); scalar *= tfactor; return scalar; } @@ -128,11 +111,6 @@ 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; @@ -155,46 +133,6 @@ 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(int i, double *v) -{ - if (tbias) tbias->restore_bias(i,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(); -} diff --git a/src/compute_temp.h b/src/compute_temp.h index 763fa534e3..eeae8479f5 100644 --- a/src/compute_temp.h +++ b/src/compute_temp.h @@ -26,17 +26,10 @@ class ComputeTemp : public Compute { double compute_scalar(); void compute_vector(); - void remove_bias(int, double *); - void remove_bias_all(); - void restore_bias(int, double *); - void restore_bias_all(); - private: int fix_dof; double tfactor; - Compute *tbias; // ptr to additional bias compute - void dof_compute(); }; diff --git a/src/compute_temp_com.cpp b/src/compute_temp_com.cpp index ac89291bee..9891421a74 100644 --- a/src/compute_temp_com.cpp +++ b/src/compute_temp_com.cpp @@ -64,14 +64,8 @@ void ComputeTempCOM::init() for (int i = 0; i < modify->nfix; i++) fix_dof += modify->fix[i]->dof(igroup); dof_compute(); - masstotal = group->mass(igroup); - tbias = NULL; - 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]; - } + masstotal = group->mass(igroup); } /* ---------------------------------------------------------------------- */ @@ -79,8 +73,8 @@ void ComputeTempCOM::init() void ComputeTempCOM::dof_compute() { double natoms = group->count(igroup); - dof = domain->dimension * natoms; - if (tbias) dof -= tbias->dof_remove(natoms); + int nper = domain->dimension; + dof = nper * natoms; dof -= extra_dof + fix_dof; if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; @@ -94,12 +88,6 @@ 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); @@ -124,10 +112,8 @@ 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 || tbias) dof_compute(); + if (dynamic) dof_compute(); scalar *= tfactor; return scalar; } @@ -141,11 +127,6 @@ 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); @@ -176,8 +157,6 @@ 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; } @@ -188,12 +167,9 @@ void ComputeTempCOM::compute_vector() void ComputeTempCOM::remove_bias(int i, double *v) { - if (tbias) tbias->remove_bias(i,v); - if (atom->mask[i] & groupbit) { - v[0] -= vbias[0]; - v[1] -= vbias[1]; - v[2] -= vbias[2]; - } + v[0] -= vbias[0]; + v[1] -= vbias[1]; + v[2] -= vbias[2]; } /* ---------------------------------------------------------------------- @@ -202,8 +178,6 @@ void ComputeTempCOM::remove_bias(int i, double *v) void ComputeTempCOM::remove_bias_all() { - if (tbias) tbias->remove_bias_all(); - double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -223,12 +197,9 @@ void ComputeTempCOM::remove_bias_all() void ComputeTempCOM::restore_bias(int i, double *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); + v[0] += vbias[0]; + v[1] += vbias[1]; + v[2] += vbias[2]; } /* ---------------------------------------------------------------------- @@ -248,6 +219,4 @@ void ComputeTempCOM::restore_bias_all() v[i][1] += vbias[1]; v[i][2] += vbias[2]; } - - if (tbias) tbias->restore_bias_all(); } diff --git a/src/compute_temp_com.h b/src/compute_temp_com.h index c289d29b79..3c64875822 100644 --- a/src/compute_temp_com.h +++ b/src/compute_temp_com.h @@ -34,11 +34,10 @@ class ComputeTempCOM : public Compute { private: int fix_dof; double tfactor,masstotal; - double vbias[3]; // stored velocity bias for one atom - Compute *tbias; // ptr to additional bias compute void dof_compute(); + }; } diff --git a/src/compute_temp_deform.cpp b/src/compute_temp_deform.cpp index e9d7f5dd6f..ad496ee13c 100644 --- a/src/compute_temp_deform.cpp +++ b/src/compute_temp_deform.cpp @@ -73,13 +73,6 @@ void ComputeTempDeform::init() fix_dof += modify->fix[i]->dof(igroup); dof_compute(); - tbias = NULL; - 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++) @@ -99,7 +92,6 @@ 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; @@ -113,12 +105,6 @@ 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; @@ -154,10 +140,8 @@ double ComputeTempDeform::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 || tbias) dof_compute(); + if (dynamic) dof_compute(); scalar *= tfactor; return scalar; } @@ -170,11 +154,6 @@ 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; @@ -210,8 +189,6 @@ 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; } @@ -222,22 +199,18 @@ void ComputeTempDeform::compute_vector() void ComputeTempDeform::remove_bias(int i, double *v) { - if (tbias) tbias->remove_bias(i,v); - - if (atom->mask[i] & groupbit) { - double lamda[3]; - double *h_rate = domain->h_rate; - double *h_ratelo = domain->h_ratelo; + 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]; - } + 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]; } /* ---------------------------------------------------------------------- @@ -246,8 +219,6 @@ void ComputeTempDeform::remove_bias(int i, double *v) void ComputeTempDeform::remove_bias_all() { - if (tbias) tbias->remove_bias_all(); - double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -283,12 +254,9 @@ void ComputeTempDeform::remove_bias_all() void ComputeTempDeform::restore_bias(int i, double *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); + v[0] += vbias[0]; + v[1] += vbias[1]; + v[2] += vbias[2]; } /* ---------------------------------------------------------------------- @@ -308,8 +276,6 @@ void ComputeTempDeform::restore_bias_all() v[i][1] += vbiasall[i][1]; v[i][2] += vbiasall[i][2]; } - - if (tbias) tbias->restore_bias_all(); } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_deform.h b/src/compute_temp_deform.h index a96e337e41..df904dc94c 100644 --- a/src/compute_temp_deform.h +++ b/src/compute_temp_deform.h @@ -35,11 +35,9 @@ class ComputeTempDeform : public Compute { 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 dof_compute(); }; diff --git a/src/compute_temp_partial.cpp b/src/compute_temp_partial.cpp index a4a11bdf5b..2e06bfcd90 100644 --- a/src/compute_temp_partial.cpp +++ b/src/compute_temp_partial.cpp @@ -67,13 +67,6 @@ void ComputeTempPartial::init() for (int i = 0; i < modify->nfix; i++) fix_dof += modify->fix[i]->dof(igroup); dof_compute(); - - tbias = NULL; - 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]; - } } /* ---------------------------------------------------------------------- */ @@ -81,8 +74,9 @@ void ComputeTempPartial::init() void ComputeTempPartial::dof_compute() { double natoms = group->count(igroup); - dof = (xflag+yflag+zflag) * natoms; - if (tbias) dof -= tbias->dof_remove(natoms); + int nper = xflag+yflag+zflag; + if (domain->dimension == 2) nper = xflag+yflag; + dof = nper * natoms; dof -= extra_dof + fix_dof; if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; @@ -90,14 +84,9 @@ void ComputeTempPartial::dof_compute() /* ---------------------------------------------------------------------- */ -double ComputeTempPartial::dof_remove(double &natoms) +int ComputeTempPartial::dof_remove(int i) { - 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; + return 0; } /* ---------------------------------------------------------------------- */ @@ -106,12 +95,6 @@ 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; @@ -133,10 +116,8 @@ 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 || tbias) dof_compute(); + if (dynamic) dof_compute(); scalar *= tfactor; return scalar; } @@ -149,11 +130,6 @@ 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; @@ -176,8 +152,6 @@ 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; } @@ -188,21 +162,17 @@ void ComputeTempPartial::compute_vector() void ComputeTempPartial::remove_bias(int i, double *v) { - if (tbias) tbias->remove_bias(i,v); - - 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; - } + 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; } } @@ -212,8 +182,6 @@ void ComputeTempPartial::remove_bias(int i, double *v) void ComputeTempPartial::remove_bias_all() { - if (tbias) tbias->remove_bias_all(); - double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -249,12 +217,9 @@ void ComputeTempPartial::remove_bias_all() void ComputeTempPartial::restore_bias(int i, double *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); + if (!xflag) v[0] += vbias[0]; + if (!yflag) v[1] += vbias[1]; + if (!zflag) v[2] += vbias[2]; } /* ---------------------------------------------------------------------- @@ -270,12 +235,10 @@ void ComputeTempPartial::restore_bias_all() 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 (!xflag) v[i][0] += vbiasall[i][0]; + if (!yflag) v[i][1] += vbiasall[i][1]; + if (!zflag) v[i][2] += vbiasall[i][2]; } - - if (tbias) tbias->restore_bias_all(); } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_partial.h b/src/compute_temp_partial.h index 12b4a7f12e..0505265ed8 100644 --- a/src/compute_temp_partial.h +++ b/src/compute_temp_partial.h @@ -26,7 +26,7 @@ class ComputeTempPartial : public Compute { double compute_scalar(); void compute_vector(); - double dof_remove(double &); + int dof_remove(int); void remove_bias(int, double *); void remove_bias_all(); void restore_bias(int, double *); @@ -37,11 +37,9 @@ class ComputeTempPartial : public Compute { 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 dof_compute(); }; diff --git a/src/compute_temp_ramp.cpp b/src/compute_temp_ramp.cpp index 68ae64f315..fe79202310 100644 --- a/src/compute_temp_ramp.cpp +++ b/src/compute_temp_ramp.cpp @@ -131,13 +131,6 @@ void ComputeTempRamp::init() for (int i = 0; i < modify->nfix; i++) fix_dof += modify->fix[i]->dof(igroup); dof_compute(); - - tbias = NULL; - 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]; - } } /* ---------------------------------------------------------------------- */ @@ -145,8 +138,8 @@ void ComputeTempRamp::init() void ComputeTempRamp::dof_compute() { double natoms = group->count(igroup); - dof = domain->dimension * natoms; - if (tbias) dof -= tbias->dof_remove(natoms); + int nper = domain->dimension; + dof = nper * natoms; dof -= extra_dof + fix_dof; if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; @@ -160,12 +153,6 @@ 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; @@ -193,10 +180,8 @@ 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 || tbias) dof_compute(); + if (dynamic) dof_compute(); scalar *= tfactor; return scalar; } @@ -210,11 +195,6 @@ 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; @@ -247,8 +227,6 @@ 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; } @@ -259,16 +237,11 @@ void ComputeTempRamp::compute_vector() void ComputeTempRamp::remove_bias(int i, double *v) { - if (tbias) tbias->remove_bias(i,v); - - 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]; - } + 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]; } /* ---------------------------------------------------------------------- @@ -277,8 +250,6 @@ void ComputeTempRamp::remove_bias(int i, double *v) void ComputeTempRamp::remove_bias_all() { - if (tbias) tbias->remove_bias_all(); - double **v = atom->v; int *mask = atom->mask; int nlocal = atom->nlocal; @@ -308,8 +279,7 @@ void ComputeTempRamp::remove_bias_all() void ComputeTempRamp::restore_bias(int i, double *v) { - if (atom->mask[i] & groupbit) v[v_dim] += vbias[v_dim]; - if (tbias) tbias->restore_bias(i,v); + v[v_dim] += vbias[v_dim]; } /* ---------------------------------------------------------------------- @@ -326,8 +296,6 @@ void ComputeTempRamp::restore_bias_all() 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(); } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_ramp.h b/src/compute_temp_ramp.h index 4462638fc6..986ee09a34 100644 --- a/src/compute_temp_ramp.h +++ b/src/compute_temp_ramp.h @@ -39,11 +39,9 @@ class ComputeTempRamp : public Compute { double v_lo,v_hi; 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 dof_compute(); }; diff --git a/src/compute_temp_region.cpp b/src/compute_temp_region.cpp index fb01a8f7d2..69475e5bbc 100644 --- a/src/compute_temp_region.cpp +++ b/src/compute_temp_region.cpp @@ -61,25 +61,16 @@ ComputeTempRegion::~ComputeTempRegion() void ComputeTempRegion::init() { - dof = 0; - - tbias = NULL; - 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]; - } + dof = 0.0; } /* ---------------------------------------------------------------------- */ -double ComputeTempRegion::dof_remove(double &natoms) +int ComputeTempRegion::dof_remove(int i) { - double rmdof = 0.0; - if (tbias) rmdof = tbias->dof_remove(natoms); - natoms -= natoms_region; - rmdof += domain->dimension * natoms; - return rmdof; + double *x = atom->x[i]; + if (domain->regions[iregion]->match(x[0],x[1],x[2])) return 0; + return 1; } /* ---------------------------------------------------------------------- */ @@ -88,12 +79,6 @@ 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; @@ -102,34 +87,30 @@ double ComputeTempRegion::compute_scalar() int *mask = atom->mask; int nlocal = atom->nlocal; + Region *region = domain->regions[iregion]; int count = 0; double t = 0.0; if (mass) { for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit && - domain->regions[iregion]->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])) { count++; t += (v[i][0]*v[i][0] + v[i][1]*v[i][1] + v[i][2]*v[i][2]) * mass[type[i]]; } } else { for (int i = 0; i < nlocal; i++) - if (mask[i] & groupbit && - domain->regions[iregion]->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])) { count++; 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(); double tarray[2],tarray_all[2]; tarray[0] = count; tarray[1] = t; MPI_Allreduce(tarray,tarray_all,2,MPI_DOUBLE,MPI_SUM,world); - natoms_region = tarray_all[0]; - dof = domain->dimension * natoms_region - extra_dof; + dof = domain->dimension * tarray_all[0] - extra_dof; if (dof > 0) scalar = force->mvv2e * tarray_all[1] / (dof * force->boltz); else scalar = 0.0; return scalar; @@ -143,11 +124,6 @@ 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; @@ -156,12 +132,12 @@ void ComputeTempRegion::compute_vector() int *mask = atom->mask; int nlocal = atom->nlocal; + Region *region = domain->regions[iregion]; double massone,t[6]; for (i = 0; i < 6; i++) t[i] = 0.0; for (i = 0; i < nlocal; i++) - if (mask[i] & groupbit && - domain->regions[iregion]->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 (mass) massone = mass[type[i]]; else massone = rmass[i]; t[0] += massone * v[i][0]*v[i][0]; @@ -172,8 +148,6 @@ 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; } @@ -184,18 +158,14 @@ void ComputeTempRegion::compute_vector() void ComputeTempRegion::remove_bias(int i, double *v) { - if (tbias) tbias->remove_bias(i,v); - - 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; - } + 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; } } @@ -205,8 +175,6 @@ void ComputeTempRegion::remove_bias(int i, double *v) void ComputeTempRegion::remove_bias_all() { - if (tbias) tbias->remove_bias_all(); - double **x = atom->x; double **v = atom->v; int *mask = atom->mask; @@ -219,9 +187,11 @@ void ComputeTempRegion::remove_bias_all() "compute/temp:vbiasall"); } + Region *region = domain->regions[iregion]; + for (int i = 0; i < nlocal; i++) if (mask[i] & groupbit) { - if (domain->regions[iregion]->match(x[i][0],x[i][1],x[i][2])) + if (region->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]; @@ -239,12 +209,9 @@ void ComputeTempRegion::remove_bias_all() void ComputeTempRegion::restore_bias(int i, double *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); + v[0] += vbias[0]; + v[1] += vbias[1]; + v[2] += vbias[2]; } /* ---------------------------------------------------------------------- @@ -264,8 +231,6 @@ void ComputeTempRegion::restore_bias_all() v[i][1] += vbiasall[i][1]; v[i][2] += vbiasall[i][2]; } - - if (tbias) tbias->restore_bias_all(); } /* ---------------------------------------------------------------------- */ diff --git a/src/compute_temp_region.h b/src/compute_temp_region.h index 4f80ec9df7..7dc5087a64 100644 --- a/src/compute_temp_region.h +++ b/src/compute_temp_region.h @@ -26,7 +26,7 @@ class ComputeTempRegion : public Compute { double compute_scalar(); void compute_vector(); - double dof_remove(double &); + int dof_remove(int); void remove_bias(int, double *); void remove_bias_all(); void restore_bias(int, double *); @@ -35,12 +35,9 @@ 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 int maxbias; // size of vbiasall array - Compute *tbias; // ptr to additional bias compute }; } diff --git a/src/compute_temp_sphere.cpp b/src/compute_temp_sphere.cpp index 05eefdf775..fcbca34fae 100644 --- a/src/compute_temp_sphere.cpp +++ b/src/compute_temp_sphere.cpp @@ -12,6 +12,7 @@ ------------------------------------------------------------------------- */ #include "mpi.h" +#include "string.h" #include "compute_temp_sphere.h" #include "atom.h" #include "force.h" @@ -33,7 +34,8 @@ using namespace LAMMPS_NS; ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) : Compute(lmp, narg, arg) { - if (narg != 3) error->all("Illegal compute temp command"); + if (narg != 3 || narg != 4) + error->all("Illegal compute temp/sphere command"); scalar_flag = vector_flag = 1; size_vector = 6; @@ -41,6 +43,15 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) : extvector = 1; tempflag = 1; + tempbias = 0; + id_bias = NULL; + if (narg == 4) { + tempbias = 1; + int n = strlen(arg[3]) + 1; + id_bias = new char[n]; + strcpy(id_bias,arg[3]); + } + vector = new double[6]; inertia = new double[atom->ntypes+1]; } @@ -57,20 +68,26 @@ ComputeTempSphere::~ComputeTempSphere() void ComputeTempSphere::init() { + if (tempbias) { + int i = modify->find_compute(id_bias); + if (i < 0) error->all("Could not find compute ID for temperature bias"); + tbias = modify->compute[i]; + if (tbias->tempflag == 0) + error->all("Bias compute does not calculate temperature"); + if (tbias->tempbias == 0) + error->all("Bias compute does not calculate a velocity bias"); + if (tbias->igroup != igroup) + error->all("Bias compute group does not match compute group"); + tbias->init(); + if (strcmp(tbias->style,"temp/region") == 0) tempbias = 2; + else tempbias = 1; + } + fix_dof = 0; for (int i = 0; i < modify->nfix; i++) fix_dof += modify->fix[i]->dof(igroup); dof_compute(); - tempbias = 0; - tbias = NULL; - 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]; - } - if (atom->mass) { double *mass = atom->mass; double **shape = atom->shape; @@ -88,9 +105,25 @@ void ComputeTempSphere::init() 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); + int nper = 6; + if (domain->dimension == 2) nper = 3; + dof = nper * natoms; + + if (tempbias) { + if (tempbias == 1) dof -= tbias->dof_remove(-1) * natoms; + else { + int *mask = atom->mask; + int nlocal = atom->nlocal; + int count = 0; + for (int i = 0; i < nlocal; i++) + if (mask[i] & groupbit) + if (tbias->dof_remove(i)) count++; + int count_all; + MPI_Allreduce(&count,&count_all,1,MPI_INT,MPI_SUM,world); + dof -= nper * count_all; + } + } + dof -= extra_dof + fix_dof; if (dof > 0) tfactor = force->mvv2e / (dof * force->boltz); else tfactor = 0.0; @@ -102,7 +135,7 @@ double ComputeTempSphere::compute_scalar() { invoked |= INVOKED_SCALAR; - if (tbias) { + if (tempbias) { if (!(tbias->invoked & INVOKED_SCALAR)) double tmp = tbias->compute_scalar(); tbias->remove_bias_all(); @@ -136,10 +169,10 @@ double ComputeTempSphere::compute_scalar() } } - if (tbias) tbias->restore_bias_all(); + if (tempbias) tbias->restore_bias_all(); MPI_Allreduce(&t,&scalar,1,MPI_DOUBLE,MPI_SUM,world); - if (dynamic || tbias) dof_compute(); + if (dynamic || tempbias == 2) dof_compute(); scalar *= tfactor; return scalar; } @@ -152,7 +185,7 @@ void ComputeTempSphere::compute_vector() invoked |= INVOKED_VECTOR; - if (tbias) { + if (tempbias) { if (!(tbias->invoked & INVOKED_VECTOR)) tbias->compute_vector(); tbias->remove_bias_all(); } @@ -209,7 +242,7 @@ void ComputeTempSphere::compute_vector() } } - if (tbias) tbias->restore_bias_all(); + if (tempbias) tbias->restore_bias_all(); MPI_Allreduce(t,vector,6,MPI_DOUBLE,MPI_SUM,world); for (i = 0; i < 6; i++) vector[i] *= force->mvv2e; @@ -221,16 +254,7 @@ void ComputeTempSphere::compute_vector() 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(); + tbias->remove_bias(i,v); } /* ---------------------------------------------------------------------- @@ -240,16 +264,5 @@ void ComputeTempSphere::remove_bias_all() void ComputeTempSphere::restore_bias(int i, double *v) { - if (tbias) tbias->restore_bias(i,v); + tbias->restore_bias(i,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(); -} - diff --git a/src/compute_temp_sphere.h b/src/compute_temp_sphere.h index 09e2fd8faa..c294ddbf7f 100644 --- a/src/compute_temp_sphere.h +++ b/src/compute_temp_sphere.h @@ -27,15 +27,13 @@ class ComputeTempSphere : public Compute { void compute_vector(); void remove_bias(int, double *); - void remove_bias_all(); void restore_bias(int, double *); - void restore_bias_all(); private: int fix_dof; double tfactor; double *inertia; - + char *id_bias; Compute *tbias; // ptr to additional bias compute void dof_compute();