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changes to files with THERMO_ENERGY mask in standard packages

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This commit is contained in:
Plimpton
2021-01-21 13:56:50 -07:00
parent dbb923e1b2
commit b5525a19bc
16 changed files with 30 additions and 66 deletions
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11
src/LATTE/fix_latte.cpp
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@ -70,8 +70,9 @@ FixLatte::FixLatte(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
virial_flag = 1;
thermo_virial = 1;
energy_global_flag = 1;
virial_global_flag = 1;
thermo_energy = thermo_virial = 1;
// store ID of compute pe/atom used to generate Coulomb potential for LATTE
// null pointer means LATTE will compute Coulombic potential
@ -117,12 +118,9 @@ FixLatte::~FixLatte()
int FixLatte::setmask()
{
int mask = 0;
//mask |= INITIAL_INTEGRATE;
//mask |= FINAL_INTEGRATE;
mask |= PRE_REVERSE;
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
return mask;
}
@ -267,9 +265,6 @@ void FixLatte::post_force(int vflag)
// hardwire these unsupported flags for now
int coulombflag = 0;
// pe_peratom = 0;
// virial_global = 1; // set via vflag_global at some point
// virial_peratom = 0;
neighflag = 0;
// set flags used by LATTE

4
src/MC/fix_gcmc.cpp
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@ -2334,9 +2334,9 @@ double FixGCMC::energy_full()
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
// NOTE: all fixes with THERMO_ENERGY mask set and which
// NOTE: all fixes with energy_global_flag set and which
// operate at pre_force() or post_force() or end_of_step()
// and which user has enable via fix_modify thermo yes,
// and which user has enabled via fix_modify energy yes,
// will contribute to total MC energy via pe->compute_scalar()
update->eflag_global = update->ntimestep;

4
src/MC/fix_widom.cpp
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@ -1061,9 +1061,9 @@ double FixWidom::energy_full()
if (modify->n_pre_force) modify->pre_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
// NOTE: all fixes with THERMO_ENERGY mask set and which
// NOTE: all fixes with energy_global_flag set and which
// operate at pre_force() or post_force() or end_of_step()
// and which user has enable via fix_modify thermo yes,
// and which user has enabled via fix_modify energy yes,
// will contribute to total MC energy via pe->compute_scalar()
update->eflag_global = update->ntimestep;

8
src/MESSAGE/fix_client_md.cpp
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@ -42,7 +42,8 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
{
if (lmp->clientserver != 1)
error->all(FLERR,"Fix client/md requires LAMMPS be running as a client");
if (atom->map_style == Atom::MAP_NONE) error->all(FLERR,"Fix client/md requires atom map");
if (atom->map_style == Atom::MAP_NONE)
error->all(FLERR,"Fix client/md requires atom map");
if (sizeof(tagint) != 4)
error->all(FLERR,"Fix client/md only supports 32-bit atom IDs");
@ -54,8 +55,8 @@ FixClientMD::FixClientMD(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
virial_flag = 1;
thermo_virial = 1;
energy_global_flag = virial_global_flag = 1;
thermo_energy = thermo_virial = 1;
inv_nprocs = 1.0 / comm->nprocs;
if (domain->dimension == 2)
@ -89,7 +90,6 @@ int FixClientMD::setmask()
int mask = 0;
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
return mask;
}

2
src/MISC/fix_efield.cpp
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@ -49,6 +49,7 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
vector_flag = 1;
scalar_flag = 1;
size_vector = 3;
energy_global_flag = 1;
global_freq = 1;
extvector = 1;
extscalar = 1;
@ -138,7 +139,6 @@ FixEfield::~FixEfield()
int FixEfield::setmask()
{
int mask = 0;
mask |= THERMO_ENERGY;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;

3
src/MISC/fix_orient_bcc.cpp
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@ -67,7 +67,7 @@ FixOrientBCC::FixOrientBCC(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
energy_global_flag = 1;
peratom_flag = 1;
size_peratom_cols = 2;
peratom_freq = 1;
@ -202,7 +202,6 @@ int FixOrientBCC::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}

3
src/MISC/fix_orient_fcc.cpp
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@ -65,7 +65,7 @@ FixOrientFCC::FixOrientFCC(LAMMPS *lmp, int narg, char **arg) :
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
energy_global_flag = 1;
peratom_flag = 1;
size_peratom_cols = 2;
peratom_freq = 1;
@ -200,7 +200,6 @@ int FixOrientFCC::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}

7
src/MOLECULE/fix_cmap.cpp
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@ -70,10 +70,10 @@ FixCMAP::FixCMAP(LAMMPS *lmp, int narg, char **arg) :
restart_global = 1;
restart_peratom = 1;
peatom_flag = 1;
virial_flag = 1;
energy_global_flag = energy_peratom_flag = 1;
virial_global_flag = virial_peratom_flag = 1;
thermo_energy = thermo_virial = 1;
centroidstressflag = CENTROID_NOTAVAIL;
thermo_virial = 1;
peratom_freq = 1;
scalar_flag = 1;
global_freq = 1;
@ -154,7 +154,6 @@ int FixCMAP::setmask()
mask |= PRE_NEIGHBOR;
mask |= PRE_REVERSE;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
mask |= MIN_POST_FORCE;
return mask;

2
src/REPLICA/fix_hyper_global.cpp
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@ -50,6 +50,7 @@ FixHyperGlobal::FixHyperGlobal(LAMMPS *lmp, int narg, char **arg) :
hyperflag = 1;
scalar_flag = 1;
energy_global_flag = 1;
vector_flag = 1;
size_vector = 12;
global_freq = 1;
@ -104,7 +105,6 @@ int FixHyperGlobal::setmask()
int mask = 0;
mask |= PRE_NEIGHBOR;
mask |= PRE_REVERSE;
mask |= THERMO_ENERGY;
return mask;
}

3
src/REPLICA/fix_hyper_local.cpp
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@ -31,7 +31,6 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -63,6 +62,7 @@ FixHyperLocal::FixHyperLocal(LAMMPS *lmp, int narg, char **arg) :
hyperflag = 2;
scalar_flag = 1;
energy_global_flag = 1;
vector_flag = 1;
size_vector = 26;
//size_vector = 28; // can add 2 for debugging
@ -237,7 +237,6 @@ int FixHyperLocal::setmask()
mask |= PRE_NEIGHBOR;
mask |= PRE_REVERSE;
mask |= MIN_PRE_NEIGHBOR;
mask |= THERMO_ENERGY;
return mask;
}

4
src/RIGID/fix_rigid_nh.cpp
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@ -49,6 +49,8 @@ FixRigidNH::FixRigidNH(LAMMPS *lmp, int narg, char **arg) :
eta_dot_b(nullptr), f_eta_b(nullptr), rfix(nullptr), id_temp(nullptr),
id_press(nullptr), temperature(nullptr), pressure(nullptr)
{
if (tstat_flag || pstat_flag) ecouple_flag = 1;
// error checks: could be moved up to FixRigid
if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||
@ -186,8 +188,6 @@ int FixRigidNH::setmask()
{
int mask = 0;
mask = FixRigid::setmask();
if (tstat_flag || pstat_flag) mask |= THERMO_ENERGY;
return mask;
}

4
src/RIGID/fix_rigid_nh_small.cpp
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@ -51,6 +51,8 @@ FixRigidNHSmall::FixRigidNHSmall(LAMMPS *lmp, int narg, char **arg) :
f_eta_b(nullptr), rfix(nullptr), id_temp(nullptr), id_press(nullptr),
temperature(nullptr), pressure(nullptr)
{
if (tstat_flag || pstat_flag) ecouple_flag = 1;
// error checks
if ((p_flag[0] == 1 && p_period[0] <= 0.0) ||
@ -199,8 +201,6 @@ int FixRigidNHSmall::setmask()
{
int mask = 0;
mask = FixRigidSmall::setmask();
if (tstat_flag || pstat_flag) mask |= THERMO_ENERGY;
return mask;
}

4
src/SHOCK/fix_msst.cpp
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@ -33,8 +33,6 @@
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace FixConst;
@ -55,6 +53,7 @@ FixMSST::FixMSST(LAMMPS *lmp, int narg, char **arg) :
global_freq = 1;
extscalar = 1;
extvector = 0;
ecouple_flag = 1;
// set defaults
@ -238,7 +237,6 @@ int FixMSST::setmask()
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
mask |= THERMO_ENERGY;
return mask;
}

23
src/SPIN/fix_langevin_spin.cpp
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@ -35,7 +35,6 @@
#include "respa.h"
#include "update.h"
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
@ -47,12 +46,6 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
{
if (narg != 6) error->all(FLERR,"Illegal langevin/spin command");
dynamic_group_allow = 1;
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
nevery = 1;
temp = utils::numeric(FLERR,arg[3],false,lmp);
alpha_t = utils::numeric(FLERR,arg[4],false,lmp);
seed = utils::inumeric(FLERR,arg[5],false,lmp);
@ -77,7 +70,6 @@ FixLangevinSpin::FixLangevinSpin(LAMMPS *lmp, int narg, char **arg) :
// random = new RanPark(lmp,seed + comm->me);
random = new RanMars(lmp,seed + comm->me);
}
/* ---------------------------------------------------------------------- */
@ -92,10 +84,6 @@ FixLangevinSpin::~FixLangevinSpin()
int FixLangevinSpin::setmask()
{
int mask = 0;
mask |= POST_FORCE;
mask |= POST_FORCE_RESPA;
mask |= END_OF_STEP;
mask |= THERMO_ENERGY;
return mask;
}
@ -156,7 +144,6 @@ void FixLangevinSpin::add_tdamping(double spi[3], double fmi[3])
void FixLangevinSpin::add_temperature(double fmi[3])
{
// double rx = sigma*(2.0*random->uniform() - 1.0);
// double ry = sigma*(2.0*random->uniform() - 1.0);
// double rz = sigma*(2.0*random->uniform() - 1.0);
@ -175,14 +162,4 @@ void FixLangevinSpin::add_temperature(double fmi[3])
fmi[0] *= gil_factor;
fmi[1] *= gil_factor;
fmi[2] *= gil_factor;
}
/* ---------------------------------------------------------------------- */
void FixLangevinSpin::post_force_respa(int vflag, int ilevel, int /*iloop*/)
{
if (ilevel == nlevels_respa-1) post_force(vflag);
}

7
src/SPIN/fix_precession_spin.cpp
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@ -44,7 +44,8 @@ enum{CONSTANT,EQUAL};
/* ---------------------------------------------------------------------- */
FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), emag(nullptr)
FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), emag(nullptr)
{
if (narg < 7) error->all(FLERR,"Illegal precession/spin command");
@ -56,6 +57,7 @@ FixPrecessionSpin::FixPrecessionSpin(LAMMPS *lmp, int narg, char **arg) : Fix(lm
scalar_flag = 1;
global_freq = 1;
extscalar = 1;
energy_global_flag = 1;
respa_level_support = 1;
ilevel_respa = 0;
@ -165,12 +167,10 @@ int FixPrecessionSpin::setmask()
int mask = 0;
mask |= POST_FORCE;
mask |= MIN_POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixPrecessionSpin::init()
@ -245,7 +245,6 @@ void FixPrecessionSpin::min_setup(int vflag)
void FixPrecessionSpin::post_force(int /* vflag */)
{
// update mag field with time (potential improvement)
if (varflag != CONSTANT) {

7
src/USER-MISC/fix_orient_eco.cpp
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@ -65,21 +65,20 @@ FixOrientECO::FixOrientECO(LAMMPS *lmp, int narg, char **arg) :
{
if (lmp->citeme) lmp->citeme->add(cite_fix_orient_eco);
// get rank of this processor
MPI_Comm_rank(world, &me);
// check for illegal command
if (narg != 7) error->all(FLERR, "Illegal fix orient/eco command");
// set fix flags
scalar_flag = 1; // computes scalar
global_freq = 1; // values can be computed at every timestep
extscalar = 1; // scalar scales with # of atoms
energy_global_flag = 1;
peratom_flag = 1; // quantities are per atom quantities
size_peratom_cols = 2; // # of per atom quantities
peratom_freq = 1; //
// parse input parameters
u_0 = utils::numeric(FLERR, arg[3],false,lmp);
sign = (u_0 >= 0.0 ? 1 : -1);
eta = utils::numeric(FLERR, arg[4],false,lmp);
@ -87,6 +86,7 @@ FixOrientECO::FixOrientECO(LAMMPS *lmp, int narg, char **arg) :
// read reference orientations from file
// work on rank 0 only
int n = strlen(arg[6]) + 1;
dir_filename = new char[n];
strcpy(dir_filename, arg[6]);
@ -151,7 +151,6 @@ FixOrientECO::~FixOrientECO() {
int FixOrientECO::setmask() {
int mask = 0;
mask |= POST_FORCE;
mask |= THERMO_ENERGY;
mask |= POST_FORCE_RESPA;
return mask;
}