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more additions to USER atom styles and bug fixes

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This commit is contained in:
Steve Plimpton
2019-12-13 13:54:12 -07:00
parent 9af08f2d54
commit db6d272303
29 changed files with 218 additions and 1289 deletions
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5
src/GRANULAR/fix_pour.cpp
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@ -40,6 +40,7 @@ using namespace MathConst;
enum{ATOM,MOLECULE};
enum{ONE,RANGE,POLY};
enum{CONSTANT,EQUAL}; // same as FixGravity
#define EPSILON 0.001
#define SMALL 1.0e-10
@ -318,6 +319,10 @@ void FixPour::init()
if (ifix == -1)
error->all(FLERR,"No fix gravity defined for fix pour");
int varflag = ((FixGravity *) modify->fix[ifix])->varflag;
if (varflag != CONSTANT)
error->all(FLERR,"Fix gravity for fix pour must be constant");
double xgrav = ((FixGravity *) modify->fix[ifix])->xgrav;
double ygrav = ((FixGravity *) modify->fix[ifix])->ygrav;
double zgrav = ((FixGravity *) modify->fix[ifix])->zgrav;

22
src/MOLECULE/atom_vec_bond.cpp
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@ -60,6 +60,20 @@ AtomVecBond::~AtomVecBond()
delete [] bond_negative;
}
/* ----------------------------------------------------------------------
grow atom arrays
must set local copy of body ptr
needed in replicate when 2 atom classes exist and pack_restart() is called
------------------------------------------------------------------------- */
void AtomVecBond::grow(int n)
{
AtomVec::grow(n);
num_bond = atom->num_bond;
bond_type = atom->bond_type;
}
/* ----------------------------------------------------------------------
modify values for AtomVec::pack_restart() to pack
------------------------------------------------------------------------- */
@ -76,8 +90,8 @@ void AtomVecBond::pack_restart_pre(int ilocal)
// flip any negative types to positive and flag which ones
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
//int *num_bond = atom->num_bond;
//int **bond_type = atom->bond_type;
any_bond_negative = 0;
for (int m = 0; m < num_bond[ilocal]; m++) {
@ -98,8 +112,8 @@ void AtomVecBond::pack_restart_post(int ilocal)
// restore the flagged types to their negative values
if (any_bond_negative) {
int *num_bond = atom->num_bond;
int **bond_type = atom->bond_type;
//int *num_bond = atom->num_bond;
//int **bond_type = atom->bond_type;
for (int m = 0; m < num_bond[ilocal]; m++)
if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];
}

4
src/MOLECULE/atom_vec_bond.h
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@ -28,6 +28,7 @@ class AtomVecBond : public AtomVec {
public:
AtomVecBond(class LAMMPS *);
~AtomVecBond();
void grow(int);
void pack_restart_pre(int);
void pack_restart_post(int);
void unpack_restart_init(int);
@ -37,6 +38,9 @@ class AtomVecBond : public AtomVec {
int any_bond_negative;
int bond_per_atom;
int *bond_negative;
int *num_bond;
int **bond_type;
};
}

8
src/MOLECULE/atom_vec_full.cpp
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@ -128,7 +128,7 @@ void AtomVecFull::pack_restart_pre(int ilocal)
int *num_improper = atom->num_improper;
int **improper_type = atom->improper_type;
int any_bond_negative = 0;
any_bond_negative = 0;
for (int m = 0; m < num_bond[ilocal]; m++) {
if (bond_type[ilocal][m] < 0) {
bond_negative[m] = 1;
@ -137,7 +137,7 @@ void AtomVecFull::pack_restart_pre(int ilocal)
} else bond_negative[m] = 0;
}
int any_angle_negative = 0;
any_angle_negative = 0;
for (int m = 0; m < num_angle[ilocal]; m++) {
if (angle_type[ilocal][m] < 0) {
angle_negative[m] = 1;
@ -146,7 +146,7 @@ void AtomVecFull::pack_restart_pre(int ilocal)
} else angle_negative[m] = 0;
}
int any_dihedral_negative = 0;
any_dihedral_negative = 0;
for (int m = 0; m < num_dihedral[ilocal]; m++) {
if (dihedral_type[ilocal][m] < 0) {
dihedral_negative[m] = 1;
@ -155,7 +155,7 @@ void AtomVecFull::pack_restart_pre(int ilocal)
} else dihedral_negative[m] = 0;
}
int any_improper_negative = 0;
any_improper_negative = 0;
for (int m = 0; m < num_improper[ilocal]; m++) {
if (improper_type[ilocal][m] < 0) {
improper_negative[m] = 1;

8
src/MOLECULE/atom_vec_molecular.cpp
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@ -128,7 +128,7 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
int *num_improper = atom->num_improper;
int **improper_type = atom->improper_type;
int any_bond_negative = 0;
any_bond_negative = 0;
for (int m = 0; m < num_bond[ilocal]; m++) {
if (bond_type[ilocal][m] < 0) {
bond_negative[m] = 1;
@ -137,7 +137,7 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
} else bond_negative[m] = 0;
}
int any_angle_negative = 0;
any_angle_negative = 0;
for (int m = 0; m < num_angle[ilocal]; m++) {
if (angle_type[ilocal][m] < 0) {
angle_negative[m] = 1;
@ -146,7 +146,7 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
} else angle_negative[m] = 0;
}
int any_dihedral_negative = 0;
any_dihedral_negative = 0;
for (int m = 0; m < num_dihedral[ilocal]; m++) {
if (dihedral_type[ilocal][m] < 0) {
dihedral_negative[m] = 1;
@ -155,7 +155,7 @@ void AtomVecMolecular::pack_restart_pre(int ilocal)
} else dihedral_negative[m] = 0;
}
int any_improper_negative = 0;
any_improper_negative = 0;
for (int m = 0; m < num_improper[ilocal]; m++) {
if (improper_type[ilocal][m] < 0) {
improper_negative[m] = 1;

1124
src/USER-AWPMD/atom_vec_wavepacket.cpp
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File diff suppressed because it is too large Load Diff

75
src/USER-AWPMD/atom_vec_wavepacket.h
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@ -11,11 +11,6 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Ilya Valuev (JIHT RAS)
------------------------------------------------------------------------- */
#ifdef ATOM_CLASS
AtomStyle(wavepacket,AtomVecWavepacket)
@ -32,77 +27,11 @@ namespace LAMMPS_NS {
class AtomVecWavepacket : public AtomVec {
public:
AtomVecWavepacket(class LAMMPS *);
~AtomVecWavepacket() {}
void grow(int);
void grow_reset();
void copy(int, int, int);
void force_clear(int, size_t);
int pack_comm(int, int *, double *, int, int *);
int pack_comm_vel(int, int *, double *, int, int *);
int pack_comm_hybrid(int, int *, double *);
void unpack_comm(int, int, double *);
void unpack_comm_vel(int, int, double *);
int unpack_comm_hybrid(int, int, double *);
int pack_reverse(int, int, double *);
int pack_reverse_hybrid(int, int, double *);
void unpack_reverse(int, int *, double *);
int unpack_reverse_hybrid(int, int *, double *);
int pack_border(int, int *, double *, int, int *);
int pack_border_vel(int, int *, double *, int, int *);
int pack_border_hybrid(int, int *, double *);
void unpack_border(int, int, double *);
void unpack_border_vel(int, int, double *);
int unpack_border_hybrid(int, int, double *);
int pack_exchange(int, double *);
int unpack_exchange(double *);
int size_restart();
int pack_restart(int, double *);
int unpack_restart(double *);
void create_atom(int, double *);
void data_atom(double *, imageint, char **);
int data_atom_hybrid(int, char **);
void data_vel(int, char **);
int data_vel_hybrid(int, char **);
void pack_data(double **);
int pack_data_hybrid(int, double *);
void write_data(FILE *, int, double **);
int write_data_hybrid(FILE *, double *);
void pack_vel(double **);
int pack_vel_hybrid(int, double *);
void write_vel(FILE *, int, double **);
int write_vel_hybrid(FILE *, double *);
void create_atom_post(int);
void data_atom_post(int);
int property_atom(char *);
void pack_property_atom(int, double *, int, int);
bigint memory_usage();
private:
tagint *tag;
int *type,*mask;
imageint *image;
double **x,**v,**f;
///\en spin: -1 or 1 for electron, 0 for ion (compatible with eff)
int *spin;
///\en charge: must be specified in the corresponding units (-1 for electron in real units, eff compatible)
double *q;
///\en width of the wavepacket (compatible with eff)
double *eradius;
///\en width velocity for the wavepacket (compatible with eff)
double *ervel;
///\en (generalized) force on width (compatible with eff)
double *erforce;
// AWPMD- specific:
///\en electron tag: must be the same for the WPs belonging to the same electron
int *etag;
///\en wavepacket split coefficients: cre, cim, size is 2*N
double *cs;
///\en force on wavepacket split coefficients: re, im, size is 2*N
double *csforce;
///\en (generalized) force on velocity, size is 3*N
double *vforce;
///\en (generalized) force on radius velocity, size is N
double *ervelforce;
};
}

6
src/USER-AWPMD/fix_nve_awpmd.cpp
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@ -74,8 +74,6 @@ void FixNVEAwpmd::init()
void FixNVEAwpmd::initial_integrate(int /* vflag */)
{
// update v,vr and x,radius of atoms in group
double **x = atom->x;
@ -84,7 +82,7 @@ void FixNVEAwpmd::initial_integrate(int /* vflag */)
double *ervel = atom->ervel;
double **f = atom->f;
double *erforce = atom->erforce;
double *vforce=atom->vforce;
double **vforce=atom->vforce;
double *ervelforce=atom->ervelforce;
double *mass = atom->mass;
@ -101,7 +99,7 @@ void FixNVEAwpmd::initial_integrate(int /* vflag */)
double dtfm = dtf / mass[type[i]];
double dtfmr=dtfm;
for(int j=0;j<3;j++){
x[i][j] += dtv*vforce[3*i+j];
x[i][j] += dtv*vforce[i][j];
v[i][j] += dtfm*f[i][j];
}
eradius[i]+= dtv*ervelforce[i];

2
src/USER-DPD/atom_vec_dpd.cpp
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@ -47,7 +47,7 @@ AtomVecDPD::AtomVecDPD(LAMMPS *lmp) : AtomVec(lmp)
fields_restart = (char *) "dpdTheta uCond uMech uChem";
fields_create = (char *) "rho dpdTheta uCond uMech uChem uCG uCGnew duChem";
fields_data_atom = (char *) "id type dpdTheta x";
fields_data_vel = (char *) "id v omega";
fields_data_vel = (char *) "id v";
setup_fields();
}

3
src/USER-EFF/atom_vec_electron.cpp
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@ -44,8 +44,6 @@ AtomVecElectron::AtomVecElectron(LAMMPS *lmp) : AtomVec(lmp)
molecular = 0;
forceclearflag = 1;
atom->ecp_flag = 0;
atom->electron_flag = 1;
atom->q_flag = atom->spin_flag = atom->eradius_flag =
atom->ervel_flag = atom->erforce_flag = 1;
@ -99,7 +97,6 @@ void AtomVecElectron::create_atom_post(int ilocal)
void AtomVecElectron::data_atom_post(int ilocal)
{
atom->ervel[ilocal] = 0.0;
if (atom->spin[ilocal] == 3) atom->ecp_flag = 1;
}
/* ----------------------------------------------------------------------

27
src/USER-EFF/pair_eff_cut.cpp
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@ -801,7 +801,7 @@ void PairEffCut::settings(int narg, char **arg)
int atype;
int iarg = 1;
int ecp_found = 0;
ecp_found = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"limit/eradius") == 0) {
@ -821,17 +821,15 @@ void PairEffCut::settings(int narg, char **arg)
else if (strcmp(arg[iarg+1],"O") == 0) ecp_type[atype] = 8;
else if (strcmp(arg[iarg+1],"Al") == 0) ecp_type[atype] = 13;
else if (strcmp(arg[iarg+1],"Si") == 0) ecp_type[atype] = 14;
else error->all(FLERR, "Note: there are no default parameters for this atom ECP\n");
else error->all(FLERR, "No default parameters for this atom ECP\n");
iarg += 2;
ecp_found = 1;
}
} else error->all(FLERR,"Illegal pair style command");
}
}
if (!ecp_found && atom->ecp_flag)
error->all(FLERR,"Need to specify ECP type on pair_style command");
// Need to introduce 2 new constants w/out changing update.cpp
if (force->qqr2e==332.06371) { // i.e. Real units chosen
h2e = 627.509; // hartree->kcal/mol
hhmss2e = 175.72044219620075; // hartree->kcal/mol * (Bohr->Angstrom)^2
@ -872,9 +870,24 @@ void PairEffCut::init_style()
if (update->whichflag == 1) {
if (force->qqr2e == 332.06371 && update->dt == 1.0)
error->all(FLERR,"You must lower the default real units timestep for pEFF ");
error->all(FLERR,"Must lower the default real units timestep for pEFF ");
}
// check if any atom's spin = 3 and ECP type was not set
int *spin = atom->spin;
int nlocal = atom->nlocal;
int flag = 0;
for (int i = 0; i < nlocal; i++)
if (spin[i] == 3) flag = 1;
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall && !ecp_found)
error->all(FLERR,"Need to specify ECP type on pair_style command");
// need a half neigh list and optionally a granular history neigh list
neighbor->request(this,instance_me);

4
src/USER-EFF/pair_eff_cut.h
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@ -46,10 +46,12 @@ class PairEffCut : public Pair {
private:
int limit_eradius_flag, pressure_with_evirials_flag;
int ecp_found;
double cut_global;
double **cut;
int ecp_type[100];
double PAULI_CORE_A[100], PAULI_CORE_B[100], PAULI_CORE_C[100], PAULI_CORE_D[100], PAULI_CORE_E[100];
double PAULI_CORE_A[100],PAULI_CORE_B[100],PAULI_CORE_C[100];
double PAULI_CORE_D[100],PAULI_CORE_E[100];
double hhmss2e, h2e;
int nmax;

22
src/USER-MESO/atom_vec_edpd.cpp
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@ -41,16 +41,16 @@ AtomVecEDPD::AtomVecEDPD(LAMMPS *lmp) : AtomVec(lmp)
// order of fields in a string does not matter
// except: fields_data_atom & fields_data_vel must match data file
fields_grow = (char *) "edpd_cv edpd_temp edpd_flux vest";
fields_copy = (char *) "edpd_cv edpd_temp edpd_flux vest";
fields_comm = (char *) "edpd_temp vest";
fields_comm_vel = (char *) "edpd_temp vest";
fields_grow = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_copy = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_comm = (char *) "edpd_temp vest vest_temp";
fields_comm_vel = (char *) "edpd_temp vest vest_temp";
fields_reverse = (char *) "edpd_flux";
fields_border = (char *) "edpd_cv edpd_temp vest";
fields_border_vel = (char *) "edpd_cv edpd_temp vest";
fields_exchange = (char *) "edpd_cv edpd_temp vest";
fields_restart = (char * ) "edpd_cv edpd_temp vest";
fields_create = (char *) "edpd_cv edpd_temp edpd_flux vest";
fields_border = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_border_vel = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_exchange = (char *) "edpd_cv edpd_temp vest vest_temp";
fields_restart = (char * ) "edpd_cv edpd_temp vest vest_temp";
fields_create = (char *) "edpd_cv edpd_temp edpd_flux vest vest_temp";
fields_data_atom = (char *) "id type edpd_temp edpd_cv x";
fields_data_vel = (char *) "id v";
@ -85,7 +85,7 @@ void AtomVecEDPD::create_atom_post(int ilocal)
{
atom->edpd_temp[ilocal] = 1.0;
atom->edpd_cv[ilocal]= 1.0e5;
atom->vest[ilocal][3] = atom->edpd_temp[ilocal];
atom->vest_temp[ilocal] = atom->edpd_temp[ilocal];
}
/* ----------------------------------------------------------------------
@ -99,5 +99,5 @@ void AtomVecEDPD::data_atom_post(int ilocal)
atom->vest[ilocal][0] = 0.0;
atom->vest[ilocal][1] = 0.0;
atom->vest[ilocal][2] = 0.0;
atom->vest[ilocal][3] = atom->edpd_temp[ilocal];
atom->vest_temp[ilocal] = atom->edpd_temp[ilocal];
}

2
src/USER-MESO/atom_vec_tdpd.cpp
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@ -63,7 +63,7 @@ void AtomVecTDPD::process_args(int narg, char **arg)
cc_species = atom->cc_species;
atom->add_peratom_change_columns("cc",cc_species);
atom->add_peratom_change_columns("cc_species",cc_species);
atom->add_peratom_change_columns("cc_flux",cc_species);
// delay setting up of fields until now

6
src/USER-MESO/fix_mvv_edpd.cpp
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@ -88,6 +88,7 @@ void FixMvvEDPD::initial_integrate(int /*vflag*/)
double *edpd_flux = atom->edpd_flux;
double *edpd_cv = atom->edpd_cv;
double **vest = atom->vest;
double *vest_temp = atom->vest_temp;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
@ -105,7 +106,7 @@ void FixMvvEDPD::initial_integrate(int /*vflag*/)
vest[i][0] = v[i][0] + dtfm * f[i][0];
vest[i][1] = v[i][1] + dtfm * f[i][1];
vest[i][2] = v[i][2] + dtfm * f[i][2];
vest[i][3] = edpd_temp[i] + dtT * edpd_flux[i];
vest_temp[i] = edpd_temp[i] + dtT * edpd_flux[i];
x[i][0] += dtv * vest[i][0];
x[i][1] += dtv * vest[i][1];
@ -131,6 +132,7 @@ void FixMvvEDPD::final_integrate()
double *edpd_flux = atom->edpd_flux;
double *edpd_cv = atom->edpd_cv;
double **vest = atom->vest;
double *vest_temp = atom->vest_temp;
double *rmass = atom->rmass;
double *mass = atom->mass;
int *type = atom->type;
@ -148,7 +150,7 @@ void FixMvvEDPD::final_integrate()
v[i][0] = vest[i][0] + dtfm * f[i][0];
v[i][1] = vest[i][1] + dtfm * f[i][1];
v[i][2] = vest[i][2] + dtfm * f[i][2];
edpd_temp[i] = vest[i][3] + dtT * edpd_flux[i];
edpd_temp[i] = vest_temp[i] + dtT * edpd_flux[i];
}
}

4
src/USER-SMD/atom_vec_smd.cpp
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@ -63,7 +63,7 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp)
fields_grow = (char *)
"de vfrac rmass x0 radius contact_radius molecule "
"smd_data_9 e vest tlsph_stress "
"smd_data_9 e vest smd_stress "
"eff_plastic_strain eff_plastic_strain_rate damage";
fields_copy = (char *)
"vfrac rmass x0 radius contact_radius molecule e "
@ -91,7 +91,7 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp)
"eff_plastic_strain eff_plastic_strain_rate smd_data_9 smd_stress damage";
fields_data_atom = (char *)
"id type molecule vfrac rmass radius contact_radius x";
fields_data_vel = (char *) "id v vest";
fields_data_vel = (char *) "id v";
// set these array sizes based on defines

4
src/atom.cpp
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@ -566,6 +566,7 @@ void Atom::peratom_create()
add_peratom("edpd_cv",&edpd_cv,DOUBLE,0);
add_peratom("edpd_temp",&edpd_temp,DOUBLE,0);
add_peratom("vest_temp",&vest_temp,DOUBLE,0);
add_peratom("edpd_flux",&edpd_flux,DOUBLE,0,1); // set per-thread flag
add_peratom("cc",&cc,DOUBLE,1);
add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
@ -625,8 +626,11 @@ void Atom::add_peratom(const char *name, void *address,
void Atom::add_peratom_change_columns(const char *name, int cols)
{
int i;
for (int i = 0; i < nperatom; i++)
if (strcmp(name,peratom[i].name) == 0) peratom[i].cols = cols;
if (i == nperatom)
error->all(FLERR,"Could not find name of peratom array for column change");
}
/* ----------------------------------------------------------------------

5
src/atom.h
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@ -124,6 +124,7 @@ class Atom : protected Pointers {
double **cc,**cc_flux; // cc = chemical concentration
double *edpd_temp,*edpd_flux; // temperature and heat flux
double *vest_temp;
double *edpd_cv; // heat capacity
int cc_species;
@ -162,10 +163,6 @@ class Atom : protected Pointers {
int sp_flag;
// USER-EFF package
int ecp_flag;
// USER-SMD package
int smd_flag;

22
src/atom_vec.cpp
View File

@ -45,6 +45,7 @@ AtomVec::AtomVec(LAMMPS *lmp) : Pointers(lmp)
forceclearflag = 0;
maxexchange = 0;
bonus_flag = 0;
size_forward_bonus = size_border_bonus = 0;
kokkosable = 0;
@ -176,7 +177,7 @@ int AtomVec::grow_nmax_bonus(int nmax_bonus)
void AtomVec::grow(int n)
{
int i,datatype,cols,maxcols;
int datatype,cols,maxcols;
void *pdata,*plength;
if (n == 0) grow_nmax();
@ -193,7 +194,7 @@ void AtomVec::grow(int n)
v = memory->grow(atom->v,nmax,3,"atom:v");
f = memory->grow(atom->f,nmax*nthreads,3,"atom:f");
for (i = 0; i < ngrow; i++) {
for (int i = 0; i < ngrow; i++) {
pdata = mgrow.pdata[i];
datatype = mgrow.datatype[i];
cols = mgrow.cols[i];
@ -1375,15 +1376,15 @@ int AtomVec::size_restart()
if (nrestart) {
for (nn = 0; nn < nrestart; nn++) {
cols = mrestart.cols[i];
cols = mrestart.cols[nn];
if (cols == 0) n += nlocal;
else if (cols > 0) n += cols*nlocal;
else {
collength = mrestart.collength[nn];
plength = mrestart.plength[nn];
for (i = 0; i < nlocal; i++) {
if (collength) ncols = (*((int ***) plength))[nlocal][collength-1];
else ncols = (*((int **) plength))[nlocal];
if (collength) ncols = (*((int ***) plength))[i][collength-1];
else ncols = (*((int **) plength))[i];
n += ncols;
}
}
@ -1435,7 +1436,7 @@ int AtomVec::pack_restart(int i, double *buf)
if (cols == 0) {
double *vec = *((double **) pdata);
buf[m++] = vec[i];
} else if (ncols > 0) {
} else if (cols > 0) {
double **array = *((double ***) pdata);
for (mm = 0; mm < cols; mm++)
buf[m++] = array[i][mm];
@ -1469,7 +1470,7 @@ int AtomVec::pack_restart(int i, double *buf)
if (cols == 0) {
bigint *vec = *((bigint **) pdata);
buf[m++] = ubuf(vec[i]).d;
} else if (ncols > 0) {
} else if (cols > 0) {
bigint **array = *((bigint ***) pdata);
for (mm = 0; mm < cols; mm++)
buf[m++] = ubuf(array[i][mm]).d;
@ -1705,7 +1706,7 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values)
vec[nlocal] = utils::numeric(FLERR,values[ivalue++],true,lmp);
} else {
double **array = *((double ***) pdata);
if (array == atom->x) { // already set by coord arg
if (array == atom->x) { // x was already set by coord arg
ivalue += cols;
continue;
}
@ -1878,9 +1879,9 @@ void AtomVec::data_vel(int ilocal, char **values)
v[ilocal][1] = utils::numeric(FLERR,values[1],true,lmp);
v[ilocal][2] = utils::numeric(FLERR,values[2],true,lmp);
if (ndata_vel) {
if (ndata_vel > 2) {
int ivalue = 3;
for (n = 0; n < ndata_vel; n++) {
for (n = 2; n < ndata_vel; n++) {
pdata = mdata_vel.pdata[n];
datatype = mdata_vel.datatype[n];
cols = mdata_vel.cols[n];
@ -2434,6 +2435,7 @@ void AtomVec::setup_fields()
else size_data_atom += cols;
}
size_data_vel = 0;
for (n = 0; n < ndata_vel; n++) {
cols = mdata_vel.cols[n];

12
src/atom_vec.h
View File

@ -74,7 +74,7 @@ class AtomVec : protected Pointers {
virtual void force_clear(int, size_t) {}
void grow(int);
virtual void grow(int);
void copy(int, int, int);
virtual void copy_bonus(int, int, int) {}
@ -122,13 +122,11 @@ class AtomVec : protected Pointers {
void data_atom(double *, imageint, char **);
virtual void data_atom_post(int) {}
void data_atom_bonus(int, char **) {}
void data_body(int, int, int, int *, double *) {}
virtual void data_atom_bonus(int, char **) {}
virtual void data_body(int, int, int, int *, double *) {}
void pack_data(double **);
void write_data(FILE *, int, double **);
virtual void pack_data_pre(int) {}
virtual void pack_data_post(int) {}
@ -145,8 +143,8 @@ class AtomVec : protected Pointers {
int pack_improper(tagint **);
void write_improper(FILE *, int, tagint **, int);
int property_atom(char *) {return -1;}
void pack_property_atom(int, double *, int, int) {}
virtual int property_atom(char *) {return -1;}
virtual void pack_property_atom(int, double *, int, int) {}
bigint memory_usage();
virtual bigint memory_usage_bonus() {}

45
src/atom_vec_body.cpp
View File

@ -40,8 +40,8 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
// size_data_bonus is not used by Atom class for body style
size_forward_bonus = 4;
size_border_bonus = 9;
size_restart_bonus_one = 9;
size_border_bonus = 10;
size_restart_bonus_one = 10;
size_data_bonus = 0;
atom->body_flag = 1;
@ -72,11 +72,9 @@ AtomVecBody::AtomVecBody(LAMMPS *lmp) : AtomVec(lmp)
fields_border_vel = (char *) "radius rmass angmom";
fields_exchange = (char *) "radius rmass angmom";
fields_restart = (char *) "radius rmass angmom";
fields_create = (char *) "radius rmass angmom tri";
fields_create = (char *) "radius rmass angmom body";
fields_data_atom = (char *) "id type body rmass x";
fields_data_vel = (char *) "id v angmom";
setup_fields();
}
/* ---------------------------------------------------------------------- */
@ -127,6 +125,20 @@ void AtomVecBody::process_args(int narg, char **arg)
size_forward_bonus += bptr->size_forward;
size_border_bonus += bptr->size_border;
setup_fields();
}
/* ----------------------------------------------------------------------
grow atom arrays
must set local copy of body ptr
needed in replicate when 2 atom classes exist and pack_restart() is called
------------------------------------------------------------------------- */
void AtomVecBody::grow(int n)
{
AtomVec::grow(n);
body = atom->body;
}
/* ----------------------------------------------------------------------
@ -150,8 +162,6 @@ void AtomVecBody::grow_bonus()
void AtomVecBody::copy_bonus(int i, int j, int delflag)
{
int *body = atom->body;
// if deleting atom J via delflag and J has bonus data, then delete it
if (delflag && body[j] >= 0) {
@ -206,8 +216,6 @@ int AtomVecBody::pack_comm_bonus(int n, int *list, double *buf)
int i,j,m;
double *quat;
int *body = atom->body;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -231,8 +239,6 @@ void AtomVecBody::unpack_comm_bonus(int n, int first, double *buf)
int i,m,last;
double *quat;
int *body = atom->body;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -254,8 +260,6 @@ int AtomVecBody::pack_border_bonus(int n, int *list, double *buf)
int i,j,m;
double *quat,*inertia;
int *body = atom->body;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
@ -287,8 +291,6 @@ int AtomVecBody::unpack_border_bonus(int n, int first, double *buf)
int i,j,m,last;
double *quat,*inertia;
int *body = atom->body;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
@ -330,8 +332,6 @@ int AtomVecBody::pack_exchange_bonus(int i, double *buf)
{
int m = 0;
int *body = atom->body;
if (body[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -363,8 +363,6 @@ int AtomVecBody::unpack_exchange_bonus(int ilocal, double *buf)
{
int m = 0;
int *body = atom->body;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
else {
@ -408,8 +406,6 @@ int AtomVecBody::size_restart_bonus()
{
int i;
int *body = atom->body;
int n = 0;
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
@ -418,8 +414,7 @@ int AtomVecBody::size_restart_bonus()
if (intdoubleratio == 1) n += bonus[body[i]].ninteger;
else n += (bonus[body[i]].ninteger+1)/2;
n += bonus[body[i]].ndouble;
}
n++;
} else n++;
}
return n;
@ -435,8 +430,6 @@ int AtomVecBody::pack_restart_bonus(int i, double *buf)
{
int m = 0;
int *body = atom->body;
if (body[i] < 0) buf[m++] = ubuf(0).d;
else {
buf[m++] = ubuf(1).d;
@ -470,8 +463,6 @@ int AtomVecBody::unpack_restart_bonus(int ilocal, double *buf)
{
int m = 0;
int *body = atom->body;
body[ilocal] = (int) ubuf(buf[m++]).i;
if (body[ilocal] == 0) body[ilocal] = -1;
else {

3
src/atom_vec_body.h
View File

@ -43,6 +43,7 @@ class AtomVecBody : public AtomVec {
~AtomVecBody();
void process_args(int, char **);
void grow(int);
void copy_bonus(int, int, int);
void clear_bonus();
int pack_comm_bonus(int, int *, double *);
@ -74,6 +75,8 @@ class AtomVecBody : public AtomVec {
int intdoubleratio; // sizeof(double) / sizeof(int)
int body_flag;
int *body;
MyPoolChunk<int> *icp;
MyPoolChunk<double> *dcp;

4
src/atom_vec_ellipsoid.cpp
View File

@ -38,7 +38,7 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp)
size_forward_bonus = 4;
size_border_bonus = 8;
size_restart_bonus_one = 7;
size_restart_bonus_one = 8;
size_data_bonus = 8;
atom->ellipsoid_flag = 1;
@ -320,7 +320,7 @@ int AtomVecEllipsoid::size_restart_bonus()
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (ellipsoid[i] >= 0) n += size_restart_bonus_one;
n++;
else n++;
}
return n;

4
src/atom_vec_line.cpp
View File

@ -37,7 +37,7 @@ AtomVecLine::AtomVecLine(LAMMPS *lmp) : AtomVec(lmp)
size_forward_bonus = 1;
size_border_bonus = 3;
size_restart_bonus_one = 2;
size_restart_bonus_one = 3;
size_data_bonus = 5;
atom->line_flag = 1;
@ -286,7 +286,7 @@ int AtomVecLine::size_restart_bonus()
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (line[i] >= 0) n += size_restart_bonus_one;
n++;
else n++;
}
return n;

10
src/atom_vec_sphere.cpp
View File

@ -61,18 +61,22 @@ AtomVecSphere::AtomVecSphere(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecSphere::process_args(int narg, char **arg)
{
if (narg == 0) return;
if (narg != 1) error->all(FLERR,"Illegal atom_style sphere command");
if (narg != 0 && narg != 1)
error->all(FLERR,"Illegal atom_style sphere command");
radvary = 0;
if (narg == 1) {
radvary = utils::numeric(FLERR,arg[0],true,lmp);
if (radvary < 0 || radvary > 1)
error->all(FLERR,"Illegal atom_style sphere command");
if (radvary == 0) return;
}
// dynamic particle radius and mass must be communicated every step
if (radvary) {
fields_comm = (char *) "radius rmass";
fields_comm_vel = (char *) "radius rmass omega";
}
// delay setting up of fields until now

6
src/atom_vec_tri.cpp
View File

@ -38,7 +38,7 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
size_forward_bonus = 4;
size_border_bonus = 17;
size_restart_bonus_one = 16;
size_restart_bonus_one = 17;
size_data_bonus = 10;
atom->tri_flag = 1;
@ -64,7 +64,7 @@ AtomVecTri::AtomVecTri(LAMMPS *lmp) : AtomVec(lmp)
fields_border_vel = (char *) "molecule radius rmass omega";
fields_exchange = (char *) "molecule radius rmass omega angmom";
fields_restart = (char *) "molecule radius rmass omega angmom";
fields_create = (char *) "molecule radius rmass omega angmom line";
fields_create = (char *) "molecule radius rmass omega angmom tri";
fields_data_atom = (char *) "id molecule type tri rmass x";
fields_data_vel = (char *) "id v omega angmom";
@ -381,7 +381,7 @@ int AtomVecTri::size_restart_bonus()
int nlocal = atom->nlocal;
for (i = 0; i < nlocal; i++) {
if (tri[i] >= 0) n += size_restart_bonus_one;
n++;
else n++;
}
return n;

21
src/fix_gravity.cpp
View File

@ -31,7 +31,7 @@ using namespace FixConst;
using namespace MathConst;
enum{CHUTE,SPHERICAL,VECTOR};
enum{CONSTANT,EQUAL};
enum{CONSTANT,EQUAL}; // same as FixPour
/* ---------------------------------------------------------------------- */
@ -134,6 +134,16 @@ FixGravity::FixGravity(LAMMPS *lmp, int narg, char **arg) :
eflag = 0;
egrav = 0.0;
// set gravity components once and for all if CONSTANT
varflag = CONSTANT;
if (mstyle != CONSTANT || vstyle != CONSTANT || pstyle != CONSTANT ||
tstyle != CONSTANT || xstyle != CONSTANT || ystyle != CONSTANT ||
zstyle != CONSTANT) varflag = EQUAL;
if (varflag == CONSTANT) set_acceleration();
}
/* ---------------------------------------------------------------------- */
@ -222,15 +232,6 @@ void FixGravity::init()
if (!input->variable->equalstyle(zvar))
error->all(FLERR,"Variable for fix gravity is invalid style");
}
varflag = CONSTANT;
if (mstyle != CONSTANT || vstyle != CONSTANT || pstyle != CONSTANT ||
tstyle != CONSTANT || xstyle != CONSTANT || ystyle != CONSTANT ||
zstyle != CONSTANT) varflag = EQUAL;
// set gravity components once and for all
if (varflag == CONSTANT) set_acceleration();
}
/* ---------------------------------------------------------------------- */

25
src/replicate.cpp
View File

@ -331,7 +331,8 @@ void Replicate::command(int narg, char **arg)
if (me == 0 && screen) {
fprintf(screen," bounding box image = (%i %i %i) to (%i %i %i)\n",
_imagelo[0],_imagelo[1],_imagelo[2],_imagehi[0],_imagehi[1],_imagehi[2]);
_imagelo[0],_imagelo[1],_imagelo[2],
_imagehi[0],_imagehi[1],_imagehi[2]);
fprintf(screen," bounding box extra memory = %.2f MB\n",
(double)size_buf_all*sizeof(double)/1024/1024);
}
@ -341,25 +342,32 @@ void Replicate::command(int narg, char **arg)
int *disp_buf_rnk;
memory->create(disp_buf_rnk, nprocs, "replicate:disp_buf_rnk");
disp_buf_rnk[0] = 0;
for (i=1; i<nprocs; ++i) disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1];
for (i = 1; i < nprocs; i++)
disp_buf_rnk[i] = disp_buf_rnk[i-1] + size_buf_rnk[i-1];
// allgather buf_all
double * buf_all;
memory->create(buf_all, size_buf_all, "replicate:buf_all");
MPI_Allgatherv(buf, n, MPI_DOUBLE, buf_all, size_buf_rnk, disp_buf_rnk, MPI_DOUBLE, world);
MPI_Allgatherv(buf,n,MPI_DOUBLE,buf_all,size_buf_rnk,disp_buf_rnk,
MPI_DOUBLE,world);
// bounding box of original unwrapped system
double _orig_lo[3], _orig_hi[3];
if (triclinic) {
_orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz;
_orig_lo[1] = domain->boxlo[1] + _imagelo[1] * old_yprd + _imagelo[2] * old_yz;
_orig_lo[0] = domain->boxlo[0] +
_imagelo[0] * old_xprd + _imagelo[1] * old_xy + _imagelo[2] * old_xz;
_orig_lo[1] = domain->boxlo[1] +
_imagelo[1] * old_yprd + _imagelo[2] * old_yz;
_orig_lo[2] = domain->boxlo[2] + _imagelo[2] * old_zprd;
_orig_hi[0] = domain->boxlo[0] + (_imagehi[0]+1) * old_xprd + (_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz;
_orig_hi[1] = domain->boxlo[1] + (_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz;
_orig_hi[0] = domain->boxlo[0] +
(_imagehi[0]+1) * old_xprd +
(_imagehi[1]+1) * old_xy + (_imagehi[2]+1) * old_xz;
_orig_hi[1] = domain->boxlo[1] +
(_imagehi[1]+1) * old_yprd + (_imagehi[2]+1) * old_yz;
_orig_hi[2] = domain->boxlo[2] + (_imagehi[2]+1) * old_zprd;
} else {
_orig_lo[0] = domain->boxlo[0] + _imagelo[0] * old_xprd;
@ -605,7 +613,8 @@ void Replicate::command(int narg, char **arg)
MPI_Reduce(&num_replicas_added, &sum, 1, MPI_INT, MPI_SUM, 0, world);
double avg = (double) sum / nprocs;
if (me == 0 && screen)
fprintf(screen," average # of replicas added to proc = %.2f out of %i (%.2f %%)\n",
fprintf(screen," average # of replicas added to proc = %.2f "
"out of %i (%.2f %%)\n",
avg,nx*ny*nz,avg/(nx*ny*nz)*100.0);
} else {