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added support for USER-AWPMD package

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This commit is contained in:
Steve Plimpton
2019-12-18 12:04:37 -07:00
parent b6374bacfb
commit ccc8f29d60
11 changed files with 86 additions and 46 deletions
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25
src/USER-AWPMD/atom_vec_wavepacket.cpp
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@ -61,6 +61,20 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
setup_fields();
}
/* ----------------------------------------------------------------------
set local copies of all grow ptrs used by this class, except defaults
needed in replicate when 2 atom classes exist and it calls pack_restart()
------------------------------------------------------------------------- */
void AtomVecWavepacket::grow_pointers()
{
q = atom->q;
spin = atom->spin;
eradius = atom->eradius;
ervel = atom->ervel;
erforce = atom->erforce;
}
/* ----------------------------------------------------------------------
clear extra forces starting at atom N
nbytes = # of bytes to clear for a per-atom vector
@ -68,7 +82,7 @@ AtomVecWavepacket::AtomVecWavepacket(LAMMPS *lmp) : AtomVec(lmp)
void AtomVecWavepacket::force_clear(int n, size_t nbytes)
{
memset(&atom->erforce[n],0,nbytes);
memset(&erforce[n],0,nbytes);
}
/* ----------------------------------------------------------------------
@ -78,7 +92,7 @@ void AtomVecWavepacket::force_clear(int n, size_t nbytes)
void AtomVecWavepacket::create_atom_post(int ilocal)
{
atom->q[ilocal] = 1.0;
q[ilocal] = 1.0;
}
/* ----------------------------------------------------------------------
@ -88,7 +102,7 @@ void AtomVecWavepacket::create_atom_post(int ilocal)
void AtomVecWavepacket::data_atom_post(int ilocal)
{
atom->ervel[ilocal] = 0.0;
ervel[ilocal] = 0.0;
}
/* ----------------------------------------------------------------------
@ -113,33 +127,28 @@ int AtomVecWavepacket::property_atom(char *name)
void AtomVecWavepacket::pack_property_atom(int index, double *buf,
int nvalues, int groupbit)
{
int *mask = atom->mask;
int nlocal = atom->nlocal;
int n = 0;
if (index == 0) {
int *spin = atom->spin;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = spin[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 1) {
double *eradius = atom->eradius;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = eradius[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 2) {
double *ervel = atom->ervel;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = ervel[i];
else buf[n] = 0.0;
n += nvalues;
}
} else if (index == 3) {
double *erforce = atom->erforce;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) buf[n] = erforce[i];
else buf[n] = 0.0;

6
src/USER-AWPMD/atom_vec_wavepacket.h
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@ -27,11 +27,17 @@ namespace LAMMPS_NS {
class AtomVecWavepacket : public AtomVec {
public:
AtomVecWavepacket(class LAMMPS *);
void grow_pointers();
void force_clear(int, size_t);
void create_atom_post(int);
void data_atom_post(int);
int property_atom(char *);
void pack_property_atom(int, double *, int, int);
private:
int *spin;
double *q,*eradius,*ervel,*erforce;
};
}

26
src/USER-AWPMD/pair_awpmd_cut.cpp
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@ -259,7 +259,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
Vector_3 xx=Vector_3(x[i][0],x[i][1],x[i][2]);
Vector_3 rv=m*Vector_3(v[i][0],v[i][1],v[i][2]);
double pv=ermscale*m*atom->ervel[i];
Vector_2 cc=Vector_2(atom->cs[2*i],atom->cs[2*i+1]);
Vector_2 cc=Vector_2(atom->cs[i][0],atom->cs[i][1]);
gmap[i]=wpmd->add_split(xx,rv,atom->eradius[i],pv,cc,1.,atom->q[i],i<nlocal ? atom->tag[i] : -atom->tag[i]);
// resetting for the case constraints were applied
v[i][0]=rv[0]/m;
@ -284,7 +284,7 @@ void PairAWPMDCut::compute(int eflag, int vflag)
} else { // electron
int iel=gmap[i];
int s=spin[i] >0 ? 0 : 1;
wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce+3*i),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce+2*i));
wpmd->get_wp_force(s,iel,(Vector_3 *)f[i],(Vector_3 *)(atom->vforce[i]),atom->erforce+i,atom->ervelforce+i,(Vector_2 *)(atom->csforce[i]));
}
}
@ -671,11 +671,11 @@ void PairAWPMDCut::min_xf_get(int /* ignore */)
double *eradius = atom->eradius;
double *erforce = atom->erforce;
double **v=atom->v;
double *vforce=atom->vforce;
double **vforce=atom->vforce;
double *ervel=atom->ervel;
double *ervelforce=atom->ervelforce;
double *cs=atom->cs;
double *csforce=atom->csforce;
double **cs=atom->cs;
double **csforce=atom->csforce;
int *spin = atom->spin;
int nlocal = atom->nlocal;
@ -686,14 +686,14 @@ void PairAWPMDCut::min_xf_get(int /* ignore */)
min_varforce[7*i] = eradius[i]*erforce[i];
for(int j=0;j<3;j++){
min_var[7*i+1+3*j] = v[i][j];
min_varforce[7*i+1+3*j] = vforce[3*i+j];
min_varforce[7*i+1+3*j] = vforce[i][j];
}
min_var[7*i+4] = ervel[i];
min_varforce[7*i+4] = ervelforce[i];
min_var[7*i+5] = cs[2*i];
min_varforce[7*i+5] = csforce[2*i];
min_var[7*i+6] = cs[2*i+1];
min_varforce[7*i+6] = csforce[2*i+1];
min_var[7*i+5] = cs[i][0];
min_varforce[7*i+5] = csforce[i][0];
min_var[7*i+6] = cs[i][1];
min_varforce[7*i+6] = csforce[i][1];
} else {
for(int j=0;j<7;j++)
@ -710,7 +710,7 @@ void PairAWPMDCut::min_x_set(int /* ignore */)
double *eradius = atom->eradius;
double **v=atom->v;
double *ervel=atom->ervel;
double *cs=atom->cs;
double **cs=atom->cs;
int *spin = atom->spin;
int nlocal = atom->nlocal;
@ -721,8 +721,8 @@ void PairAWPMDCut::min_x_set(int /* ignore */)
for(int j=0;j<3;j++)
v[i][j]=min_var[7*i+1+3*j];
ervel[i]=min_var[7*i+4];
cs[2*i]=min_var[7*i+5];
cs[2*i+1]=min_var[7*i+6];
cs[i][0]=min_var[7*i+5];
cs[i][1]=min_var[7*i+6];
}
}
}

2
src/USER-SMD/atom_vec_smd.cpp
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@ -90,7 +90,7 @@ AtomVecSMD::AtomVecSMD(LAMMPS *lmp) : AtomVec(lmp)
"x0 vest vfrac rmass radius contact_radius molecule e "
"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";
"id type molecule vfrac rmass radius contact_radius x0 x";
fields_data_vel = (char *) "id v";
// set these array sizes based on defines

8
src/atom.cpp
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@ -134,8 +134,8 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
spin = NULL;
eradius = ervel = erforce = NULL;
ervelforce = cs = csforce = NULL;
vforce = NULL;
ervelforce = NULL;
cs = csforce = vforce = NULL;
etag = NULL;
// USER-DPD package
@ -512,8 +512,8 @@ void Atom::peratom_create()
// USER-AWPMD package
add_peratom("cs",&cs,DOUBLE,0);
add_peratom("csforce",&csforce,DOUBLE,0);
add_peratom("cs",&cs,DOUBLE,2);
add_peratom("csforce",&csforce,DOUBLE,2);
add_peratom("vforce",&vforce,DOUBLE,3);
add_peratom("ervelforce",&ervelforce,DOUBLE,0);
add_peratom("etag",&etag,INT,0);

6
src/atom.h
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@ -109,8 +109,8 @@ class Atom : protected Pointers {
int *spin;
double *eradius,*ervel,*erforce;
double *ervelforce,*cs,*csforce;
double **vforce;
double *ervelforce;
double **cs,**csforce,**vforce;
int *etag;
// USER-DPD package
@ -322,7 +322,7 @@ class Atom : protected Pointers {
inline int get_map_size() {return map_tag_max+1;};
inline int get_map_maxarray() {return map_maxarray+1;};
// NOTE: placeholder method until AtomVec is refactored
// NOTE: placeholder method until KOKKOS/AtomVec is refactored
int memcheck(const char *) {return 1;}
bigint memory_usage();

7
src/atom_vec.cpp
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@ -1368,7 +1368,7 @@ int AtomVec::size_restart()
int i,nn,cols,collength,ncols;
void *plength;
// NOTE: need to worry about overflow of returned int ??
// NOTE: need to worry about overflow of returned int N
int nlocal = atom->nlocal;
@ -1738,9 +1738,9 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, char **values)
// error checks applicable to all styles
if (atom->tag[nlocal] <= 0)
if (tag[nlocal] <= 0)
error->one(FLERR,"Invalid atom ID in Atoms section of data file");
if (atom->type[nlocal] <= 0 || atom->type[nlocal] > atom->ntypes)
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
// if needed, modify unpacked values or initialize other peratom values
@ -2388,7 +2388,6 @@ void AtomVec::setup_fields()
}
// set style-specific sizes
// NOTE: check for others vars in atom_vec.cpp/h ??
comm_x_only = 1;
if (ncomm) comm_x_only = 0;

9
src/atom_vec_body.cpp
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@ -132,15 +132,12 @@ void AtomVecBody::process_args(int narg, char **arg)
}
/* ----------------------------------------------------------------------
grow atom arrays
must set local copy of body ptr
needed in replicate when 2 atom classes exist and pack_restart() is called
set local copies of all grow ptrs used by this class, except defaults
needed in replicate when 2 atom classes exist and it calls pack_restart()
------------------------------------------------------------------------- */
void AtomVecBody::grow(int n)
void AtomVecBody::grow_pointers()
{
AtomVec::grow(n);
body = atom->body;
rmass = atom->rmass;
radius = atom->radius;

2
src/atom_vec_body.h
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@ -43,7 +43,7 @@ class AtomVecBody : public AtomVec {
~AtomVecBody();
void process_args(int, char **);
void grow(int);
void grow_pointers();
void copy_bonus(int, int, int);
void clear_bonus();
int pack_comm_bonus(int, int *, double *);

38
src/atom_vec_hybrid.cpp
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@ -31,12 +31,10 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp) : AtomVec(lmp)
keywords = NULL;
fieldstrings = NULL;
bonus_flag = 0;
nstyles_bonus = 0;
styles_bonus = NULL;
// NOTE: set bonus_flag if any substyle does
// set nstyles_bonus, styles_bonus
// these strings will be concatenated from sub-style strings
// fields_data_atom & fields_data_vel start with fields common to all styles
@ -45,6 +43,8 @@ AtomVecHybrid::AtomVecHybrid(LAMMPS *lmp) : AtomVec(lmp)
fields_exchange = fields_restart = fields_create = (char *) "";
fields_data_atom = (char *) "id type x";
fields_data_vel = (char *) "id v";
fields_allocated = 0;
}
/* ---------------------------------------------------------------------- */
@ -56,7 +56,10 @@ AtomVecHybrid::~AtomVecHybrid()
for (int k = 0; k < nstyles; k++) delete [] keywords[k];
delete [] keywords;
// NOTE: need to check these have actually been allocated
for (int k = 0; k < nstyles_bonus; k++) delete styles_bonus[k];
delete [] styles_bonus;
if (!fields_allocated) return;
delete [] fields_grow;
delete [] fields_copy;
@ -198,6 +201,8 @@ void AtomVecHybrid::process_args(int narg, char **arg)
fields_data_atom = merge_fields(10,fields_data_atom,0,null);
fields_data_vel = merge_fields(11,fields_data_vel,0,null);
fields_allocated = 1;
// check concat_grow for multiple special-case fields
// may cause issues with style-specific create_atom() and data_atom() methods
// issue warnings if appear in multiple sub-styles
@ -219,6 +224,23 @@ void AtomVecHybrid::process_args(int narg, char **arg)
delete [] concat_grow;
// set bonus_flag if any substyle has bonus data
// set nstyles_bonus & styles_bonus
nstyles_bonus = 0;
for (int k = 0; k < nstyles; k++)
if (styles[k]->bonus_flag) nstyles_bonus++;
if (nstyles_bonus) {
bonus_flag = 1;
styles_bonus = new AtomVec*[nstyles_bonus];
nstyles_bonus = 0;
for (int k = 0; k < nstyles; k++) {
if (styles[k]->bonus_flag)
styles_bonus[nstyles_bonus++] = styles[k];
}
}
// parent AtomVec can now operate on merged fields
setup_fields();
@ -326,7 +348,13 @@ void AtomVecHybrid::copy_bonus(int i, int j, int delflag)
styles_bonus[k]->copy_bonus(i,j,delflag);
}
// NOTE: need a clear_bonus() ?
/* ---------------------------------------------------------------------- */
void AtomVecHybrid::clear_bonus()
{
for (int k = 0; k < nstyles_bonus; k++)
styles_bonus[k]->clear_bonus();
}
/* ---------------------------------------------------------------------- */

3
src/atom_vec_hybrid.h
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@ -38,7 +38,7 @@ class AtomVecHybrid : public AtomVec {
void grow_pointers();
void force_clear(int, size_t);
void copy_bonus(int, int, int);
void clear_bonus() {}
void clear_bonus();
int pack_comm_bonus(int, int *, double *);
void unpack_comm_bonus(int, int, double *);
int pack_border_bonus(int, int *, double *);
@ -64,6 +64,7 @@ class AtomVecHybrid : public AtomVec {
private:
int nallstyles;
char **allstyles;
int fields_allocated;
struct FieldStrings {
char **fstr;