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resolved merge conflicts with master

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This commit is contained in:
Steve Plimpton
2021-08-17 11:55:33 -06:00
parent b2f96d92df dad9942bb8
commit e6af1eecb8
8612 changed files with 510252 additions and 341930 deletions
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274
src/atom.cpp
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@ -1,6 +1,7 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://lammps.sandia.gov/, Sandia National Laboratories
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
@ -34,12 +35,17 @@
#include "library.h"
#include <algorithm>
#include <cmath>
#include <cstring>
#ifdef LMP_USER_INTEL
#ifdef LMP_INTEL
#include "neigh_request.h"
#endif
#ifdef LMP_GPU
#include "fix_gpu.h"
#endif
using namespace LAMMPS_NS;
using namespace MathConst;
@ -155,7 +161,7 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
sp = fm = fm_long = nullptr;
// USER-EFF and USER-AWPMD packages
// EFF and AWPMD packages
spin = nullptr;
eradius = ervel = erforce = nullptr;
@ -163,23 +169,27 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
cs = csforce = vforce = nullptr;
etag = nullptr;
// USER-DPD package
// CG-DNA package
id5p = nullptr;
// DPD-REACT package
uCond = uMech = uChem = uCG = uCGnew = nullptr;
duChem = dpdTheta = nullptr;
// USER-MESO package
// MESO package
cc = cc_flux = nullptr;
edpd_temp = edpd_flux = edpd_cv = nullptr;
// USER-MESONT package
// MESONT package
length = nullptr;
buckling = nullptr;
bond_nt = nullptr;
// USER-SMD package
// MACHDYN package
contact_radius = nullptr;
smd_data_9 = nullptr;
@ -188,11 +198,15 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
eff_plastic_strain_rate = nullptr;
damage = nullptr;
// USER-SPH package
// SPH package
rho = drho = esph = desph = cv = nullptr;
vest = nullptr;
// DIELECTRIC package
area = ed = em = epsilon = curvature = q_unscaled = nullptr;
// end of customization section
// --------------------------------------------------------------------
@ -352,11 +366,8 @@ void Atom::settings(Atom *old)
map_style = old->map_style;
sortfreq = old->sortfreq;
userbinsize = old->userbinsize;
if (old->firstgroupname) {
int n = strlen(old->firstgroupname) + 1;
firstgroupname = new char[n];
strcpy(firstgroupname,old->firstgroupname);
}
if (old->firstgroupname)
firstgroupname = utils::strdup(old->firstgroupname);
}
/* ----------------------------------------------------------------------
@ -465,14 +476,14 @@ void Atom::peratom_create()
add_peratom("fm",&fm,DOUBLE,3,1);
add_peratom("fm_long",&fm_long,DOUBLE,3,1);
// USER-EFF package
// EFF package
add_peratom("spin",&spin,INT,0);
add_peratom("eradius",&eradius,DOUBLE,0);
add_peratom("ervel",&ervel,DOUBLE,0);
add_peratom("erforce",&erforce,DOUBLE,0,1); // set per-thread flag
// USER-AWPMD package
// AWPMD package
add_peratom("cs",&cs,DOUBLE,2);
add_peratom("csforce",&csforce,DOUBLE,2);
@ -480,7 +491,11 @@ void Atom::peratom_create()
add_peratom("ervelforce",&ervelforce,DOUBLE,0);
add_peratom("etag",&etag,INT,0);
// USER-DPD package
// CG-DNA package
add_peratom("id5p",&id5p,tagintsize,0);
// DPD-REACT package
add_peratom("dpdTheta",&dpdTheta,DOUBLE,0);
add_peratom("uCond",&uCond,DOUBLE,0);
@ -490,7 +505,7 @@ void Atom::peratom_create()
add_peratom("uCGnew",&uCGnew,DOUBLE,0);
add_peratom("duChem",&duChem,DOUBLE,0);
// USER-MESO package
// MESO package
add_peratom("edpd_cv",&edpd_cv,DOUBLE,0);
add_peratom("edpd_temp",&edpd_temp,DOUBLE,0);
@ -499,13 +514,13 @@ void Atom::peratom_create()
add_peratom("cc",&cc,DOUBLE,1);
add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
// USER-MESONT package
// MESONT package
add_peratom("length",&length,DOUBLE,0);
add_peratom("buckling",&buckling,INT,0);
add_peratom("bond_nt",&bond_nt,tagintsize,2);
// USER-SPH package
// SPH package
add_peratom("rho",&rho,DOUBLE,0);
add_peratom("drho",&drho,DOUBLE,0,1); // set per-thread flag
@ -514,7 +529,7 @@ void Atom::peratom_create()
add_peratom("vest",&vest,DOUBLE,3);
add_peratom("cv",&cv,DOUBLE,0);
// USER-SMD package
// MACHDYN package
add_peratom("contact_radius",&contact_radius,DOUBLE,0);
add_peratom("smd_data_9",&smd_data_9,DOUBLE,1);
@ -523,6 +538,15 @@ void Atom::peratom_create()
add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0);
add_peratom("damage",&damage,DOUBLE,0);
// DIELECTRIC package
add_peratom("area",&area,DOUBLE,0);
add_peratom("ed",&ed,DOUBLE,0);
add_peratom("em",&em,DOUBLE,0);
add_peratom("epsilon",&epsilon,DOUBLE,0);
add_peratom("curvature",&curvature,DOUBLE,0);
add_peratom("q_unscaled",&q_unscaled,DOUBLE,0);
// end of customization section
// --------------------------------------------------------------------
}
@ -543,9 +567,7 @@ void Atom::add_peratom(const char *name, void *address,
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
int n = strlen(name) + 1;
peratom[nperatom].name = new char[n];
strcpy(peratom[nperatom].name,name);
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = cols;
@ -593,9 +615,7 @@ void Atom::add_peratom_vary(const char *name, void *address,
memory->srealloc(peratom,maxperatom*sizeof(PerAtom),"atom:peratom");
}
int n = strlen(name) + 1;
peratom[nperatom].name = new char[n];
strcpy(peratom[nperatom].name,name);
peratom[nperatom].name = utils::strdup(name);
peratom[nperatom].address = address;
peratom[nperatom].datatype = datatype;
peratom[nperatom].cols = -1;
@ -681,7 +701,7 @@ void Atom::create_avec(const std::string &style, int narg, char **arg, int trysu
// map style will be reset to array vs hash to by map_init()
molecular = avec->molecular;
if (molecular && tag_enable == 0)
if ((molecular != Atom::ATOMIC) && (tag_enable == 0))
error->all(FLERR,"Atom IDs must be used for molecular systems");
if (molecular != Atom::ATOMIC) map_style = MAP_YES;
}
@ -826,9 +846,7 @@ void Atom::modify_params(int narg, char **arg)
delete [] firstgroupname;
firstgroupname = nullptr;
} else {
int n = strlen(arg[iarg+1]) + 1;
firstgroupname = new char[n];
strcpy(firstgroupname,arg[iarg+1]);
firstgroupname = utils::strdup(arg[iarg+1]);
sortfreq = 0;
}
iarg += 2;
@ -1125,13 +1143,13 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
if (values[0] == nullptr)
error->all(FLERR,"Incorrect atom format in data file");
for (m = 1; m < nwords; m++) {
values[m] = strtok(nullptr," \t\n\r\f");
if (values[m] == nullptr)
for (m = 0; m < nwords; m++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
if (strlen(buf) == 0)
error->all(FLERR,"Incorrect atom format in data file");
values[m] = buf;
buf += strlen(buf)+1;
}
int imx = 0, imy = 0, imz = 0;
@ -1228,9 +1246,12 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(nullptr," \t\n\r\f");
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
@ -1282,6 +1303,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom2;
num_bond[m]++;
avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset);
}
}
if (newton_bond == 0) {
@ -1291,6 +1313,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom1;
num_bond[m]++;
avec->data_bonds_post(m, num_bond[m], atom1, atom2, id_offset);
}
}
}
@ -1580,9 +1603,12 @@ void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus, tagint id_offset)
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(nullptr," \t\n\r\f");
for (j = 0; j < nwords; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
values[j] = buf;
buf += strlen(buf)+1;
}
tagdata = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
@ -1622,8 +1648,10 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
// else skip values
for (int i = 0; i < n; i++) {
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
else tagdata = ATOTAGINT(strtok(nullptr," \t\n\r\f")) + id_offset;
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
tagdata = utils::tnumeric(FLERR,buf,false,lmp) + id_offset;
buf += strlen(buf)+1;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
@ -1633,8 +1661,15 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
else
error->one(FLERR,"Duplicate atom ID in Bodies section of data file");
ninteger = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
ndouble = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ninteger = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ndouble = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
@ -1648,17 +1683,29 @@ void Atom::data_bodies(int n, char *buf, AtomVec *avec_body, tagint id_offset)
dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++)
ivalues[j] = utils::inumeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
for (j = 0; j < ndouble; j++)
dvalues[j] = utils::numeric(FLERR,strtok(nullptr," \t\n\r\f"),false,lmp);
for (j = 0; j < ninteger; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
ivalues[j] = utils::inumeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
for (j = 0; j < ndouble; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
dvalues[j] = utils::numeric(FLERR,buf,false,lmp);
buf += strlen(buf)+1;
}
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++)
strtok(nullptr," \t\n\r\f");
for (j = 0; j < nvalues; j++) {
buf += strspn(buf," \t\n\r\f");
buf[strcspn(buf," \t\n\r\f")] = '\0';
buf += strlen(buf)+1;
}
}
}
@ -1763,7 +1810,7 @@ void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
if (lo < 1 || hi > ntypes) error->all(file,line,"Invalid type for mass set");
for (int itype = lo; itype <= hi; itype++) {
mass[itype] = atof(arg[1]);
mass[itype] = utils::numeric(FLERR,arg[1],false,lmp);
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all(file,line,"Invalid mass value");
@ -2164,7 +2211,7 @@ void Atom::setup_sort_bins()
bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
bininvz = nbinz / (bboxhi[2]-bboxlo[2]);
#ifdef LMP_USER_INTEL
#ifdef LMP_INTEL
int intel_neigh = 0;
if (neighbor->nrequest) {
if (neighbor->requests[0]->intel) intel_neigh = 1;
@ -2209,7 +2256,36 @@ void Atom::setup_sort_bins()
bboxhi[1] = bboxlo[1] + static_cast<double>(nbiny) / bininvy;
bboxhi[2] = bboxlo[2] + static_cast<double>(nbinz) / bininvz;
}
#endif
#endif
#ifdef LMP_GPU
if (userbinsize == 0.0) {
int ifix = modify->find_fix("package_gpu");
if (ifix >= 0) {
const double subx = domain->subhi[0] - domain->sublo[0];
const double suby = domain->subhi[1] - domain->sublo[1];
const double subz = domain->subhi[2] - domain->sublo[2];
FixGPU *fix = static_cast<FixGPU *>(modify->fix[ifix]);
binsize = fix->binsize(subx, suby, subz, atom->nlocal,
neighbor->cutneighmax);
bininv = 1.0 / binsize;
nbinx = static_cast<int> (ceil(subx * bininv));
nbiny = static_cast<int> (ceil(suby * bininv));
nbinz = static_cast<int> (ceil(subz * bininv));
if (domain->dimension == 2) nbinz = 1;
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
bininvx = bininv;
bininvy = bininv;
bininvz = bininv;
}
}
#endif
if (1.0*nbinx*nbiny*nbinz > INT_MAX)
error->one(FLERR,"Too many atom sorting bins");
@ -2401,9 +2477,7 @@ int Atom::add_custom(const char *name, int flag, int cols)
nivector++;
ivname = (char **) memory->srealloc(ivname,nivector*sizeof(char *),
"atom:ivname");
int n = strlen(name) + 1;
ivname[index] = new char[n];
strcpy(ivname[index],name);
ivname[index] = utils::strdup(name);
ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
"atom:ivector");
memory->create(ivector[index],nmax,"atom:ivector");
@ -2413,9 +2487,7 @@ int Atom::add_custom(const char *name, int flag, int cols)
ndvector++;
dvname = (char **) memory->srealloc(dvname,ndvector*sizeof(char *),
"atom:dvname");
int n = strlen(name) + 1;
dvname[index] = new char[n];
strcpy(dvname[index],name);
dvname[index] = utils::strdup(name);
dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *),
"atom:dvector");
memory->create(dvector[index],nmax,"atom:dvector");
@ -2425,9 +2497,7 @@ int Atom::add_custom(const char *name, int flag, int cols)
niarray++;
ianame = (char **) memory->srealloc(ianame,niarray*sizeof(char *),
"atom:ianame");
int n = strlen(name) + 1;
ianame[index] = new char[n];
strcpy(ianame[index],name);
ianame[index] = utils::strdup(name);
iarray = (int ***) memory->srealloc(iarray,niarray*sizeof(int **),
"atom:iarray");
memory->create(iarray[index],nmax,cols,"atom:iarray");
@ -2440,9 +2510,7 @@ int Atom::add_custom(const char *name, int flag, int cols)
ndarray++;
daname = (char **) memory->srealloc(daname,ndarray*sizeof(char *),
"atom:daname");
int n = strlen(name) + 1;
daname[index] = new char[n];
strcpy(daname[index],name);
daname[index] = utils::strdup(name);
darray = (double ***) memory->srealloc(darray,ndarray*sizeof(double **),
"atom:darray");
memory->create(darray[index],nmax,cols,"atom:darray");
@ -2676,7 +2744,13 @@ void *Atom::extract(const char *name)
if (strcmp(name,"cv") == 0) return (void *) cv;
if (strcmp(name,"vest") == 0) return (void *) vest;
// USER-SMD package
// MESONT package
if (strcmp(name,"length") == 0) return (void *) length;
if (strcmp(name,"buckling") == 0) return (void *) buckling;
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
// MACHDYN package
if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
@ -2687,22 +2761,29 @@ void *Atom::extract(const char *name)
return (void *) eff_plastic_strain_rate;
if (strcmp(name, "damage") == 0) return (void *) damage;
// USER-DPD package
// DPD-REACT pakage
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
// USER-MESO package
// DPD-MESO package
if (strcmp(name,"edpd_temp") == 0) return (void *) edpd_temp;
// USER-MESONT package
if (strcmp(name,"length") == 0) return (void *) length;
if (strcmp(name,"buckling") == 0) return (void *) buckling;
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
// DIELECTRIC package
if (strcmp(name,"area") == 0) return (void *) area;
if (strcmp(name,"ed") == 0) return (void *) ed;
if (strcmp(name,"em") == 0) return (void *) em;
if (strcmp(name,"epsilon") == 0) return (void *) epsilon;
if (strcmp(name,"curvature") == 0) return (void *) curvature;
if (strcmp(name,"q_unscaled") == 0) return (void *) q_unscaled;
// end of customization section
// --------------------------------------------------------------------
// custom vectors and arrays
// OLDSTYLE code
if (strstr(name,"i_") == name || strstr(name,"d_") == name ||
strstr(name,"i2_") == name || strstr(name,"d2_") == name) {
int which = 0;
@ -2724,9 +2805,6 @@ void *Atom::extract(const char *name)
if (which && array) return (void *) darray[index];
}
// end of customization section
// --------------------------------------------------------------------
return nullptr;
}
@ -2791,8 +2869,14 @@ int Atom::extract_datatype(const char *name)
if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D;
// USER-SMD package
// MESONT package
if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"buckling") == 0) return LAMMPS_INT;
if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D;
// MACHDYN package
if (strcmp(name, "contact_radius") == 0) return LAMMPS_DOUBLE;
if (strcmp(name, "smd_data_9") == 0) return LAMMPS_DOUBLE_2D;
if (strcmp(name, "smd_stress") == 0) return LAMMPS_DOUBLE_2D;
@ -2800,21 +2884,28 @@ int Atom::extract_datatype(const char *name)
if (strcmp(name, "eff_plastic_strain_rate") == 0) return LAMMPS_DOUBLE;
if (strcmp(name, "damage") == 0) return LAMMPS_DOUBLE;
// USER-DPD package
// DPD-REACT package
if (strcmp(name,"dpdTheta") == 0) return LAMMPS_DOUBLE;
// USER-MESO package
// DPD-MESO package
if (strcmp(name,"edpd_temp") == 0) return LAMMPS_DOUBLE;
// USER-MESONT package
// DIELECTRIC package
if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"buckling") == 0) return LAMMPS_INT;
if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D;
if (strcmp(name,"area") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"ed") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"em") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"epsilon") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"curvature") == 0) return LAMMPS_DOUBLE;
if (strcmp(name,"q_unscaled") == 0) return LAMMPS_DOUBLE;
// end of customization section
// --------------------------------------------------------------------
// custom vectors and arrays
// OLDSTYLE code
if (strstr(name,"i_") == name || strstr(name,"d_") == name ||
strstr(name,"i2_") == name || strstr(name,"d2_") == name) {
@ -2834,9 +2925,6 @@ int Atom::extract_datatype(const char *name)
if (which == 0) return LAMMPS_INT;
else return LAMMPS_DOUBLE;
}
// end of customization section
// --------------------------------------------------------------------
return -1;
}
@ -2851,12 +2939,12 @@ double Atom::memory_usage()
{
double bytes = avec->memory_usage();
bytes += max_same*sizeof(int);
bytes += (double)max_same*sizeof(int);
if (map_style == MAP_ARRAY)
bytes += memory->usage(map_array,map_maxarray);
else if (map_style == MAP_HASH) {
bytes += map_nbucket*sizeof(int);
bytes += map_nhash*sizeof(HashElem);
bytes += (double)map_nbucket*sizeof(int);
bytes += (double)map_nhash*sizeof(HashElem);
}
if (maxnext) {
bytes += memory->usage(next,maxnext);