git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
244
src/atom.cpp
244
src/atom.cpp
@ -5,7 +5,7 @@
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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@ -135,14 +135,14 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
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map_style = 0;
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map_tag_max = 0;
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map_nhash = 0;
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nprimes = 38;
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primes = new int[nprimes];
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int plist[] = {5041,10007,20011,30011,40009,50021,60013,70001,80021,
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90001,100003,110017,120011,130003,140009,150001,160001,
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170003,180001,190027,200003,210011,220009,230003,240007,
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250007,260003,270001,280001,290011,300007,310019,320009,
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330017,340007,350003,362881,3628801};
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90001,100003,110017,120011,130003,140009,150001,160001,
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170003,180001,190027,200003,210011,220009,230003,240007,
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250007,260003,270001,280001,290011,300007,310019,320009,
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330017,340007,350003,362881,3628801};
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for (int i = 0; i < nprimes; i++) primes[i] = plist[i];
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// default atom style = atomic
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@ -264,7 +264,7 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
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sphere_flag = ellipsoid_flag = line_flag = tri_flag = 0;
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peri_flag = electron_flag = 0;
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molecule_flag = q_flag = mu_flag = 0;
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rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
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vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
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@ -295,7 +295,7 @@ void Atom::create_avec(const char *style, int narg, char **arg, char *suffix)
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------------------------------------------------------------------------- */
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AtomVec *Atom::new_avec(const char *style, int narg, char **arg,
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char *suffix, int &sflag)
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char *suffix, int &sflag)
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{
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if (suffix && lmp->suffix_enable) {
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sflag = 1;
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@ -379,7 +379,7 @@ AtomVec *Atom::style_match(const char *style)
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AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) avec;
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for (int i = 0; i < avec_hybrid->nstyles; i++)
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if (strcmp(avec_hybrid->keywords[i],style) == 0)
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return avec_hybrid->styles[i];
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return avec_hybrid->styles[i];
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}
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return NULL;
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}
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@ -401,20 +401,20 @@ void Atom::modify_params(int narg, char **arg)
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if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
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else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
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else error->all(FLERR,"Illegal atom_modify command");
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if (domain->box_exist)
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error->all(FLERR,
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"Atom_modify map command after simulation box is defined");
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if (domain->box_exist)
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error->all(FLERR,
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"Atom_modify map command after simulation box is defined");
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iarg += 2;
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} else if (strcmp(arg[iarg],"first") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
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if (strcmp(arg[iarg+1],"all") == 0) {
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delete [] firstgroupname;
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firstgroupname = NULL;
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delete [] firstgroupname;
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firstgroupname = NULL;
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} else {
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int n = strlen(arg[iarg+1]) + 1;
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firstgroupname = new char[n];
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strcpy(firstgroupname,arg[iarg+1]);
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sortfreq = 0;
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int n = strlen(arg[iarg+1]) + 1;
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firstgroupname = new char[n];
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strcpy(firstgroupname,arg[iarg+1]);
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sortfreq = 0;
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}
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iarg += 2;
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} else if (strcmp(arg[iarg],"sort") == 0) {
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@ -422,10 +422,10 @@ void Atom::modify_params(int narg, char **arg)
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sortfreq = atoi(arg[iarg+1]);
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userbinsize = atof(arg[iarg+2]);
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if (sortfreq < 0 || userbinsize < 0.0)
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error->all(FLERR,"Illegal atom_modify command");
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if (sortfreq >= 0 && firstgroupname)
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error->all(FLERR,"Atom_modify sort and first options "
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"cannot be used together");
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error->all(FLERR,"Illegal atom_modify command");
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if (sortfreq >= 0 && firstgroupname)
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error->all(FLERR,"Atom_modify sort and first options "
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"cannot be used together");
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iarg += 3;
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} else error->all(FLERR,"Illegal atom_modify command");
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}
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@ -515,18 +515,18 @@ void Atom::map_clear()
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ibucket = global % map_nbucket;
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index = map_bucket[ibucket];
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while (index > -1) {
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if (map_hash[index].global == global) break;
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previous = index;
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index = map_hash[index].next;
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if (map_hash[index].global == global) break;
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previous = index;
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index = map_hash[index].next;
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}
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if (index == -1) continue;
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// delete the hash entry and add it to free list
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// special logic if entry is 1st in the bucket
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if (previous == -1) map_bucket[ibucket] = map_hash[index].next;
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else map_hash[previous].next = map_hash[index].next;
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map_hash[index].next = map_free;
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map_free = index;
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map_nused--;
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@ -538,7 +538,7 @@ void Atom::map_clear()
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set global -> local map for all of my own and ghost atoms
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loop in reverse order so that nearby images take precedence over far ones
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and owned atoms take precedence over images
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this enables valid lookups of bond topology atoms
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this enables valid lookups of bond topology atoms
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for hash table option:
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if hash table too small, re-init
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global ID may already be in table if image atom was set
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@ -565,13 +565,13 @@ void Atom::map_set()
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ibucket = global % map_nbucket;
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index = map_bucket[ibucket];
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while (index > -1) {
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if (map_hash[index].global == global) break;
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previous = index;
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index = map_hash[index].next;
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if (map_hash[index].global == global) break;
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previous = index;
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index = map_hash[index].next;
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}
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if (index > -1) {
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map_hash[index].local = i;
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continue;
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map_hash[index].local = i;
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continue;
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}
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// take one entry from free list
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@ -603,7 +603,7 @@ void Atom::map_one(int global, int local)
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else {
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// search for key
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// if found it, just overwrite local value with index
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int previous = -1;
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int ibucket = global % map_nbucket;
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int index = map_bucket[ibucket];
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@ -616,11 +616,11 @@ void Atom::map_one(int global, int local)
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map_hash[index].local = local;
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return;
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}
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// take one entry from free list
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// add the new global/local pair as entry at end of bucket list
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// special logic if this entry is 1st in bucket
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index = map_free;
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map_free = map_hash[map_free].next;
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if (previous == -1) map_bucket[ibucket] = index;
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@ -708,7 +708,7 @@ int Atom::tag_consecutive()
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{
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int idmin = MAXTAGINT;
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int idmax = 0;
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for (int i = 0; i < nlocal; i++) {
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idmin = MIN(idmin,tag[i]);
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idmax = MAX(idmax,tag[i]);
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@ -826,18 +826,18 @@ void Atom::data_atoms(int n, char *buf)
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next = strchr(buf,'\n');
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values[0] = strtok(buf," \t\n\r\f");
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if (values[0] == NULL)
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if (values[0] == NULL)
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error->all(FLERR,"Incorrect atom format in data file");
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for (m = 1; m < nwords; m++) {
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values[m] = strtok(NULL," \t\n\r\f");
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if (values[m] == NULL)
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error->all(FLERR,"Incorrect atom format in data file");
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if (values[m] == NULL)
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error->all(FLERR,"Incorrect atom format in data file");
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}
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if (imageflag)
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imagedata = ((atoi(values[iptr+2]) + 512 & 1023) << 20) |
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((atoi(values[iptr+1]) + 512 & 1023) << 10) |
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(atoi(values[iptr]) + 512 & 1023);
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((atoi(values[iptr+1]) + 512 & 1023) << 10) |
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(atoi(values[iptr]) + 512 & 1023);
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else imagedata = (512 << 20) | (512 << 10) | 512;
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xdata[0] = atof(values[xptr]);
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@ -850,8 +850,8 @@ void Atom::data_atoms(int n, char *buf)
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} else coord = xdata;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2])
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2])
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avec->data_atom(xdata,imagedata,values);
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buf = next + 1;
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@ -964,8 +964,8 @@ void Atom::data_bonds(int n, char *buf)
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next = strchr(buf,'\n');
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*next = '\0';
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sscanf(buf,"%d %d %d %d",&tmp,&itype,&atom1,&atom2);
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if (atom1 <= 0 || atom1 > map_tag_max ||
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atom2 <= 0 || atom2 > map_tag_max)
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if (atom1 <= 0 || atom1 > map_tag_max ||
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atom2 <= 0 || atom2 > map_tag_max)
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error->one(FLERR,"Invalid atom ID in Bonds section of data file");
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if (itype <= 0 || itype > nbondtypes)
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error->one(FLERR,"Invalid bond type in Bonds section of data file");
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@ -976,9 +976,9 @@ void Atom::data_bonds(int n, char *buf)
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}
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if (newton_bond == 0) {
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if ((m = map(atom2)) >= 0) {
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bond_type[m][num_bond[m]] = itype;
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bond_atom[m][num_bond[m]] = atom1;
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num_bond[m]++;
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bond_type[m][num_bond[m]] = itype;
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bond_atom[m][num_bond[m]] = atom1;
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num_bond[m]++;
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}
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}
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buf = next + 1;
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@ -999,9 +999,9 @@ void Atom::data_angles(int n, char *buf)
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next = strchr(buf,'\n');
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*next = '\0';
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sscanf(buf,"%d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3);
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if (atom1 <= 0 || atom1 > map_tag_max ||
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atom2 <= 0 || atom2 > map_tag_max ||
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atom3 <= 0 || atom3 > map_tag_max)
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if (atom1 <= 0 || atom1 > map_tag_max ||
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atom2 <= 0 || atom2 > map_tag_max ||
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atom3 <= 0 || atom3 > map_tag_max)
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error->one(FLERR,"Invalid atom ID in Angles section of data file");
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if (itype <= 0 || itype > nangletypes)
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error->one(FLERR,"Invalid angle type in Angles section of data file");
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@ -1014,18 +1014,18 @@ void Atom::data_angles(int n, char *buf)
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}
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if (newton_bond == 0) {
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if ((m = map(atom1)) >= 0) {
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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}
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if ((m = map(atom3)) >= 0) {
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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angle_type[m][num_angle[m]] = itype;
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angle_atom1[m][num_angle[m]] = atom1;
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angle_atom2[m][num_angle[m]] = atom2;
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angle_atom3[m][num_angle[m]] = atom3;
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num_angle[m]++;
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}
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}
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buf = next + 1;
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@ -1046,14 +1046,14 @@ void Atom::data_dihedrals(int n, char *buf)
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next = strchr(buf,'\n');
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*next = '\0';
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sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
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if (atom1 <= 0 || atom1 > map_tag_max ||
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atom2 <= 0 || atom2 > map_tag_max ||
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atom3 <= 0 || atom3 > map_tag_max ||
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atom4 <= 0 || atom4 > map_tag_max)
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if (atom1 <= 0 || atom1 > map_tag_max ||
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atom2 <= 0 || atom2 > map_tag_max ||
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atom3 <= 0 || atom3 > map_tag_max ||
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atom4 <= 0 || atom4 > map_tag_max)
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error->one(FLERR,"Invalid atom ID in Dihedrals section of data file");
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if (itype <= 0 || itype > ndihedraltypes)
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error->one(FLERR,
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"Invalid dihedral type in Dihedrals section of data file");
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"Invalid dihedral type in Dihedrals section of data file");
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if ((m = map(atom2)) >= 0) {
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dihedral_type[m][num_dihedral[m]] = itype;
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dihedral_atom1[m][num_dihedral[m]] = atom1;
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@ -1064,28 +1064,28 @@ void Atom::data_dihedrals(int n, char *buf)
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}
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if (newton_bond == 0) {
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if ((m = map(atom1)) >= 0) {
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dihedral_type[m][num_dihedral[m]] = itype;
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dihedral_atom1[m][num_dihedral[m]] = atom1;
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dihedral_atom2[m][num_dihedral[m]] = atom2;
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dihedral_atom3[m][num_dihedral[m]] = atom3;
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dihedral_atom4[m][num_dihedral[m]] = atom4;
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num_dihedral[m]++;
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dihedral_type[m][num_dihedral[m]] = itype;
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dihedral_atom1[m][num_dihedral[m]] = atom1;
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dihedral_atom2[m][num_dihedral[m]] = atom2;
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dihedral_atom3[m][num_dihedral[m]] = atom3;
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dihedral_atom4[m][num_dihedral[m]] = atom4;
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num_dihedral[m]++;
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}
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if ((m = map(atom3)) >= 0) {
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dihedral_type[m][num_dihedral[m]] = itype;
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dihedral_atom1[m][num_dihedral[m]] = atom1;
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dihedral_atom2[m][num_dihedral[m]] = atom2;
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dihedral_atom3[m][num_dihedral[m]] = atom3;
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dihedral_atom4[m][num_dihedral[m]] = atom4;
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num_dihedral[m]++;
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dihedral_type[m][num_dihedral[m]] = itype;
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dihedral_atom1[m][num_dihedral[m]] = atom1;
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dihedral_atom2[m][num_dihedral[m]] = atom2;
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dihedral_atom3[m][num_dihedral[m]] = atom3;
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dihedral_atom4[m][num_dihedral[m]] = atom4;
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num_dihedral[m]++;
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}
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if ((m = map(atom4)) >= 0) {
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dihedral_type[m][num_dihedral[m]] = itype;
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dihedral_atom1[m][num_dihedral[m]] = atom1;
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dihedral_atom2[m][num_dihedral[m]] = atom2;
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dihedral_atom3[m][num_dihedral[m]] = atom3;
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dihedral_atom4[m][num_dihedral[m]] = atom4;
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num_dihedral[m]++;
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dihedral_type[m][num_dihedral[m]] = itype;
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dihedral_atom1[m][num_dihedral[m]] = atom1;
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dihedral_atom2[m][num_dihedral[m]] = atom2;
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dihedral_atom3[m][num_dihedral[m]] = atom3;
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dihedral_atom4[m][num_dihedral[m]] = atom4;
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num_dihedral[m]++;
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}
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}
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buf = next + 1;
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@ -1106,14 +1106,14 @@ void Atom::data_impropers(int n, char *buf)
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next = strchr(buf,'\n');
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*next = '\0';
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sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
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if (atom1 <= 0 || atom1 > map_tag_max ||
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atom2 <= 0 || atom2 > map_tag_max ||
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atom3 <= 0 || atom3 > map_tag_max ||
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atom4 <= 0 || atom4 > map_tag_max)
|
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if (atom1 <= 0 || atom1 > map_tag_max ||
|
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atom2 <= 0 || atom2 > map_tag_max ||
|
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atom3 <= 0 || atom3 > map_tag_max ||
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atom4 <= 0 || atom4 > map_tag_max)
|
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error->one(FLERR,"Invalid atom ID in Impropers section of data file");
|
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if (itype <= 0 || itype > nimpropertypes)
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error->one(FLERR,
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"Invalid improper type in Impropers section of data file");
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"Invalid improper type in Impropers section of data file");
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if ((m = map(atom2)) >= 0) {
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improper_type[m][num_improper[m]] = itype;
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improper_atom1[m][num_improper[m]] = atom1;
|
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@ -1124,28 +1124,28 @@ void Atom::data_impropers(int n, char *buf)
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}
|
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if (newton_bond == 0) {
|
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if ((m = map(atom1)) >= 0) {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
}
|
||||
if ((m = map(atom3)) >= 0) {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
}
|
||||
if ((m = map(atom4)) >= 0) {
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
improper_type[m][num_improper[m]] = itype;
|
||||
improper_atom1[m][num_improper[m]] = atom1;
|
||||
improper_atom2[m][num_improper[m]] = atom2;
|
||||
improper_atom3[m][num_improper[m]] = atom3;
|
||||
improper_atom4[m][num_improper[m]] = atom4;
|
||||
num_improper[m]++;
|
||||
}
|
||||
}
|
||||
buf = next + 1;
|
||||
@ -1180,7 +1180,7 @@ void Atom::set_mass(const char *str)
|
||||
int n = sscanf(str,"%d %lg",&itype,&mass_one);
|
||||
if (n != 2) error->all(FLERR,"Invalid mass line in data file");
|
||||
|
||||
if (itype < 1 || itype > ntypes)
|
||||
if (itype < 1 || itype > ntypes)
|
||||
error->all(FLERR,"Invalid type for mass set");
|
||||
|
||||
mass[itype] = mass_one;
|
||||
@ -1197,7 +1197,7 @@ void Atom::set_mass(const char *str)
|
||||
void Atom::set_mass(int itype, double value)
|
||||
{
|
||||
if (mass == NULL) error->all(FLERR,"Cannot set mass for this atom style");
|
||||
if (itype < 1 || itype > ntypes)
|
||||
if (itype < 1 || itype > ntypes)
|
||||
error->all(FLERR,"Invalid type for mass set");
|
||||
|
||||
mass[itype] = value;
|
||||
@ -1281,7 +1281,7 @@ int Atom::radius_consistency(int itype, double &rad)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int Atom::shape_consistency(int itype,
|
||||
double &shapex, double &shapey, double &shapez)
|
||||
double &shapex, double &shapey, double &shapez)
|
||||
{
|
||||
double zero[3] = {0.0, 0.0, 0.0};
|
||||
double one[3] = {-1.0, -1.0, -1.0};
|
||||
@ -1435,7 +1435,7 @@ void Atom::sort()
|
||||
while (permute[empty] != i) {
|
||||
avec->copy(permute[empty],empty,0);
|
||||
empty = current[empty] = permute[empty];
|
||||
}
|
||||
}
|
||||
avec->copy(nlocal,empty,0);
|
||||
current[empty] = permute[empty];
|
||||
}
|
||||
@ -1471,13 +1471,13 @@ void Atom::setup_sort_bins()
|
||||
else if (!lmp->cuda) binsize = 0.5 * neighbor->cutneighmax;
|
||||
else {
|
||||
if (domain->dimension == 3) {
|
||||
double vol = (domain->boxhi[0]-domain->boxlo[0]) *
|
||||
(domain->boxhi[1]-domain->boxlo[1]) *
|
||||
(domain->boxhi[2]-domain->boxlo[2]);
|
||||
double vol = (domain->boxhi[0]-domain->boxlo[0]) *
|
||||
(domain->boxhi[1]-domain->boxlo[1]) *
|
||||
(domain->boxhi[2]-domain->boxlo[2]);
|
||||
binsize = pow(1.0*CUDA_CHUNK/natoms*vol,1.0/3.0);
|
||||
} else {
|
||||
double area = (domain->boxhi[0]-domain->boxlo[0]) *
|
||||
(domain->boxhi[1]-domain->boxlo[1]);
|
||||
double area = (domain->boxhi[0]-domain->boxlo[0]) *
|
||||
(domain->boxhi[1]-domain->boxlo[1]);
|
||||
binsize = pow(1.0*CUDA_CHUNK/natoms*area,1.0/2.0);
|
||||
}
|
||||
}
|
||||
@ -1487,7 +1487,7 @@ void Atom::setup_sort_bins()
|
||||
|
||||
// nbin xyz = local bins
|
||||
// bbox lo/hi = bounding box of my sub-domain
|
||||
|
||||
|
||||
if (domain->triclinic)
|
||||
domain->bbox(domain->sublo_lamda,domain->subhi_lamda,bboxlo,bboxhi);
|
||||
else {
|
||||
@ -1498,12 +1498,12 @@ void Atom::setup_sort_bins()
|
||||
bboxhi[1] = domain->subhi[1];
|
||||
bboxhi[2] = domain->subhi[2];
|
||||
}
|
||||
|
||||
|
||||
nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv);
|
||||
nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv);
|
||||
nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv);
|
||||
if (domain->dimension == 2) nbinz = 1;
|
||||
|
||||
|
||||
if (nbinx == 0) nbinx = 1;
|
||||
if (nbiny == 0) nbiny = 1;
|
||||
if (nbinz == 0) nbinz = 1;
|
||||
@ -1512,7 +1512,7 @@ void Atom::setup_sort_bins()
|
||||
bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
|
||||
bininvz = nbinz / (bboxhi[2]-bboxlo[2]);
|
||||
|
||||
if (1.0*nbinx*nbiny*nbinz > INT_MAX)
|
||||
if (1.0*nbinx*nbiny*nbinz > INT_MAX)
|
||||
error->one(FLERR,"Too many atom sorting bins");
|
||||
|
||||
nbins = nbinx*nbiny*nbinz;
|
||||
@ -1670,7 +1670,7 @@ int Atom::memcheck(const char *str)
|
||||
strcpy(padded," ");
|
||||
strcat(padded,str);
|
||||
strcat(padded," ");
|
||||
|
||||
|
||||
if (strstr(memstr,padded)) {
|
||||
delete [] padded;
|
||||
return 0;
|
||||
|
||||
Reference in New Issue
Block a user