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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8226 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2012-06-06 22:47:51 +00:00
parent f46eb9dedb
commit ef9e700545
1408 changed files with 58053 additions and 57983 deletions
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262
src/special.cpp
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@ -5,7 +5,7 @@
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
@ -44,7 +44,7 @@ Special::~Special()
/* ----------------------------------------------------------------------
create 1-2, 1-3, 1-4 lists of topology neighbors
store in onetwo, onethree, onefour for each atom
store 3 counters in nspecial[i]
store 3 counters in nspecial[i]
------------------------------------------------------------------------- */
void Special::build()
@ -70,7 +70,7 @@ void Special::build()
// setup ring of procs
int next = me + 1;
int prev = me -1;
int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@ -110,7 +110,7 @@ void Special::build()
size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++)
buf[size++] = bond_atom[i][j];
buf[size++] = bond_atom[i][j];
// cycle buffer around ring of procs back to self
// when receive buffer, scan tags for atoms I own
@ -119,15 +119,15 @@ void Special::build()
messtag = 1;
for (loop = 0; loop < nprocs; loop++) {
for (i = 0; i < size; i++) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) nspecial[m][0]++;
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) nspecial[m][0]++;
}
if (me != next) {
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
@ -182,8 +182,8 @@ void Special::build()
size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_bond[i]; j++) {
buf[size++] = tag[i];
buf[size++] = bond_atom[i][j];
buf[size++] = tag[i];
buf[size++] = bond_atom[i][j];
}
// cycle buffer around ring of procs back to self
@ -193,15 +193,15 @@ void Special::build()
messtag = 2;
for (loop = 0; loop < nprocs; loop++) {
for (i = 1; i < size; i += 2) {
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) onetwo[m][count[m]++] = buf[i-1];
m = atom->map(buf[i]);
if (m >= 0 && m < nlocal) onetwo[m][count[m]++] = buf[i-1];
}
if (me != next) {
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
@ -259,8 +259,8 @@ void Special::build()
n = buf[i];
num12 = buf[i+1];
for (j = 0; j < num12; j++) {
m = atom->map(buf[i+2+j]);
if (m >= 0 && m < nlocal) n += nspecial[m][0] - 1;
m = atom->map(buf[i+2+j]);
if (m >= 0 && m < nlocal) n += nspecial[m][0] - 1;
}
buf[i] = n;
i += 2 + num12;
@ -346,11 +346,11 @@ void Special::build()
num13 = buf[i+2];
n = buf[i+3];
for (j = 0; j < num12; j++) {
m = atom->map(buf[i+4+j]);
if (m >= 0 && m < nlocal)
for (k = 0; k < nspecial[m][0]; k++)
if (onetwo[m][k] != original)
buf[i+4+num12+(n++)] = onetwo[m][k];
m = atom->map(buf[i+4+j]);
if (m >= 0 && m < nlocal)
for (k = 0; k < nspecial[m][0]; k++)
if (onetwo[m][k] != original)
buf[i+4+num12+(n++)] = onetwo[m][k];
}
buf[i+3] = n;
i += 4 + num12 + num13;
@ -373,7 +373,7 @@ void Special::build()
if (buf[j+3] != nspecial[i][1])
error->one(FLERR,"1-3 bond count is inconsistent");
j += 4 + nspecial[i][0];
for (k = 0; k < nspecial[i][1]; k++)
for (k = 0; k < nspecial[i][1]; k++)
onethree[i][k] = buf[j++];
}
@ -426,8 +426,8 @@ void Special::build()
n = buf[i];
num13 = buf[i+1];
for (j = 0; j < num13; j++) {
m = atom->map(buf[i+2+j]);
if (m >= 0 && m < nlocal) n += nspecial[m][0];
m = atom->map(buf[i+2+j]);
if (m >= 0 && m < nlocal) n += nspecial[m][0];
}
buf[i] = n;
i += 2 + num13;
@ -473,7 +473,7 @@ void Special::build()
// info for each atom = 3 scalars + list of 1-3 neighs + list of 1-4 neighs
nbuf = 0;
for (i = 0; i < nlocal; i++)
for (i = 0; i < nlocal; i++)
nbuf += 3 + nspecial[i][1] + nspecial[i][2];
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
@ -510,10 +510,10 @@ void Special::build()
num14 = buf[i+1];
n = buf[i+2];
for (j = 0; j < num13; j++) {
m = atom->map(buf[i+3+j]);
if (m >= 0 && m < nlocal)
for (k = 0; k < nspecial[m][0]; k++)
buf[i+3+num13+(n++)] = onetwo[m][k];
m = atom->map(buf[i+3+j]);
if (m >= 0 && m < nlocal)
for (k = 0; k < nspecial[m][0]; k++)
buf[i+3+num13+(n++)] = onetwo[m][k];
}
buf[i+2] = n;
i += 3 + num13 + num14;
@ -536,7 +536,7 @@ void Special::build()
if (buf[j+2] != nspecial[i][2])
error->one(FLERR,"1-4 bond count is inconsistent");
j += 3 + nspecial[i][1];
for (k = 0; k < nspecial[i][2]; k++)
for (k = 0; k < nspecial[i][2]; k++)
onefour[i][k] = buf[j++];
}
@ -551,7 +551,7 @@ void Special::build()
/* ----------------------------------------------------------------------
concatenate onetwo, onethree, onefour into master atom->special list
remove duplicates
convert nspecial[0], nspecial[1], nspecial[2] into cumulative counters
convert nspecial[0], nspecial[1], nspecial[2] into cumulative counters
------------------------------------------------------------------------- */
void Special::combine()
@ -589,22 +589,22 @@ void Special::combine()
for (j = 0; j < nspecial[i][0]; j++) {
m = onetwo[i][j];
if (atom->map(m) < 0) {
unique++;
atom->map_one(m,0);
unique++;
atom->map_one(m,0);
}
}
for (j = 0; j < nspecial[i][1]; j++) {
m = onethree[i][j];
if (atom->map(m) < 0) {
unique++;
atom->map_one(m,0);
unique++;
atom->map_one(m,0);
}
}
for (j = 0; j < nspecial[i][2]; j++) {
m = onefour[i][j];
if (atom->map(m) < 0) {
unique++;
atom->map_one(m,0);
unique++;
atom->map_one(m,0);
}
}
@ -657,8 +657,8 @@ void Special::combine()
for (j = 0; j < nspecial[i][0]; j++) {
m = onetwo[i][j];
if (atom->map(m) < 0) {
special[i][unique++] = m;
atom->map_one(m,0);
special[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][0] = unique;
@ -666,8 +666,8 @@ void Special::combine()
for (j = 0; j < nspecial[i][1]; j++) {
m = onethree[i][j];
if (atom->map(m) < 0) {
special[i][unique++] = m;
atom->map_one(m,0);
special[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][1] = unique;
@ -675,8 +675,8 @@ void Special::combine()
for (j = 0; j < nspecial[i][2]; j++) {
m = onefour[i][j];
if (atom->map(m) < 0) {
special[i][unique++] = m;
atom->map_one(m,0);
special[i][unique++] = m;
atom->map_one(m,0);
}
}
nspecial[i][2] = unique;
@ -702,7 +702,7 @@ void Special::angle_trim()
int i,j,m,n,iglobal,jglobal,ilocal,jlocal;
MPI_Request request;
MPI_Status status;
int *num_angle = atom->num_angle;
int *num_dihedral = atom->num_dihedral;
int **angle_atom1 = atom->angle_atom1;
@ -720,19 +720,19 @@ void Special::angle_trim()
double onethreecount = 0.0;
for (i = 0; i < nlocal; i++)
onethreecount += nspecial[i][1] - nspecial[i][0];
double allcount;
MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-3 neighbors before angle trim\n",allcount);
" %g = # of 1-3 neighbors before angle trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-3 neighbors before angle trim\n",allcount);
" %g = # of 1-3 neighbors before angle trim\n",allcount);
}
// if angles or dihedrals are defined,
// flag each 1-3 neigh if it appears in an angle or dihedral
@ -745,7 +745,7 @@ void Special::angle_trim()
maxcount = MAX(maxcount,nspecial[i][1]-nspecial[i][0]);
int **dflag;
memory->create(dflag,nlocal,maxcount,"special::dflag");
for (i = 0; i < nlocal; i++) {
n = nspecial[i][1] - nspecial[i][0];
for (j = 0; j < n; j++) dflag[i][j] = 0;
@ -754,31 +754,31 @@ void Special::angle_trim()
// nbufmax = largest buffer needed to hold info from any proc
// info for each atom = list of 1,3 atoms in each angle stored by atom
// and list of 1,3 and 2,4 atoms in each dihedral stored by atom
int nbuf = 0;
for (i = 0; i < nlocal; i++) nbuf += 2*num_angle[i] + 2*2*num_dihedral[i];
int nbufmax;
MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
int *buf = new int[nbufmax];
int *bufcopy = new int[nbufmax];
// fill buffer with list of 1,3 atoms in each angle
// and with list of 1,3 and 2,4 atoms in each dihedral
int size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_angle[i]; j++) {
buf[size++] = angle_atom1[i][j];
buf[size++] = angle_atom3[i][j];
buf[size++] = angle_atom1[i][j];
buf[size++] = angle_atom3[i][j];
}
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++) {
buf[size++] = dihedral_atom1[i][j];
buf[size++] = dihedral_atom3[i][j];
buf[size++] = dihedral_atom2[i][j];
buf[size++] = dihedral_atom4[i][j];
buf[size++] = dihedral_atom1[i][j];
buf[size++] = dihedral_atom3[i][j];
buf[size++] = dihedral_atom2[i][j];
buf[size++] = dihedral_atom4[i][j];
}
// cycle buffer around ring of procs back to self
@ -786,7 +786,7 @@ void Special::angle_trim()
// when find one, scan its 1-3 neigh list and mark I,J as in an angle
int next = me + 1;
int prev = me -1;
int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@ -794,48 +794,48 @@ void Special::angle_trim()
for (int loop = 0; loop < nprocs; loop++) {
i = 0;
while (i < size) {
iglobal = buf[i];
jglobal = buf[i+1];
ilocal = atom->map(iglobal);
jlocal = atom->map(jglobal);
if (ilocal >= 0 && ilocal < nlocal)
for (m = nspecial[ilocal][0]; m < nspecial[ilocal][1]; m++)
if (jglobal == special[ilocal][m]) {
dflag[ilocal][m-nspecial[ilocal][0]] = 1;
break;
}
if (jlocal >= 0 && jlocal < nlocal)
for (m = nspecial[jlocal][0]; m < nspecial[jlocal][1]; m++)
if (iglobal == special[jlocal][m]) {
dflag[jlocal][m-nspecial[jlocal][0]] = 1;
break;
}
i += 2;
iglobal = buf[i];
jglobal = buf[i+1];
ilocal = atom->map(iglobal);
jlocal = atom->map(jglobal);
if (ilocal >= 0 && ilocal < nlocal)
for (m = nspecial[ilocal][0]; m < nspecial[ilocal][1]; m++)
if (jglobal == special[ilocal][m]) {
dflag[ilocal][m-nspecial[ilocal][0]] = 1;
break;
}
if (jlocal >= 0 && jlocal < nlocal)
for (m = nspecial[jlocal][0]; m < nspecial[jlocal][1]; m++)
if (iglobal == special[jlocal][m]) {
dflag[jlocal][m-nspecial[jlocal][0]] = 1;
break;
}
i += 2;
}
if (me != next) {
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
// delete 1-3 neighbors if they are not flagged in dflag
// preserve 1-4 neighbors
int offset;
for (i = 0; i < nlocal; i++) {
offset = m = nspecial[i][0];
for (j = nspecial[i][0]; j < nspecial[i][1]; j++)
if (dflag[i][j-offset]) special[i][m++] = special[i][j];
if (dflag[i][j-offset]) special[i][m++] = special[i][j];
offset = m;
for (j = nspecial[i][1]; j < nspecial[i][2]; j++)
special[i][m++] = special[i][j];
special[i][m++] = special[i][j];
nspecial[i][1] = offset;
nspecial[i][2] = m;
}
// clean up
memory->destroy(dflag);
@ -849,7 +849,7 @@ void Special::angle_trim()
for (i = 0; i < nlocal; i++) {
m = nspecial[i][0];
for (j = nspecial[i][1]; j < nspecial[i][2]; j++)
special[i][m++] = special[i][j];
special[i][m++] = special[i][j];
nspecial[i][1] = nspecial[i][0];
nspecial[i][2] = m;
}
@ -860,17 +860,17 @@ void Special::angle_trim()
onethreecount = 0.0;
for (i = 0; i < nlocal; i++)
onethreecount += nspecial[i][1] - nspecial[i][0];
MPI_Allreduce(&onethreecount,&allcount,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-3 neighbors after angle trim\n",allcount);
" %g = # of 1-3 neighbors after angle trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-3 neighbors after angle trim\n",allcount);
}
" %g = # of 1-3 neighbors after angle trim\n",allcount);
}
}
/* ----------------------------------------------------------------------
@ -903,10 +903,10 @@ void Special::dihedral_trim()
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-4 neighbors before dihedral trim\n",allcount);
" %g = # of 1-4 neighbors before dihedral trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-4 neighbors before dihedral trim\n",allcount);
" %g = # of 1-4 neighbors before dihedral trim\n",allcount);
}
// if dihedrals are defined, flag each 1-4 neigh if it appears in a dihedral
@ -943,8 +943,8 @@ void Special::dihedral_trim()
int size = 0;
for (i = 0; i < nlocal; i++)
for (j = 0; j < num_dihedral[i]; j++) {
buf[size++] = dihedral_atom1[i][j];
buf[size++] = dihedral_atom4[i][j];
buf[size++] = dihedral_atom1[i][j];
buf[size++] = dihedral_atom4[i][j];
}
// cycle buffer around ring of procs back to self
@ -952,7 +952,7 @@ void Special::dihedral_trim()
// when find one, scan its 1-4 neigh list and mark I,J as in a dihedral
int next = me + 1;
int prev = me -1;
int prev = me -1;
if (next == nprocs) next = 0;
if (prev < 0) prev = nprocs - 1;
@ -960,43 +960,43 @@ void Special::dihedral_trim()
for (int loop = 0; loop < nprocs; loop++) {
i = 0;
while (i < size) {
iglobal = buf[i];
jglobal = buf[i+1];
ilocal = atom->map(iglobal);
jlocal = atom->map(jglobal);
if (ilocal >= 0 && ilocal < nlocal)
for (m = nspecial[ilocal][1]; m < nspecial[ilocal][2]; m++)
if (jglobal == special[ilocal][m]) {
dflag[ilocal][m-nspecial[ilocal][1]] = 1;
break;
}
if (jlocal >= 0 && jlocal < nlocal)
for (m = nspecial[jlocal][1]; m < nspecial[jlocal][2]; m++)
if (iglobal == special[jlocal][m]) {
dflag[jlocal][m-nspecial[jlocal][1]] = 1;
break;
}
i += 2;
iglobal = buf[i];
jglobal = buf[i+1];
ilocal = atom->map(iglobal);
jlocal = atom->map(jglobal);
if (ilocal >= 0 && ilocal < nlocal)
for (m = nspecial[ilocal][1]; m < nspecial[ilocal][2]; m++)
if (jglobal == special[ilocal][m]) {
dflag[ilocal][m-nspecial[ilocal][1]] = 1;
break;
}
if (jlocal >= 0 && jlocal < nlocal)
for (m = nspecial[jlocal][1]; m < nspecial[jlocal][2]; m++)
if (iglobal == special[jlocal][m]) {
dflag[jlocal][m-nspecial[jlocal][1]] = 1;
break;
}
i += 2;
}
if (me != next) {
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
MPI_Send(buf,size,MPI_INT,next,messtag,world);
MPI_Wait(&request,&status);
MPI_Get_count(&status,MPI_INT,&size);
for (j = 0; j < size; j++) buf[j] = bufcopy[j];
}
}
// delete 1-4 neighbors if they are not flagged in dflag
int offset;
for (i = 0; i < nlocal; i++) {
offset = m = nspecial[i][1];
for (j = nspecial[i][1]; j < nspecial[i][2]; j++)
if (dflag[i][j-offset]) special[i][m++] = special[i][j];
if (dflag[i][j-offset]) special[i][m++] = special[i][j];
nspecial[i][2] = m;
}
// clean up
memory->destroy(dflag);
@ -1018,9 +1018,9 @@ void Special::dihedral_trim()
if (me == 0) {
if (screen)
fprintf(screen,
" %g = # of 1-4 neighbors after dihedral trim\n",allcount);
" %g = # of 1-4 neighbors after dihedral trim\n",allcount);
if (logfile)
fprintf(logfile,
" %g = # of 1-4 neighbors after dihedral trim\n",allcount);
" %g = # of 1-4 neighbors after dihedral trim\n",allcount);
}
}