git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9473 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
549
src/special.cpp
549
src/special.cpp
@ -17,11 +17,16 @@
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#include "atom.h"
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#include "atom_vec.h"
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#include "force.h"
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#include "comm.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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// allocate space for static class variable
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Special *Special::sptr;
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/* ---------------------------------------------------------------------- */
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Special::Special(LAMMPS *lmp) : Pointers(lmp)
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@ -49,10 +54,9 @@ Special::~Special()
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void Special::build()
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{
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int i,j,k,m,n,loop,size,original;
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int num12,num13,num14;
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int max,maxall,messtag,nbuf,nbufmax;
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int *buf,*bufcopy,*count;
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int i,j,k,m,n,size;
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int max,maxall,nbuf;
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int *buf;
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MPI_Request request;
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MPI_Status status;
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@ -100,10 +104,7 @@ void Special::build()
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nbuf = 0;
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for (i = 0; i < nlocal; i++) nbuf += num_bond[i];
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MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
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buf = new int[nbufmax];
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bufcopy = new int[nbufmax];
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memory->create(buf,nbuf,"special:buf");
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// fill buffer with global tags of bond partners of my atoms
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@ -116,23 +117,10 @@ void Special::build()
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// when receive buffer, scan tags for atoms I own
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// when find one, increment nspecial count for that atom
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messtag = 1;
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for (loop = 0; loop < nprocs; loop++) {
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for (i = 0; i < size; i++) {
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m = atom->map(buf[i]);
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if (m >= 0 && m < nlocal) nspecial[m][0]++;
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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MPI_Send(buf,size,MPI_INT,next,messtag,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&size);
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for (j = 0; j < size; j++) buf[j] = bufcopy[j];
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}
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}
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sptr = this;
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comm->ring(size,sizeof(int),buf,1,ring_one,NULL);
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delete [] buf;
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delete [] bufcopy;
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memory->destroy(buf);
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}
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// ----------------------------------------------------
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@ -153,7 +141,7 @@ void Special::build()
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// count = accumulating counter
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count = new int[nlocal];
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memory->create(count,nlocal,"special:count");
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for (i = 0; i < nlocal; i++) count[i] = 0;
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// add bond partners stored by atom to onetwo list
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@ -172,10 +160,7 @@ void Special::build()
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nbuf = 0;
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for (i = 0; i < nlocal; i++) nbuf += 2*num_bond[i];
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MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
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buf = new int[nbufmax];
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bufcopy = new int[nbufmax];
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memory->create(buf,nbuf,"special:buf");
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// fill buffer with global tags of both atoms in bond
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@ -190,26 +175,13 @@ void Special::build()
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// when receive buffer, scan 2nd-atom tags for atoms I own
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// when find one, add 1st-atom tag to onetwo list for 2nd atom
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messtag = 2;
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for (loop = 0; loop < nprocs; loop++) {
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for (i = 1; i < size; i += 2) {
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m = atom->map(buf[i]);
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if (m >= 0 && m < nlocal) onetwo[m][count[m]++] = buf[i-1];
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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MPI_Send(buf,size,MPI_INT,next,messtag,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&size);
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for (j = 0; j < size; j++) buf[j] = bufcopy[j];
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}
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}
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sptr = this;
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comm->ring(size,sizeof(int),buf,2,ring_two,NULL);
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delete [] buf;
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delete [] bufcopy;
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memory->destroy(buf);
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}
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delete [] count;
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memory->destroy(count);
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// -----------------------------------------------------
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// done if special_bonds for 1-3, 1-4 are set to 1.0
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@ -230,10 +202,7 @@ void Special::build()
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nbuf = 0;
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for (i = 0; i < nlocal; i++) nbuf += 2 + nspecial[i][0];
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MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
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buf = new int[nbufmax];
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bufcopy = new int[nbufmax];
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memory->create(buf,nbuf,"special:buf");
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// fill buffer with:
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// (1) = counter for 1-3 neighbors, initialized to 0
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@ -252,27 +221,8 @@ void Special::build()
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// when find one, increment 1-3 count by # of 1-2 neighbors of my atom,
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// subtracting one since my list will contain original atom
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messtag = 3;
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for (loop = 0; loop < nprocs; loop++) {
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i = 0;
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while (i < size) {
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n = buf[i];
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num12 = buf[i+1];
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for (j = 0; j < num12; j++) {
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m = atom->map(buf[i+2+j]);
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if (m >= 0 && m < nlocal) n += nspecial[m][0] - 1;
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}
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buf[i] = n;
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i += 2 + num12;
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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MPI_Send(buf,size,MPI_INT,next,messtag,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&size);
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for (j = 0; j < size; j++) buf[j] = bufcopy[j];
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}
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}
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sptr = this;
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comm->ring(size,sizeof(int),buf,3,ring_three,buf);
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// extract count from buffer that has cycled back to me
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// nspecial[i][1] = # of 1-3 neighbors of atom i
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@ -283,8 +233,7 @@ void Special::build()
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j += 2 + nspecial[i][0];
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}
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delete [] buf;
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delete [] bufcopy;
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memory->destroy(buf);
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// ----------------------------------------------------
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// create onethree[i] = list of 1-3 neighbors for atom i
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@ -307,10 +256,7 @@ void Special::build()
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nbuf = 0;
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for (i = 0; i < nlocal; i++) nbuf += 4 + nspecial[i][0] + nspecial[i][1];
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MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
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buf = new int[nbufmax];
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bufcopy = new int[nbufmax];
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memory->create(buf,nbuf,"special:buf");
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// fill buffer with:
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// (1) = global tag of original atom
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@ -337,32 +283,8 @@ void Special::build()
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// exclude the atom whose tag = original
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// this process may include duplicates but they will be culled later
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messtag = 4;
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for (loop = 0; loop < nprocs; loop++) {
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i = 0;
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while (i < size) {
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original = buf[i];
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num12 = buf[i+1];
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num13 = buf[i+2];
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n = buf[i+3];
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for (j = 0; j < num12; j++) {
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m = atom->map(buf[i+4+j]);
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if (m >= 0 && m < nlocal)
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for (k = 0; k < nspecial[m][0]; k++)
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if (onetwo[m][k] != original)
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buf[i+4+num12+(n++)] = onetwo[m][k];
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}
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buf[i+3] = n;
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i += 4 + num12 + num13;
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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MPI_Send(buf,size,MPI_INT,next,messtag,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&size);
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for (j = 0; j < size; j++) buf[j] = bufcopy[j];
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}
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}
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sptr = this;
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comm->ring(size,sizeof(int),buf,4,ring_four,buf);
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// fill onethree with buffer values that have been returned to me
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// sanity check: accumulated buf[i+3] count should equal
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@ -377,8 +299,7 @@ void Special::build()
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onethree[i][k] = buf[j++];
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}
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delete [] buf;
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delete [] bufcopy;
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memory->destroy(buf);
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// done if special_bonds for 1-4 are set to 1.0
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@ -397,10 +318,7 @@ void Special::build()
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nbuf = 0;
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for (i = 0; i < nlocal; i++) nbuf += 2 + nspecial[i][1];
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MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
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buf = new int[nbufmax];
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bufcopy = new int[nbufmax];
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memory->create(buf,nbuf,"special:buf");
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// fill buffer with:
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// (1) = counter for 1-4 neighbors, initialized to 0
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@ -419,27 +337,8 @@ void Special::build()
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// when find one, increment 1-4 count by # of 1-2 neighbors of my atom
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// may include duplicates and original atom but they will be culled later
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messtag = 5;
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for (loop = 0; loop < nprocs; loop++) {
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i = 0;
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while (i < size) {
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n = buf[i];
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num13 = buf[i+1];
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for (j = 0; j < num13; j++) {
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m = atom->map(buf[i+2+j]);
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if (m >= 0 && m < nlocal) n += nspecial[m][0];
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}
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buf[i] = n;
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i += 2 + num13;
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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MPI_Send(buf,size,MPI_INT,next,messtag,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&size);
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for (j = 0; j < size; j++) buf[j] = bufcopy[j];
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}
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}
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sptr = this;
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comm->ring(size,sizeof(int),buf,5,ring_five,buf);
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// extract count from buffer that has cycled back to me
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// nspecial[i][2] = # of 1-4 neighbors of atom i
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@ -450,8 +349,7 @@ void Special::build()
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j += 2 + nspecial[i][1];
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}
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delete [] buf;
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delete [] bufcopy;
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memory->destroy(buf);
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// ----------------------------------------------------
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// create onefour[i] = list of 1-4 neighbors for atom i
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@ -475,10 +373,7 @@ void Special::build()
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nbuf = 0;
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for (i = 0; i < nlocal; i++)
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nbuf += 3 + nspecial[i][1] + nspecial[i][2];
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MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
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buf = new int[nbufmax];
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bufcopy = new int[nbufmax];
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memory->create(buf,nbuf,"special:buf");
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// fill buffer with:
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// (1) = # of 1-3 neighbors
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@ -502,30 +397,8 @@ void Special::build()
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// incrementing the count in buf(i+4)
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// this process may include duplicates but they will be culled later
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messtag = 6;
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for (loop = 0; loop < nprocs; loop++) {
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i = 0;
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while (i < size) {
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num13 = buf[i];
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num14 = buf[i+1];
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n = buf[i+2];
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for (j = 0; j < num13; j++) {
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m = atom->map(buf[i+3+j]);
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if (m >= 0 && m < nlocal)
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for (k = 0; k < nspecial[m][0]; k++)
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buf[i+3+num13+(n++)] = onetwo[m][k];
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}
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buf[i+2] = n;
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i += 3 + num13 + num14;
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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MPI_Send(buf,size,MPI_INT,next,messtag,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&size);
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for (j = 0; j < size; j++) buf[j] = bufcopy[j];
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}
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}
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sptr = this;
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comm->ring(size,sizeof(int),buf,6,ring_six,buf);
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// fill onefour with buffer values that have been returned to me
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// sanity check: accumulated buf[i+2] count should equal
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@ -540,8 +413,7 @@ void Special::build()
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onefour[i][k] = buf[j++];
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}
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delete [] buf;
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delete [] bufcopy;
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memory->destroy(buf);
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combine();
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if (force->special_angle) angle_trim();
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@ -699,7 +571,7 @@ void Special::combine()
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void Special::angle_trim()
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{
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int i,j,m,n,iglobal,jglobal,ilocal,jlocal;
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int i,j,m,n;
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MPI_Request request;
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MPI_Status status;
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@ -743,7 +615,6 @@ void Special::angle_trim()
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int maxcount = 0;
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for (i = 0; i < nlocal; i++)
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maxcount = MAX(maxcount,nspecial[i][1]-nspecial[i][0]);
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int **dflag;
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memory->create(dflag,nlocal,maxcount,"special::dflag");
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for (i = 0; i < nlocal; i++) {
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@ -757,12 +628,8 @@ void Special::angle_trim()
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int nbuf = 0;
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for (i = 0; i < nlocal; i++) nbuf += 2*num_angle[i] + 2*2*num_dihedral[i];
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int nbufmax;
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MPI_Allreduce(&nbuf,&nbufmax,1,MPI_INT,MPI_MAX,world);
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int *buf = new int[nbufmax];
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int *bufcopy = new int[nbufmax];
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int *buf;
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memory->create(buf,nbuf,"special:buf");
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// fill buffer with list of 1,3 atoms in each angle
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// and with list of 1,3 and 2,4 atoms in each dihedral
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@ -785,41 +652,8 @@ void Special::angle_trim()
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// when receive buffer, scan list of 1,3 atoms looking for atoms I own
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// when find one, scan its 1-3 neigh list and mark I,J as in an angle
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int next = me + 1;
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int prev = me -1;
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if (next == nprocs) next = 0;
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if (prev < 0) prev = nprocs - 1;
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int messtag = 7;
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for (int loop = 0; loop < nprocs; loop++) {
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i = 0;
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while (i < size) {
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iglobal = buf[i];
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jglobal = buf[i+1];
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ilocal = atom->map(iglobal);
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jlocal = atom->map(jglobal);
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if (ilocal >= 0 && ilocal < nlocal)
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for (m = nspecial[ilocal][0]; m < nspecial[ilocal][1]; m++)
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if (jglobal == special[ilocal][m]) {
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dflag[ilocal][m-nspecial[ilocal][0]] = 1;
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break;
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}
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if (jlocal >= 0 && jlocal < nlocal)
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for (m = nspecial[jlocal][0]; m < nspecial[jlocal][1]; m++)
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if (iglobal == special[jlocal][m]) {
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dflag[jlocal][m-nspecial[jlocal][0]] = 1;
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break;
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}
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i += 2;
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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MPI_Send(buf,size,MPI_INT,next,messtag,world);
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MPI_Wait(&request,&status);
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MPI_Get_count(&status,MPI_INT,&size);
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for (j = 0; j < size; j++) buf[j] = bufcopy[j];
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}
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}
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sptr = this;
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comm->ring(size,sizeof(int),buf,7,ring_seven,NULL);
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// delete 1-3 neighbors if they are not flagged in dflag
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// preserve 1-4 neighbors
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@ -839,8 +673,7 @@ void Special::angle_trim()
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// clean up
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memory->destroy(dflag);
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delete [] buf;
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delete [] bufcopy;
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memory->destroy(buf);
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// if no angles or dihedrals are defined,
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// delete all 1-3 neighs, preserving 1-4 neighs
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@ -880,7 +713,7 @@ void Special::angle_trim()
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void Special::dihedral_trim()
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{
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int i,j,m,n,iglobal,jglobal,ilocal,jlocal;
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int i,j,m,n;
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MPI_Request request;
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MPI_Status status;
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@ -918,7 +751,6 @@ void Special::dihedral_trim()
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int maxcount = 0;
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for (i = 0; i < nlocal; i++)
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maxcount = MAX(maxcount,nspecial[i][2]-nspecial[i][1]);
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int **dflag;
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memory->create(dflag,nlocal,maxcount,"special::dflag");
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for (i = 0; i < nlocal; i++) {
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@ -931,12 +763,8 @@ void Special::dihedral_trim()
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int nbuf = 0;
|
||||
for (i = 0; i < nlocal; i++) nbuf += 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];
|
||||
int *buf;
|
||||
memory->create(buf,nbuf,"special:buf");
|
||||
|
||||
// fill buffer with list of 1,4 atoms in each dihedral
|
||||
|
||||
@ -951,41 +779,8 @@ void Special::dihedral_trim()
|
||||
// when receive buffer, scan list of 1,4 atoms looking for atoms I own
|
||||
// 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;
|
||||
if (next == nprocs) next = 0;
|
||||
if (prev < 0) prev = nprocs - 1;
|
||||
|
||||
int messtag = 8;
|
||||
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;
|
||||
}
|
||||
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];
|
||||
}
|
||||
}
|
||||
sptr = this;
|
||||
comm->ring(size,sizeof(int),buf,8,ring_eight,NULL);
|
||||
|
||||
// delete 1-4 neighbors if they are not flagged in dflag
|
||||
|
||||
@ -1000,8 +795,7 @@ void Special::dihedral_trim()
|
||||
// clean up
|
||||
|
||||
memory->destroy(dflag);
|
||||
delete [] buf;
|
||||
delete [] bufcopy;
|
||||
memory->destroy(buf);
|
||||
|
||||
// if no dihedrals are defined, delete all 1-4 neighs
|
||||
|
||||
@ -1024,3 +818,254 @@ void Special::dihedral_trim()
|
||||
" %g = # of 1-4 neighbors after dihedral trim\n",allcount);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan tags for atoms I own
|
||||
when find one, increment nspecial count for that atom
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_one(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int **nspecial = atom->nspecial;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int m;
|
||||
|
||||
for (int i = 0; i < ndatum; i++) {
|
||||
m = atom->map(buf[i]);
|
||||
if (m >= 0 && m < nlocal) nspecial[m][0]++;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan 2nd-atom tags for atoms I own
|
||||
when find one, add 1st-atom tag to onetwo list for 2nd atom
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_two(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int **onetwo = sptr->onetwo;
|
||||
int *count = sptr->count;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int m;
|
||||
|
||||
for (int i = 1; i < ndatum; i += 2) {
|
||||
m = atom->map(buf[i]);
|
||||
if (m >= 0 && m < nlocal) onetwo[m][count[m]++] = buf[i-1];
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan list of 1-2 neighbors for atoms I own
|
||||
when find one, increment 1-3 count by # of 1-2 neighbors of my atom,
|
||||
subtracting one since my list will contain original atom
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_three(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int **nspecial = atom->nspecial;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int i,j,m,n,num12;
|
||||
|
||||
i = 0;
|
||||
while (i < ndatum) {
|
||||
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;
|
||||
}
|
||||
buf[i] = n;
|
||||
i += 2 + num12;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan list of 1-2 neighbors for atoms I own
|
||||
when find one, add its neighbors to 1-3 list
|
||||
increment the count in buf(i+4)
|
||||
exclude the atom whose tag = original
|
||||
this process may include duplicates but they will be culled later
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_four(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int **nspecial = atom->nspecial;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int **onetwo = sptr->onetwo;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int i,j,k,m,n,original,num12,num13;
|
||||
|
||||
i = 0;
|
||||
while (i < ndatum) {
|
||||
original = buf[i];
|
||||
num12 = buf[i+1];
|
||||
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];
|
||||
}
|
||||
buf[i+3] = n;
|
||||
i += 4 + num12 + num13;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan list of 1-3 neighbors for atoms I own
|
||||
when find one, increment 1-4 count by # of 1-2 neighbors of my atom
|
||||
may include duplicates and original atom but they will be culled later
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_five(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int **nspecial = atom->nspecial;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int i,j,m,n,num13;
|
||||
|
||||
i = 0;
|
||||
while (i < ndatum) {
|
||||
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];
|
||||
}
|
||||
buf[i] = n;
|
||||
i += 2 + num13;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan list of 1-3 neighbors for atoms I own
|
||||
when find one, add its neighbors to 1-4 list
|
||||
incrementing the count in buf(i+4)
|
||||
this process may include duplicates but they will be culled later
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_six(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int **nspecial = atom->nspecial;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int **onetwo = sptr->onetwo;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int i,j,k,m,n,num13,num14;
|
||||
|
||||
i = 0;
|
||||
while (i < ndatum) {
|
||||
num13 = buf[i];
|
||||
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];
|
||||
}
|
||||
buf[i+2] = n;
|
||||
i += 3 + num13 + num14;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan list of 1,3 atoms looking for atoms I own
|
||||
when find one, scan its 1-3 neigh list and mark I,J as in an angle
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_seven(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int **nspecial = atom->nspecial;
|
||||
int **special = atom->special;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int **dflag = sptr->dflag;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int i,m,iglobal,jglobal,ilocal,jlocal;
|
||||
|
||||
i = 0;
|
||||
while (i < ndatum) {
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
when receive buffer, scan list of 1,4 atoms looking for atoms I own
|
||||
when find one, scan its 1-4 neigh list and mark I,J as in a dihedral
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::ring_eight(int ndatum, char *cbuf)
|
||||
{
|
||||
Atom *atom = sptr->atom;
|
||||
int **nspecial = atom->nspecial;
|
||||
int **special = atom->special;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int **dflag = sptr->dflag;
|
||||
|
||||
int *buf = (int *) cbuf;
|
||||
int i,m,iglobal,jglobal,ilocal,jlocal;
|
||||
|
||||
i = 0;
|
||||
while (i < ndatum) {
|
||||
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;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user