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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12245 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2014-08-01 23:40:44 +00:00
parent 00a803f04b
commit a12cc9cce8
5 changed files with 151 additions and 18 deletions
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85
src/comm_tiled.cpp
View File

@ -417,24 +417,39 @@ void CommTiled::setup()
noverlap = 0;
iswap = 2*idim;
n = nsendproc[iswap];
for (i = 0; i < n; i++) {
proc = sendproc[iswap][i];
if (proc == me) continue;
if ((this->*box_touch)(proc,idim,0)) overlap[noverlap++] = proc;
}
noverlap1 = noverlap;
iswap = 2*idim;
n = nsendproc[iswap];
for (i = 0; i < n; i++) {
proc = sendproc[iswap][i];
if (proc == me) continue;
if ((this->*box_touch)(proc,idim,0)) {
for (j = 0; j < noverlap1; j++)
if (overlap[j] == proc) break;
if (j < noverlap1) continue;
if (noverlap == maxoverlap) {
maxoverlap += DELTA_PROCS;
memory->grow(overlap,maxoverlap,"comm:overlap");
}
overlap[noverlap++] = proc;
}
}
noverlap1 = noverlap;
iswap = 2*idim+1;
n = nsendproc[iswap];
MPI_Barrier(world);
for (i = 0; i < n; i++) {
proc = sendproc[iswap][i];
if (proc == me) continue;
if ((this->*box_touch)(proc,idim,1)) {
for (j = 0; j < noverlap1; j++)
if (overlap[j] == proc) break;
if (j < noverlap1) continue;
if (noverlap == maxoverlap) {
maxoverlap += DELTA_PROCS;
memory->grow(overlap,maxoverlap,"comm:overlap");
}
overlap[noverlap++] = proc;
}
}
MPI_Barrier(world);
// reallocate esendproc and erecvproc if needed based on noverlap
@ -447,13 +462,14 @@ void CommTiled::setup()
}
nexchproc[idim] = noverlap;
for (i = 0; i < noverlap; i++) exchproc[iswap][i] = overlap[i];
for (i = 0; i < noverlap; i++) exchproc[idim][i] = overlap[i];
}
// reallocate MPI Requests and Statuses as needed
int nmax = 0;
for (iswap = 0; iswap < nswap; iswap++) nmax = MAX(nmax,nprocmax[iswap]);
for (i = 0; i < nswap; i++) nmax = MAX(nmax,nprocmax[i]);
for (i = 0; i < dimension; i++) nmax = MAX(nmax,nexchprocmax[i]);
if (nmax > maxreqstat) {
maxreqstat = nmax;
delete [] requests;
@ -463,11 +479,13 @@ void CommTiled::setup()
}
// DEBUG
/*
MPI_Barrier(world);
printf("SUBBOX %d: %g %g: %g %g\n",me,sublo[0],sublo[1],subhi[0],subhi[1]);
MPI_Barrier(world);
/*
for (i = 0; i < nswap; i++) {
if (nsendproc[i] == 1)
printf("SETUP SEND %d %d: nsend %d self %d sproc0 %d: "
@ -503,8 +521,25 @@ void CommTiled::setup()
i,me,nrecvproc[i],sendother[i],recvproc[i][0],recvproc[i][1]);
}
MPI_Barrier(world);
*/
for (i = 0; i < dimension; i++) {
if (nexchproc[i] == 1)
printf("SETUP EXCH %d %d: nexch %d exch %d\n",
i,me,nexchproc[i],exchproc[i][0]);
else if (nexchproc[i] == 2)
printf("SETUP EXCH2 %d %d: nexch %d exch %d %d\n",
i,me,nexchproc[i],exchproc[i][0],exchproc[i][1]);
else if (nexchproc[i] == 3)
printf("SETUP EXCH2 %d %d: nexch %d exch %d %d %d\n",
i,me,nexchproc[i],exchproc[i][0],exchproc[i][1],exchproc[i][2]);
else if (nexchproc[i] == 4)
printf("SETUP EXCH2 %d %d: nexch %d exch %d %d %d %d\n",
i,me,nexchproc[i],exchproc[i][0],exchproc[i][1],
exchproc[i][2],exchproc[i][3]);
}
MPI_Barrier(world);
}
/* ----------------------------------------------------------------------
@ -781,13 +816,18 @@ void CommTiled::exchange()
// receiver may receive multiple messages, realloc buf_recv if needed
nexch = nexchproc[dim];
if (!nexch) continue;
//MPI_Barrier(world);
printf("EXCH dim %d me %d nexch %d %d\n",dim,me,nexch,exchproc[0][0]);
//MPI_Barrier(world);
for (m = 0; m < nexch; m++)
MPI_Irecv(&exchnum[dim][m],1,MPI_INT,
exchproc[dim][m],0,world,&requests[m]);
for (m = 0; m < nexch; m++)
MPI_Send(&nsend,1,MPI_INT,exchproc[dim][m],0,world);
MPI_Waitall(nrecv,requests,statuses);
MPI_Waitall(nexch,requests,statuses);
nrecv = 0;
for (m = 0; m < nexch; m++) nrecv += exchnum[dim][m];
@ -801,7 +841,11 @@ void CommTiled::exchange()
}
for (m = 0; m < nexch; m++)
MPI_Send(buf_send,nsend,MPI_DOUBLE,exchproc[dim][m],0,world);
MPI_Waitall(nrecv,requests,statuses);
MPI_Waitall(nexch,requests,statuses);
//MPI_Barrier(world);
printf("DONE EXCH dim %d me %d nexch %d %d\n",dim,me,nexch,exchproc[0][0]);
//MPI_Barrier(world);
// check incoming atoms to see if I own it and they are in my box
// if so, add to my list
@ -820,6 +864,11 @@ void CommTiled::exchange()
}
m += static_cast<int> (buf_recv[m]);
}
//MPI_Barrier(world);
printf("DONE UNPACK dim %d me %d nexch %d %d\n",
dim,me,nexch,exchproc[0][0]);
//MPI_Barrier(world);
}
if (atom->firstgroupname) atom->first_reorder();
@ -1891,7 +1940,7 @@ void CommTiled::deallocate_swap(int n)
delete [] nexchproc;
delete [] nexchprocmax;
for (int i = 0; i < n; i++) {
for (int i = 0; i < n/2; i++) {
delete [] exchproc[i];
delete [] exchnum[i];
}

41
src/domain.cpp
View File

@ -1740,3 +1740,44 @@ void Domain::box_corners()
corners[7][0] = 1.0; corners[7][1] = 1.0; corners[7][2] = 1.0;
lamda2x(corners[7],corners[7]);
}
/* ----------------------------------------------------------------------
compute 8 corner pts of my triclinic sub-box
8 are ordered with x changing fastest, then y, finally z
could be more efficient if just coded with xy,yz,xz explicitly
------------------------------------------------------------------------- */
void Domain::subbox_corners()
{
corners[0][0] = sublo_lamda[0]; corners[0][1] = sublo_lamda[1];
corners[0][2] = sublo_lamda[2];
lamda2x(corners[0],corners[0]);
corners[1][0] = subhi_lamda[0]; corners[1][1] = sublo_lamda[1];
corners[1][2] = sublo_lamda[2];
lamda2x(corners[1],corners[1]);
corners[2][0] = sublo_lamda[0]; corners[2][1] = subhi_lamda[1];
corners[2][2] = sublo_lamda[2];
lamda2x(corners[2],corners[2]);
corners[3][0] = subhi_lamda[0]; corners[3][1] = subhi_lamda[1];
corners[3][2] = sublo_lamda[2];
lamda2x(corners[3],corners[3]);
corners[4][0] = sublo_lamda[0]; corners[4][1] = sublo_lamda[1];
corners[4][2] = subhi_lamda[2];
lamda2x(corners[4],corners[4]);
corners[5][0] = subhi_lamda[0]; corners[5][1] = sublo_lamda[1];
corners[5][2] = subhi_lamda[2];
lamda2x(corners[5],corners[5]);
corners[6][0] = sublo_lamda[0]; corners[6][1] = subhi_lamda[1];
corners[6][2] = subhi_lamda[2];
lamda2x(corners[6],corners[6]);
corners[7][0] = subhi_lamda[0]; corners[7][1] = subhi_lamda[1];
corners[7][2] = subhi_lamda[2];
lamda2x(corners[7],corners[7]);
}

1
src/domain.h
View File

@ -128,6 +128,7 @@ class Domain : protected Pointers {
void x2lamda(double *, double *, double *, double *);
void bbox(double *, double *, double *, double *);
void box_corners();
void subbox_corners();
// minimum image convention check
// return 1 if any distance > 1/2 of box size

40
src/dump_image.cpp
View File

@ -122,6 +122,7 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
boxflag = YES;
boxdiam = 0.02;
axesflag = NO;
subboxflag = NO;
// parse optional args
@ -285,6 +286,15 @@ DumpImage::DumpImage(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Illegal dump image command");
iarg += 4;
} else if (strcmp(arg[iarg],"subbox") == 0) {
if (iarg+3 > narg) error->all(FLERR,"Illegal dump image command");
if (strcmp(arg[iarg+1],"yes") == 0) subboxflag = YES;
else if (strcmp(arg[iarg+1],"no") == 0) subboxflag = NO;
else error->all(FLERR,"Illegal dump image command");
subboxdiam = force->numeric(FLERR,arg[iarg+2]);
if (subboxdiam < 0.0) error->all(FLERR,"Illegal dump image command");
iarg += 3;
} else if (strcmp(arg[iarg],"shiny") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal dump image command");
double shiny = force->numeric(FLERR,arg[iarg+1]);
@ -826,6 +836,36 @@ void DumpImage::create_image()
}
}
// render outline of my sub-box, orthogonal or triclinic
if (subboxflag) {
double diameter = MIN(boxxhi-boxxlo,boxyhi-boxylo);
if (domain->dimension == 3) diameter = MIN(diameter,boxzhi-boxzlo);
diameter *= boxdiam;
double *sublo = domain->sublo;
double *subhi = domain->subhi;
double (*boxcorners)[3];
double box[8][3];
if (domain->triclinic == 0) {
box[0][0] = sublo[0]; box[0][1] = sublo[1]; box[0][2] = sublo[2];
box[1][0] = subhi[0]; box[1][1] = sublo[1]; box[1][2] = sublo[2];
box[2][0] = sublo[0]; box[2][1] = subhi[1]; box[2][2] = sublo[2];
box[3][0] = subhi[0]; box[3][1] = subhi[1]; box[3][2] = sublo[2];
box[4][0] = sublo[0]; box[4][1] = sublo[1]; box[4][2] = subhi[2];
box[5][0] = subhi[0]; box[5][1] = sublo[1]; box[5][2] = subhi[2];
box[6][0] = sublo[0]; box[6][1] = subhi[1]; box[6][2] = subhi[2];
box[7][0] = subhi[0]; box[7][1] = subhi[1]; box[7][2] = subhi[2];
boxcorners = box;
} else {
domain->subbox_corners();
boxcorners = domain->corners;
}
image->draw_box(boxcorners,diameter);
}
// render outline of simulation box, orthogonal or triclinic
if (boxflag) {

2
src/dump_image.h
View File

@ -54,6 +54,8 @@ class DumpImage : public DumpCustom {
int zoomvar,perspvar; // index to zoom,persp vars
int boxflag,axesflag; // 0/1 for draw box and axes
double boxdiam,axeslen,axesdiam; // params for drawing box and axes
int subboxflag;
double subboxdiam;
int viewflag; // overall view is static or dynamic