int main(int argc,char *argv[]) {
char *cp, *ep;
char host[49];
char tmpb[CMD_BUF_SIZE];
int tmo;
#if NEWS
printf("amptest: See <news> command\n");
printf("amptest: Type h for help\n");
#endif
pname = argv[0];
printf("%s: Compiled %s %s\n",pname,__DATE__,__TIME__);
printf("%s: %s\n",pname, git_version);
tmo = 0;
while (AmpIsBlocked()) {
usleep(100000);
if (tmo++ > 50) {
printf("Amplifier is blocked by another program\n");
if (YesNo("Force","Reservation")) AmpUnBlock();
else exit(1);
}
}
AmpBlock();
printf("Amplifier reservation taken, all other programs blocked\n");
amp = AmpOpen();
if (amp == 0) {
printf("\nWARNING: Could not open driver");
printf("\n\n");
} else {
printf("Driver opened OK\n\n");
}
bzero((void *) host,49);
gethostname(host,48);
while (True) {
if (amp) sprintf(prompt,"%s:Amp[%02d]",host,cmdindx+1);
else sprintf(prompt,"%s:NoDriver:Amp[%02d]",host,cmdindx+1);
cmdbuf = &(history[cmdindx][0]);
if (strlen(cmdbuf)) printf("{%s} ",cmdbuf);
printf("%s",prompt);
bzero((void *) tmpb,CMD_BUF_SIZE);
if (gets(tmpb)==NULL) exit(1);
cp = &(tmpb[0]);
if (*cp == '!') {
cmdindx = strtoul(++cp,&ep,0) -1; cp = ep;
if (cmdindx >= HISTORIES) cmdindx = 0;
cmdbuf = &(history[cmdindx][0]);
continue;
} else if (*cp == '.') {
printf("Execute:%s\n",cmdbuf); fflush(stdout);
} else if ((*cp == '\n') || (*cp == '\0')) {
cmdindx++;
if (cmdindx >= HISTORIES) { printf("\n"); cmdindx = 0; }
cmdbuf = &(history[cmdindx][0]);
continue;
} else if (*cp == '?') {
printf("History:\n");
printf("\t!<1..24> Goto command\n");
printf("\tCR Goto next command\n");
printf("\t. Execute current command\n");
printf("\this Show command history\n");
continue;
} else {
cmdindx++; if (cmdindx >= HISTORIES) { printf("\n"); cmdindx = 0; }
strcpy(cmdbuf,tmpb);
}
bzero((void *) val_bufs,sizeof(val_bufs));
GetAtoms(cmdbuf);
DoCmd(0);
}
}
int main(int argc,char *argv[]) {
char *cp;
char host[49];
char tmpb[CMD_BUF_SIZE];
int c;
#if NEWS
printf("xmemtest: See <news> command\n");
printf("xmemtest: Type h for help\n");
#endif
pname = argv[0];
printf("%s: Compiled %s %s\n",pname,__DATE__,__TIME__);
for (;;) {
c = getopt(argc, argv, "c:h");
if (c < 0)
break;
switch (c) {
case 'c':
if (set_conf_path(optarg))
printf("\nWarning: path invalid or too long\n");
break;
case 'h':
usage_complete();
exit(0);
}
}
xmem = XmemOpen();
if (xmem == 0) {
printf("\nWARNING: Could not open driver");
printf("\n\n");
} else {
printf("Driver opened OK: Using XMEM module: 1\n\n");
}
ReadSegTable(0);
ReadNodeTableFile(0);
printf("\n");
bzero((void *) host,49);
gethostname(host,48);
while (True) {
if (xmem) sprintf(prompt,"%s:Xmem[%02d]",host,cmdindx+1);
else sprintf(prompt,"%s:NoDriver:Xmem[%02d]",host,cmdindx+1);
cmdbuf = &(history[cmdindx][0]);
if (strlen(cmdbuf)) printf("{%s} ",cmdbuf);
printf("%s",prompt);
bzero((void *) tmpb,CMD_BUF_SIZE);
if (gets(tmpb)==NULL) exit(1);
cp = &(tmpb[0]);
if (*cp == '!') {
cmdindx = strtoul(++cp,&cp,0) -1;
if (cmdindx >= HISTORIES) cmdindx = 0;
cmdbuf = &(history[cmdindx][0]);
continue;
} else if (*cp == '.') {
printf("Execute:%s\n",cmdbuf); fflush(stdout);
} else if ((*cp == '\n') || (*cp == '\0')) {
cmdindx++;
if (cmdindx >= HISTORIES) { printf("\n"); cmdindx = 0; }
cmdbuf = &(history[cmdindx][0]);
continue;
} else if (*cp == '?') {
printf("History:\n");
printf("\t!<1..24> Goto command\n");
printf("\tCR Goto next command\n");
printf("\t. Execute current command\n");
printf("\this Show command history\n");
continue;
} else {
cmdindx++; if (cmdindx >= HISTORIES) { printf("\n"); cmdindx = 0; }
strcpy(cmdbuf,tmpb);
}
bzero((void *) val_bufs,sizeof(val_bufs));
GetAtoms(cmdbuf);
DoCmd(0);
}
}
int main(int argc,char *argv[]) {
char *cp, *ep;
char host[49];
char tmpb[CMD_BUF_SIZE];
printf("vmeiotest: See <news> command\n");
printf("vmeiotest: Type h for help\n");
pname = argv[0];
printf("%s: Compiled %s %s\n",pname,__DATE__,__TIME__);
bzero((void *) host,49);
gethostname(host,48);
if (argc > 1)
strcat(dev_name,argv[1]);
else
strcat(dev_name,"vmeio");
if ((vmeio[lun] = __vsl_open_name(lun,dev_name)) == NULL) {
printf("Warning: Can't open support library\n");
perror(DRV_NAME);
exit(1);
}
memlen = 1024;
mem = malloc(memlen);
get_window_parameters(lun);
read_regs(dev_name);
while (True) {
cmdbuf = &(history[cmdindx][0]);
if (strlen(cmdbuf)) printf("{%s} ",cmdbuf);
fflush(stdout);
if (vmeio) sprintf(prompt,"%s:%s[%02d]",host,dev_name,cmdindx+1);
else sprintf(prompt,"%s:NoDriver:Vmeio[%02d]",host,cmdindx+1);
printf("%s",prompt);
bzero((void *) tmpb,CMD_BUF_SIZE);
if (fgets(tmpb,CMD_BUF_SIZE,stdin)==NULL) exit(1);
cp = tmpb;
if (*cp == '!') {
cmdindx = strtoul(++cp,&ep,0) -1;
cp = ep;
if (cmdindx >= HISTORIES) cmdindx = 0;
cmdbuf = &(history[cmdindx][0]);
continue;
} else if (*cp == '.') {
printf("Execute:%s\n",cmdbuf); fflush(stdout);
} else if ((*cp == '\n') || (*cp == '\0')) {
cmdindx++;
if (cmdindx >= HISTORIES) { printf("\n"); cmdindx = 0; }
cmdbuf = &(history[cmdindx][0]);
continue;
} else if (*cp == '?') {
printf("History:\n");
printf("\t!<1..24> Goto command\n");
printf("\tCR Goto next command\n");
printf("\t. Execute current command\n");
printf("\this Show command history\n");
continue;
} else {
cmdindx++; if (cmdindx >= HISTORIES) { printf("\n"); cmdindx = 0; }
strcpy(cmdbuf,tmpb);
}
bzero((void *) val_bufs,sizeof(val_bufs));
GetAtoms(cmdbuf);
DoCmd(0);
}
}
int main(int argc,char *argv[])
{
int rp, pr, dev;
char *cp;
char host[49];
char tmpb[CMD_BUF_SIZE];
pname = argv[0];
printf("%s: Compiled %s %s\n",pname,__DATE__,__TIME__);
if (argc > 1)
dev = strtoul(argv[1],&cp,0);
do_open(dev);
show_dev(1);
bzero((void *) host,49);
gethostname(host,48);
while (True) {
sprintf(prompt,"%s:Icv196.%d[%02d]",host,get_lun(),cmdindx+1);
printf("%s",prompt);
cmdbuf = &(history[cmdindx][0]);
bzero((void *) tmpb,CMD_BUF_SIZE);
if (fgets(tmpb,CMD_BUF_SIZE,stdin) == NULL) break;
cp = &(tmpb[0]);
pr = 0; /* Dont print a history */
rp = 0; /* Dont repeat a command */
while ((*cp == '-')
|| (*cp == '+')
|| (*cp == '.')
|| (*cp == '!')) {
pr = 1; /* Print command on */
if (*cp == '!') {
cp++;
cmdindx = strtoul(cp,&cp,0) -1;
if (cmdindx >= HISTORIES) cmdindx = 0;
if (cmdindx < 0) cmdindx = HISTORIES -1;
rp = 1;
break;
}
if (*cp == '-') {
if (--cmdindx < 0) cmdindx = HISTORIES -1;
cmdbuf = &(history[cmdindx][0]);
}
if (*cp == '+') {
if (++cmdindx >= HISTORIES) cmdindx = 0;
cmdbuf = &(history[cmdindx][0]);
}
if (*cp == '.') {
rp = 1;
break;
}
cp++;
}
if (pr) {
printf("{%s}\t ",cmdbuf); fflush(stdout);
if (!rp) continue;
}
if (!rp) strcpy(cmdbuf,tmpb);
bzero((void *) val_bufs,sizeof(val_bufs));
GetAtoms(cmdbuf);
DoCmd(0);
if ((!rp) && (++cmdindx >= HISTORIES)) cmdindx = 0;
}
exit(0);
}
{
SetName("Hask");
}
void
MoleculesHaskell::
Init(const bool) throw (...)
{
struct ParallelScript::NamedFunctions_s
funcs[] =
{
{"generateMolecules@16", (void **)&GenerateMolecules},
{0, 0}
};
ScriptInit(L"MoleculesHaskell.dll", funcs);
GenerateMolecules((float *)GetAtoms().GetData(), (int)GetCount(), GetHeight(), GetWidth());
CUmodule
module = 0;
TryCUDA(cuModuleLoad(&module, "MoleculesHaskell.ptx"));
m_kernel = 0;
TryCUDA(cuModuleGetFunction(&m_kernel, module, "DoAtoms"));
}
void
MoleculesHaskell::
Execute() throw (...)
{
//printf("0");
size_t
height = GetHeight(),
width = GetWidth(),
int main()
{
// get list of dat/*.dat, and sort them
char files[5000][11];
int nfile = FilesList(files, "dat");
qsort(&files[0], nfile, sizeof(files[0]), CompStrInt);
if(nfile < 1) return -1; // exit if no files
// read following system information from cube.in
// number of atoms -> nat
// number of atomic types -> ntyp
// number of each atom in system -> num[]
// proton number of each atom in the same order with num[] -> z[]
// 3x3 matrix of the cell dimensions -> celldm[3][3]
int nat = 0, ntyp = 0, num[30], z[30];
double celldm[3][3];
ReadInput(&nat, &ntyp, num, z, celldm);
// we will need
// the inverse of celldm matrix -> inv[3][3]
// and lengths of cell vectors -> norm[3]
double inv[3][3];
double norm[3] = {
VecLen(celldm[0]),
VecLen(celldm[1]),
VecLen(celldm[2])
};
Inv3D(celldm, inv);
// a string for
// the name of the dat file to read -> fname[20]
// the name of the cube file to write -> cname[20]
// a FILE for the file i/o
char fname[20], cname[20];
FILE *f;
// read the grid information from the files[0]
int ngrid[3];
sprintf(fname, "dat/%s", files[0]);
f = fopen(fname, "r");
ReadDatHeader(f, ngrid);
fclose(f);
// let's calculate ngrid[0] * ngrid[1] once and for all.
int dim = ngrid[0] * ngrid[1];
// calculate the voxel sizes
double vsize[3][3];
memcpy(vsize, celldm, sizeof(celldm));
for(int i = 0; i < 3; ++i)
{
VecScale(vsize[i], 1.0/ngrid[i]);
}
int dummy[3];
#pragma omp parallel for private(f, fname, cname) shared(dummy)
for(int file = 0; file < nfile; ++file)
{
// set cube file name
sprintf(cname, "cube/%d.cube", atoi(files[file]));
// if the file exists, skip
if (access(cname, F_OK) == -1)
{
// create a Cube to read dat file into
Cube *c = CubeInit(nat, ngrid);
CubeSetVoxels(c, vsize);
// Read the next dat file (header info is read to skip this part)
sprintf(fname, "dat/%s", files[file]);
f = fopen(fname, "r");
ReadDatHeader(f, dummy);
ReadDatData(f, ngrid, dim, c);
fclose(f);
// get ionic positions for the corresponding frame from cp.pos
GetAtoms(atoi(files[file]), c, nat, z, num);
int pos = 0;
char com[255] = "";
double rho;
for (int i = 0; i < c->nat; i++)
{
if(Surround(i, c, 0.4, 1) > THR && c->atoms[i].Z == 22)
{
rho = Surround(i, c, 2.1, 0) ;
printf("%d %lf %lf\n", atoi(files[file]), c->atoms[i].coor[2], rho);
pos += sprintf(com + pos, "%d ", i);
}
fflush(stdout);
}
CubeBeautify(c, THR);
CubeTrim(&c, THR);
sprintf(c->comment[0], "%-10.6f %-10.6f %-10.6f %-10.6f %-10.6f %-10.6f",
norm[0]*B2A, norm[1]*B2A, norm[2]*B2A,
DEG*acos(VecDot(celldm[0], celldm[2])/(norm[2]*norm[0])),
DEG*acos(VecDot(celldm[1], celldm[2])/(norm[1]*norm[2])),
DEG*acos(VecDot(celldm[0], celldm[1])/(norm[0]*norm[1])));
strcpy(c->comment[1], com);
printf("%s %s", files[file], com);
CubeWrite(c, cname);
CubeDelete(c);
}
}
return 0;
}
#include <Accelerator.h>
// cons
MoleculesOptimised::
MoleculesOptimised() :
Molecules(),
ParallelReference()
{
SetName("Opt ");
}
void
MoleculesOptimised::
Init(const bool) throw (...)
{
m_atoms = &GetAtoms();
}
void
MoleculesOptimised::
Execute() throw (...)
/*{
// This version is optimised accoring to:
// http://y-less.com/wordpress/?p=117
size_t
height = GetHeight(),
width = GetWidth(),
count = GetCount();
// Target array for the effects.
float
* d = GetStore(),
