void calculateChargesPotential(LSMSCommunication &comm, LSMSSystemParameters &lsms, LocalTypeInfo &local, CrystalParameters &crystal, int chargeSwitch)
{
Real *qsub;
Array3d<Real> rhoTemp;
//qsub = new Real[crystal.num_types];
qsub = (Real*)shmalloc(crystal.num_types*sizeof(Real));
for (int i=0; i<crystal.num_types; i++) qsub[i] = 0.0;
rhoTemp.resize(lsms.global.iprpts+1, 2, local.num_local);
rhoTemp = 0.0;
printf("%d:calculateCharges\n",comm.comm.rank);
calculateCharges(comm, lsms, local, crystal, qsub, rhoTemp, chargeSwitch);
// for (int i=0; i<crystal.num_types; i++) printf("i, qsub = %5d %25.15f\n", i, qsub[i]);
printf("%d:calculatePotential\n",comm.comm.rank);
calculatePotential(comm, lsms, local, crystal, qsub, rhoTemp, chargeSwitch);
printf("%d:end of calculatePotential\n",comm.comm.rank);
//delete[] qsub;
shfree(qsub);
return;
}
void traceJigData(struct part *part, struct xyz *positions) {
double x;
int i;
struct jig *j;
__p = __line;
__p += sprintf(__p, "%10.4f ", Iteration * Dt / PICOSEC);
for (i=0; i<part->num_jigs; i++) {
j = part->jigs[i];
switch (j->type) {
case DihedralMeter:
case AngleMeter:
__p += sprintf(__p, " %15.5f", j->data);
break;
case Ground:
x=vlen(j->xdata)/1e4;
__p += sprintf(__p, " %15.2f", x / j->data);
j->data=0.0;
vsetc(j->xdata, 0.0);
break;
case RadiusMeter:
case LinearMotor:
// convert from picometers to angstroms
__p += sprintf(__p, " %15.4f", 0.01 * j->data);
j->data = 0.0;
break;
case Thermometer:
case Thermostat:
__p += sprintf(__p, " %15.2f", j->data);
j->data = 0.0;
break;
case RotaryMotor:
__p += sprintf(__p, " %15.3f %15.3f", j->data, j->data2);
j->data = 0.0;
j->data2 = 0.0;
break;
}
}
if (PrintPotentialEnergy) {
double potential_energy = calculatePotential(part, positions);
double kinetic_energy = calculateKinetic(part);
__p += sprintf(__p, " %15.6f", potential_energy);
__p += sprintf(__p, " %15.6f", kinetic_energy);
__p += sprintf(__p, " %15.6f", potential_energy + kinetic_energy);
}
sprintf(__p, "\n"); // each snapshot is one line
write_traceline(__line);
}
int
main(int argc, char **argv)
{
struct part *part;
int opt, n;
int dump_part = 0;
int printStructurePotentialEnergy = 0;
int needVDW = 1;
char *printPotential = NULL;
double printPotentialInitial = -1; // pm
double printPotentialIncrement = -1; // pm
double printPotentialLimit = -1; // pm
char *fileNameTemplate = NULL;
char *outputFilename = NULL;
reinit_globals();
if (signal(SIGTERM, &SIGTERMhandler) == SIG_ERR) {
perror("signal(SIGTERM)");
exit(1);
}
CommandLine = assembleCommandLine(argc, argv);
while ((opt = getopt_long(argc, argv,
"hnmEi:f:s:t:xXONI:K:rD:o:q:B:",
option_vec, NULL)) != -1) {
switch(opt) {
case 'h':
usage();
case OPT_DUMP_PART:
dump_part = 1;
break;
case OPT_WRITE_GROMACS_TOPOLOGY:
GromacsOutputBaseName = optarg;
break;
case OPT_PATH_TO_CPP:
PathToCpp = optarg;
break;
case OPT_SYSTEM_PARAMETERS:
SystemParametersFileName = optarg;
break;
case OPT_PRINT_POTENTIAL:
printPotential = optarg;
break;
case OPT_INITIAL:
printPotentialInitial = atof(optarg);
break;
case OPT_INCREMENT:
printPotentialIncrement = atof(optarg);
break;
case OPT_LIMIT:
printPotentialLimit = atof(optarg);
break;
case OPT_DIRECT_EVALUATE:
DirectEvaluate = 1;
break;
case OPT_INTERPOLATE:
DirectEvaluate = 0;
break;
case OPT_SIMPLE_MOVIE_FORCE_SCALE:
SimpleMovieForceScale = atof(optarg);
break;
case OPT_MIN_THRESH_CUT_RMS:
MinimizeThresholdCutoverRMS = atof(optarg);
break;
case OPT_MIN_THRESH_CUT_MAX:
MinimizeThresholdCutoverMax = atof(optarg);
break;
case OPT_MIN_THRESH_END_RMS:
MinimizeThresholdEndRMS = atof(optarg);
break;
case OPT_MIN_THRESH_END_MAX:
MinimizeThresholdEndMax = atof(optarg);
break;
case OPT_VDW_CUTOFF_RADIUS:
VanDerWaalsCutoffRadius = atof(optarg);
break;
case OPT_VDW_CUTOFF_FACTOR:
VanDerWaalsCutoffFactor = atof(optarg);
break;
case OPT_ENABLE_ELECTROSTATIC:
EnableElectrostatic = atoi(optarg);
break;
case OPT_TIME_REVERSAL:
TimeReversal = 1;
break;
case OPT_THERMOSTAT_GAMMA:
ThermostatGamma = atof(optarg);
break;
case OPT_PRINT_ENERGIES:
PrintPotentialEnergy = 1;
break;
case OPT_NEIGHBOR_SEARCHING:
NeighborSearching = atoi(optarg);
break;
case 'n':
// ignored
break;
case 'm':
ToMinimize=1;
break;
case 'E':
printStructurePotentialEnergy=1;
break;
case 'i':
IterPerFrame = atoi(optarg);
break;
case 'f':
NumFrames = atoi(optarg);
break;
case 's':
Dt = atof(optarg);
break;
case 't':
Temperature = atof(optarg);
break;
case 'x':
DumpAsText = 1;
break;
case 'X':
DumpIntermediateText = 1;
break;
case 'O':
OutputFormat = 1;
break;
case 'N':
OutputFormat = 2;
break;
case OPT_OUTPUT_FORMAT_3:
OutputFormat = 3;
break;
case 'I':
IDKey = optarg;
break;
case 'K':
KeyRecordInterval = atoi(optarg);
break;
case 'r':
PrintFrameNums = 1;
break;
case 'D':
n = atoi(optarg);
if (n < 32 && n >= 0) {
debug_flags |= 1 << n;
}
break;
case 'o':
outputFilename = optarg;
break;
case 'q':
TraceFileName = optarg;
break;
case 'B':
BaseFileName = optarg;
break;
case ':':
case '?':
default:
usage();
exit(1);
}
}
if (optind + 1 == argc) { // (optind < argc) if not paranoid
fileNameTemplate = argv[optind];
}
if (DEBUG(D_PRINT_BEND_STRETCH)) { // -D8
initializeBondTable();
printBendStretch();
exit(0);
}
if (DumpAsText) {
OutputFormat = 0;
}
if (!fileNameTemplate) {
usage();
}
InputFileName = replaceExtension(fileNameTemplate, "mmp");
if (BaseFileName != NULL) {
int i1;
int i2;
struct xyz *basePositions;
struct xyz *initialPositions;
basePositions = readXYZ(BaseFileName, &i1);
if (basePositions == NULL) {
fprintf(stderr, "could not read base positions file from -B<filename>\n");
exit(1);
}
initialPositions = readXYZ(InputFileName, &i2);
if (initialPositions == NULL) {
fprintf(stderr, "could not read comparison positions file\n");
exit(1);
}
if (i1 != i2) {
fprintf(stderr, "structures to compare must have same number of atoms\n");
exit(1);
}
exit(doStructureCompare(i1, basePositions, initialPositions,
NumFrames, 1e-8, 1e-4, 1.0+1e-4));
}
if (outputFilename) {
OutputFileName = copy_string(outputFilename);
} else {
char *extension;
switch (OutputFormat) {
case 0:
extension = "xyz";
break;
case 1:
case 2:
default:
extension = "dpb";
break;
case 3:
extension = "gro";
break;
}
OutputFileName = replaceExtension(fileNameTemplate, extension);
}
if (TraceFileName) {
TraceFile = fopen(TraceFileName, "w");
if (TraceFile == NULL) {
perror(TraceFileName);
exit(1);
}
} else {
TraceFile = fdopen(1, "w");
if (TraceFile == NULL) {
perror("fdopen stdout as TraceFile");
exit(1);
}
}
traceFileVersion(); // call this before any other writes to trace file.
// tell where and how the simulator was built. We never build the
// standalone simulator with distutils.
fprintf(TraceFile, "%s", tracePrefix);
initializeBondTable();
if (IterPerFrame <= 0) IterPerFrame = 1;
if (printPotential) {
printPotentialAndGradientFunctions(printPotential,
printPotentialInitial,
printPotentialIncrement,
printPotentialLimit);
exit(0);
}
part = readMMP(InputFileName);
if (EXCEPTION) {
exit(1);
}
if (GromacsOutputBaseName != NULL) {
needVDW = 0;
}
initializePart(part, needVDW);
createPatterns();
matchPartToAllPatterns(part);
if (printStructurePotentialEnergy) {
struct xyz *force = (struct xyz *)allocate(sizeof(struct xyz) * part->num_atoms);
double potentialEnergy = calculatePotential(part, part->positions);
calculateGradient(part, part->positions, force);
printf("%e %e %e %e (Potential energy in aJ, gradient of atom 1)\n", potentialEnergy, force[1].x, force[1].y, force[1].z);
exit(0);
}
if (dump_part) {
//
// this segment is convenient to run valgrind on to test the
// part and bond table destructors. By the time we reach the
// exit() there should be no malloc'd blocks remaining.
//
// valgrind -v --leak-check=full --leak-resolution=high --show-reachable=yes simulator --dump-part part.mmp
//
printPart(stdout, part);
destroyPart(part);
part = NULL;
destroyBondTable();
fclose(TraceFile);
destroyAccumulator(CommandLine);
free(InputFileName);
free(OutputFileName);
exit(0);
}
if (GromacsOutputBaseName != NULL) {
printGromacsToplogy(GromacsOutputBaseName, part);
destroyPart(part);
part = NULL;
destroyBondTable();
fclose(TraceFile);
destroyAccumulator(CommandLine);
free(InputFileName);
free(OutputFileName);
done("");
exit(0);
}
constrainGlobals();
traceHeader(part);
if (ToMinimize) {
NumFrames = max(NumFrames,(int)sqrt((double)part->num_atoms));
Temperature = 0.0;
} else {
traceJigHeader(part);
}
OutputFile = fopen(OutputFileName, DumpAsText ? "w" : "wb");
if (OutputFile == NULL) {
perror(OutputFileName);
exit(1);
}
writeOutputHeader(OutputFile, part);
if (ToMinimize) {
minimizeStructure(part);
exit(0);
}
else {
dynamicsMovie(part);
}
done("");
return 0;
}
