void traceJigHeader(struct part *part) {
struct jig *j;
int i;
int ncol;
__p = __line;
__p += sprintf(__p, "# Time ");
for (i=0; i<part->num_jigs; i++) {
j = part->jigs[i];
j->data=0.0;
j->data2=0.0;
vsetc(j->xdata,0.0);
switch (j->type) {
case Ground: __p += sprintf(__p, "Anchor "); break;
case Thermometer: __p += sprintf(__p, "T.meter "); break;
case DihedralMeter: __p += sprintf(__p, "Dihedral "); break;
case AngleMeter: __p += sprintf(__p, "Angle "); break;
case RadiusMeter: __p += sprintf(__p, "Distance "); break;
case Thermostat: __p += sprintf(__p, "T.stat "); break;
case LinearMotor: __p += sprintf(__p, "Lmotor "); break;
case RotaryMotor: __p += sprintf(__p, "speed torque ");
}
}
sprintf(__p, "\n");
write_traceline(__line);
__p = __line;
__p += sprintf(__p, "# picosec ");
for (i=0; i<part->num_jigs; i++) {
j = part->jigs[i];
ncol = countOutputColumns(j);
if (ncol > 0) {
__p += sprintf(__p, " %-15.15s", j->name);
while (ncol-- > 1)
// 16 spaces
__p += sprintf(__p, " %-15.15s", " ");
}
}
if (PrintPotentialEnergy) {
__p += sprintf(__p, " %-15.15s", "P.Energy");
__p += sprintf(__p, " %-15.15s", "K.Energy");
__p += sprintf(__p, " %-15.15s", "T.Energy");
}
sprintf(__p, "\n");
write_traceline(__line);
__p = __line;
sprintf(__p, "#\n");
write_traceline(__line);
}
static void
trace_makeVirtualAtom(struct patternMatch *match, struct atom *a)
{
char buf[1024];
char buf1[64];
sprintf(buf, "# Pattern makeVirtualAtom: [%d] %s %d %d ",
match->sequenceNumber,
trace_atomID(a),
a->virtualConstructionAtoms,
a->virtualFunction);
strcat(buf, trace_atomID(a->creationParameters.v.virtual1));
strcat(buf, " ");
strcat(buf, trace_atomID(a->creationParameters.v.virtual2));
strcat(buf, " ");
strcat(buf, trace_atomID(a->creationParameters.v.virtual3));
strcat(buf, " ");
strcat(buf, trace_atomID(a->creationParameters.v.virtual4));
sprintf(buf1, " %f %f %f\n",
a->creationParameters.v.virtualA,
a->creationParameters.v.virtualB,
a->creationParameters.v.virtualC);
strcat(buf, buf1);
write_traceline(buf);
}
static void
trace_makeVanDerWaals(struct patternMatch *match, struct atom *a1, struct atom *a2)
{
char buf[1024];
sprintf(buf, "# Pattern makeVanDerWaals: [%d] %s ", match->sequenceNumber, trace_atomID(a1));
strcat(buf, trace_atomID(a2));
strcat(buf, "\n");
write_traceline(buf);
}
static void
trace_setStretchType(struct patternMatch *match, struct stretch *s)
{
char buf[1024];
char buf1[64];
sprintf(buf, "# Pattern setStretchType: [%d] %s ", match->sequenceNumber, trace_atomID(s->a1));
strcat(buf, trace_atomID(s->a2));
sprintf(buf1, " %f %f\n", s->stretchType->ks, s->stretchType->r0);
strcat(buf, buf1);
write_traceline(buf);
}
void
done(const char *format, ...)
{
va_list args;
__p = __line;
__p += sprintf(__p, "# Done: ");
va_start(args, format);
__p += vsprintf(__p, format, args);
va_end(args);
sprintf(__p, "\n");
write_traceline(__line);
}
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);
}
static void
trace_makeBond(struct patternMatch *match, struct bond *b)
{
char buf[1024];
char buf1[64];
struct bondStretch *stretchType;
sprintf(buf, "# Pattern makeBond: [%d] %s ", match->sequenceNumber, trace_atomID(b->a1));
strcat(buf, trace_atomID(b->a2));
stretchType = getBondStretch(b->a1->type->protons,
b->a2->type->protons,
b->order);
sprintf(buf1, " %f %f\n", stretchType->ks, stretchType->r0);
strcat(buf, buf1);
write_traceline(buf);
}
void
printError(const char *file, int line, int error_type,
int doPerror, const char *format, ...)
{
va_list args;
char *errorType;
int toStderr = 0;
switch (error_type) {
case TYPE_ERROR:
errorType = "Error";
toStderr = 1;
break;
case TYPE_WARNING:
errorType = "Warning";
break;
default:
errorType = "Info";
break;
}
__p = __line;
__p += sprintf(__p, "# %s: ", errorType);
va_start(args, format);
__p += vsprintf(__p, format, args);
va_end(args);
if (doPerror) {
sprintf(__p, ": %s\n", strerror(errno));
} else {
sprintf(__p, "\n");
}
write_traceline(__line);
if (toStderr) {
fprintf(stderr, "%s", __line);
}
}
static int
readBondTableOverlay(char *filename)
{
char buf[4096];
char *token;
int lineNumber = 0;
int err;
int protons;
int group;
int period;
char *parentSymbol;
char *symbol;
char *name;
double mass;
double rvdW;
double evdW;
int nBonds;
double rCovalent;
double charge;
int isVirtual;
double ks;
double r0;
double de;
double beta;
double inflectionR;
double x1;
double y1;
double x2;
double y2;
int quality;
int quadratic;
double ktheta;
double theta0;
double cutoffRadiusStart;
double cutoffRadiusEnd;
double value;
double angleUnits = 1.0; // default to radians
FILE *f = fopen(filename, "r");
if (f == NULL) {
// silent about not finding file
return 0;
}
write_traceline("# reading parameter file: %s\n", filename);
while (fgets(buf, 4096, f)) {
lineNumber++;
token = strtok(buf, " \n");
if (token) {
if (!strncmp(token, "#", 1) ) {
continue;
} else if (!strcmp(token, "units")) {
err = 0;
name = strtok(NULL, " \n");
if (!strcmp(name, "degrees")) {
angleUnits = Pi / 180.0;
} else if (!strcmp(name, "radians")) {
angleUnits = 1.0;
} else {
fprintf(stderr, "unknown unit at file %s line %d\n", filename, lineNumber);
}
if (err || name == NULL) {
fprintf(stderr, "format error at file %s line %d\n", filename, lineNumber);
}
} else if (!strcmp(token, "element")) {
err = 0;
protons = tokenizeInt(&err);
group = tokenizeInt(&err);
period = tokenizeInt(&err);
parentSymbol = strtok(NULL, " \n");
symbol = strtok(NULL, " \n");
name = strtok(NULL, " \n");
mass = tokenizeDouble(&err);
rvdW = tokenizeDouble(&err);
evdW = tokenizeDouble(&err);
nBonds = tokenizeInt(&err);
rCovalent = tokenizeDouble(&err);
charge = tokenizeDouble(&err);
isVirtual = tokenizeInt(&err);
if (err || symbol == NULL || name == NULL) {
fprintf(stderr, "format error at file %s line %d\n", filename, lineNumber);
} else {
setElement(protons, group, period, parentSymbol, symbol, name, mass, rvdW, evdW, nBonds, rCovalent, charge, isVirtual);
DPRINT13(D_READER, "setElement: %d %d %d %s %s %s %f %f %f %d %f %f %d\n", protons, group, period, parentSymbol, symbol, name, mass, rvdW, evdW, nBonds, rCovalent, charge, isVirtual);
}
} else if (!strcmp(token, "stretch")) {
err = 0;
ks = tokenizeDouble(&err);
r0 = tokenizeDouble(&err);
de = tokenizeDouble(&err);
beta = tokenizeDouble(&err);
inflectionR = tokenizeDouble(&err);
quality = tokenizeInt(&err);
quadratic = tokenizeInt(&err);
name = strtok(NULL, " \n");
if (err || name == NULL) {
fprintf(stderr, "format error at file %s line %d\n", filename, lineNumber);
} else {
addInitialBondStretch(ks, r0, de, beta, inflectionR, quality, quadratic, name);
DPRINT8(D_READER, "addBondStretch: %f %f %f %f %f %d %d %s\n", ks, r0, de, beta, inflectionR, quality, quadratic, name);
}
} else if (!strcmp(token, "bend")) {
err = 0;
ktheta = tokenizeDouble(&err);
theta0 = tokenizeDouble(&err) * angleUnits;
quality = tokenizeInt(&err);
name = strtok(NULL, " \n");
if (err || name == NULL) {
fprintf(stderr, "format error at file %s line %d\n", filename, lineNumber);
} else {
addInitialBendData(ktheta, theta0, quality, name);
DPRINT4(D_READER, "addBendData: %f %f %d %s\n", ktheta, theta0, quality, name);
}
} else if (!strcmp(token, "vdw")) {
err = 0;
rvdW = tokenizeDouble(&err);
evdW = tokenizeDouble(&err);
cutoffRadiusStart = tokenizeDouble(&err);
cutoffRadiusEnd = tokenizeDouble(&err);
name = strtok(NULL, " \n");
if (err || name == NULL) {
fprintf(stderr, "format error at file %s line %d\n", filename, lineNumber);
} else {
addVanDerWaalsInteraction(name, rvdW, evdW, cutoffRadiusStart, cutoffRadiusEnd);
DPRINT5(D_READER, "addVanDerWaalsInteraction: %f %f %f %f %s\n", rvdW, evdW, cutoffRadiusStart, cutoffRadiusEnd, name);
}
} else if (!strcmp(token, "pattern")) {
err = 0;
name = strtok(NULL, " \n");
value = tokenizeDouble(&err);
if (err || name == NULL) {
fprintf(stderr, "format error at file %s line %d\n", filename, lineNumber);
} else {
addPatternParameter(name, value, angleUnits, NULL);
DPRINT2(D_READER, "addPatternParameter: %s %f\n", name, value);
}
} else if (!strcmp(token, "strut")) {
err = 0;
name = strtok(NULL, " \n");
ks = tokenizeDouble(&err);
r0 = tokenizeDouble(&err);
x1 = tokenizeDouble(&err);
y1 = tokenizeDouble(&err);
x2 = tokenizeDouble(&err);
y2 = tokenizeDouble(&err);
if (err || name == NULL) {
fprintf(stderr, "format error at file %s line %d\n", filename, lineNumber);
} else {
addStrutDefinition(name, ks, r0, x1, y1, x2, y2);
DPRINT7(D_READER, "addStrutDefinition: %s %f %f %f %f %f %f\n", name, ks, r0, x1, y1, x2, y2);
}
//} else {
//fprintf(stderr, "unrecognized line type at file %s line %d: %s\n", filename, lineNumber, token);
}
}
}
fclose(f);
return 1;
}
void
dynamicsMovie(struct part *part)
{
struct xyz *averagePositions = (struct xyz *)allocate(sizeof(struct xyz) * part->num_atoms);
struct xyz *oldPositions = (struct xyz *)allocate(sizeof(struct xyz) * part->num_atoms);
struct xyz *newPositions = (struct xyz *)allocate(sizeof(struct xyz) * part->num_atoms);
struct xyz *positions = (struct xyz *)allocate(sizeof(struct xyz) * part->num_atoms);
struct xyz *force = (struct xyz *)allocate(sizeof(struct xyz) * part->num_atoms);
struct xyz *tmp;
int i;
#ifndef WIN32
int timefailure = 0;
struct timeval start;
struct timeval end;
double elapsedSeconds;
char timebuffer[256];
#endif
setThermalVelocities(part, Temperature);
for (i = 0; i < part->num_atoms; i++) {
vset(positions[i], part->positions[i]);
vsub2(oldPositions[i], positions[i], part->velocities[i]);
}
#ifndef WIN32
// we should probably use times() to get user and system time
// instead of wall time, but the clock ticks conversions appear to
// be system dependant.
if (gettimeofday(&start, NULL)) {
timefailure = errno;
errno = 0;
}
#endif
if (TimeReversal) {
dynamicsMovieRun(part, averagePositions, &oldPositions, &newPositions, &positions, force, 0, NumFrames/2);
tmp = newPositions;
newPositions = positions;
positions = tmp;
dynamicsMovieRun(part, averagePositions, &oldPositions, &newPositions, &positions, force, NumFrames/2, NumFrames);
} else {
dynamicsMovieRun(part, averagePositions, &oldPositions, &newPositions, &positions, force, 0, NumFrames);
}
#ifndef WIN32
if (gettimeofday(&end, NULL)) {
timefailure = errno;
}
if (timefailure) {
errno = timefailure;
perror("gettimeofday");
errno = 0;
} else {
end.tv_sec -= start.tv_sec;
end.tv_usec -= start.tv_usec;
if (end.tv_usec < 0) {
end.tv_sec--;
end.tv_usec += 1000000;
}
elapsedSeconds = (double)end.tv_sec + (double)end.tv_usec / 1e6;
write_traceline("# Duration: %s, %f sec/frame, %f sec/iteration\n",
formatSeconds(elapsedSeconds, timebuffer),
elapsedSeconds / (double)i,
elapsedSeconds / (double)(i * IterPerFrame));
}
#endif
writeOutputTrailer(OutputFile, part, NumFrames);
free(averagePositions);
free(oldPositions);
free(newPositions);
free(positions);
free(force);
}
void traceHeader(struct part *part)
{
int i, ncols;
struct jig *j;
struct tm *ptr;
time_t tm;
tm = time(NULL);
ptr = localtime(&tm);
if (CommandLine != NULL && CommandLine[0] != '\0') {
write_traceline("# Command Line: %s\n", CommandLine);
}
printGlobals();
// asctime provides '\n' so we needn't add one
write_traceline("# Date and Time: %s", asctime(ptr));
if (InputFileName != NULL && InputFileName[0] != '\0') {
write_traceline("# Input File: %s\n", InputFileName);
}
if (GromacsOutputBaseName != NULL && GromacsOutputBaseName[0] != '\0') {
write_traceline("# Gromacs Output Base Name: %s\n", GromacsOutputBaseName);
}
if (OutputFileName != NULL && OutputFileName[0] != '\0') {
write_traceline("# Output File: %s\n", OutputFileName);
}
if (TraceFileName != NULL && TraceFileName[0] != '\0') {
write_traceline("# Trace File: %s\n", TraceFileName);
}
if (IDKey != NULL && IDKey[0] != '\0') {
write_traceline("# IDKey: %s\n", IDKey);
}
if (ToMinimize) {
write_traceline("#\n");
write_traceline("# Run type: Energy Minimization.\n");
write_traceline("#\n");
write_traceline("# iteration RMS force (pN) maximum force (pN)\n");
write_traceline("#\n");
return;
}
write_traceline("# \n");
write_traceline("# Run type: Dynamics.\n");
write_traceline("# \n");
write_traceline("# Number of Frames: %d\n", NumFrames);
write_traceline("# Steps per Frame: %d\n", IterPerFrame);
write_traceline("# Temperature: %.1f\n", Temperature);
if (part == NULL) {
write_traceline("# Warning: no part supplied.\n");
return;
}
write_traceline("# Number of Atoms: %d\n", part->num_atoms);
write_traceline("# \n");
for (i=0; i<part->num_jigs; i++) {
j = part->jigs[i];
switch (j->type) {
case Thermostat:
write_traceline("# %s Temperature setting: %f K\n", j->name, j->j.thermostat.temperature);
break;
case LinearMotor:
write_traceline("# %s Force: %f pN\n", j->name, j->j.lmotor.force);
write_traceline("# %s Stiffness: %f N/m\n", j->name, j->j.lmotor.stiffness);
break;
case RotaryMotor:
write_traceline("# %s Zero Speed Torque: %f nN-nm\n", j->name, j->j.rmotor.stall / 1e6);
write_traceline("# %s Zero Torque Speed: %f Ghz\n", j->name, j->j.rmotor.speed / (2.0e9 * Pi));
write_traceline("# %s Initial Speed: %f Ghz\n", j->name, j->j.rmotor.omega / (2.0e9 * Pi));
write_traceline("# %s Damping coefficient: %f\n", j->name, j->j.rmotor.damping_enabled ? j->j.rmotor.dampingCoefficient : 0.0);
break;
default:
break;
}
}
write_traceline("#\n");
ncols = 0;
if (PrintPotentialEnergy) {
ncols += 3;
}
for (i=0; i<part->num_jigs; i++) {
ncols += countOutputColumns(part->jigs[i]);
}
// Column count does not include the time column. Cad uses this
// to configure plotting interface.
write_traceline("# %d columns:\n", ncols);
for (i=0; i<part->num_jigs; i++) {
j = part->jigs[i];
switch (j->type) {
case DihedralMeter:
write_traceline("# %s: dihedral (degrees)\n", j->name);
break;
case AngleMeter:
write_traceline("# %s: angle (degrees)\n", j->name);
break;
case RadiusMeter:
write_traceline("# %s: distance (angstroms)\n", j->name);
break;
case Ground:
write_traceline("# %s: torque (nn-nm)\n", j->name);
break;
case Thermometer:
write_traceline("# %s: temperature (K)\n", j->name);
break;
case Thermostat:
write_traceline("# %s: energy added (zJ)\n", j->name);
break;
case LinearMotor:
write_traceline("# %s: displacement (angstroms)\n", j->name);
break;
case RotaryMotor:
write_traceline("# %s: speed (GHz)\n", j->name);
write_traceline("# %s: torque (nn-nm)\n", j->name);
break;
}
}
if (PrintPotentialEnergy) {
write_traceline("# Structure: potential energy (attojoules)\n");
write_traceline("# Structure: kinetic energy (attojoules)\n");
write_traceline("# Structure: total energy (attojoules)\n");
}
write_traceline("#\n");
}
void
traceFileVersion()
{
write_traceline("# NanoEngineer-1.com Simulator Trace File, Version 050310\n");
write_traceline("#\n");
}
