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);
}
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);
}
void
oneDynamicsFrame(struct part *part,
int iters,
struct xyz *averagePositions,
struct xyz **pOldPositions,
struct xyz **pNewPositions,
struct xyz **pPositions,
struct xyz *force)
{
int j;
int loop;
double deltaTframe;
struct xyz f;
struct xyz *tmp;
struct jig *jig;
struct xyz *oldPositions = *pOldPositions;
struct xyz *newPositions = *pNewPositions;
struct xyz *positions = *pPositions;
// wware 060109 python exception handling
NULLPTR(part);
NULLPTR(averagePositions);
NULLPTR(oldPositions);
NULLPTR(newPositions);
NULLPTR(positions);
iters = max(iters,1);
deltaTframe = 1.0/iters;
for (j=0; j<part->num_atoms; j++) {
vsetc(averagePositions[j],0.0);
}
// See http://www.nanoengineer-1.net/mediawiki/index.php?title=Verlet_integration
// for a discussion of how dynamics is done in the simulator.
// we want:
// x(t+dt) = 2x(t) - x(t-dt) + A dt^2
// or:
// newPositions = 2 * positions - oldPositions + A dt^2
// wware 060110 don't handle Interrupted with the BAIL mechanism
for (loop=0; loop < iters && !Interrupted; loop++) {
_last_iteration = loop == iters - 1;
Iteration++;
// wware 060109 python exception handling
updateVanDerWaals(part, NULL, positions); BAIL();
calculateGradient(part, positions, force); BAIL();
/* first, for each atom, find non-accelerated new pos */
/* Atom moved from oldPositions to positions last time,
now we move it the same amount from positions to newPositions */
for (j=0; j<part->num_atoms; j++) {
// f = positions - oldPositions
vsub2(f,positions[j],oldPositions[j]);
// newPositions = positions + f
// or:
// newPositions = 2 * positions - oldPositions
vadd2(newPositions[j],positions[j],f);
// after this, we will need to add A dt^2 to newPositions
}
// pre-force jigs
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
// wware 060109 python exception handling
NULLPTR(jig);
switch (jig->type) {
case LinearMotor:
jigLinearMotor(jig, positions, newPositions, force, deltaTframe);
break;
default:
break;
}
}
/* convert forces to accelerations, giving new positions */
//FoundKE = 0.0; /* and add up total KE */
for (j=0; j<part->num_atoms; j++) {
// to complete Verlet integration, this needs to do:
// newPositions += A dt^2
//
// force[] is in pN, mass is in g, Dt in seconds, f in pm
vmul2c(f,force[j],part->atoms[j]->inverseMass); // inverseMass = Dt*Dt/mass
// XXX: 0.15 probably needs a scaling by Dt
// 0.15 = deltaX
// keMax = m v^2 / 2
// v^2 = 2 keMax / m
// v = deltaX / Dt = sqrt(2 keMax / m)
// deltaX = Dt sqrt(2 keMax / m)
// We probably don't want to do this, because a large raw
// velocity isn't a problem, it's just when that creates a
// high force between atoms that it becomes a problem. We
// check that elsewhere.
//if (!ExcessiveEnergyWarning && vlen(f)>0.15) { // 0.15 is just below H flyaway
// WARNING3("Excessive force %.6f in iteration %d on atom %d -- further warnings suppressed", vlen(f), Iteration, j+1);
// ExcessiveEnergyWarningThisFrame++;
//}
vadd(newPositions[j],f);
//vsub2(f, newPositions[j], positions[j]);
//ff = vdot(f, f);
//FoundKE += atom[j].energ * ff;
}
// Jigs are executed in the following order: motors,
// thermostats, grounds, measurements. Motions from each
// motor are added together, then thermostats operate on the
// motor output. Grounds override anything that moves atoms.
// Measurements happen after all things that could affect
// positions, including grounds.
// motors
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
if (jig->type == RotaryMotor) {
jigMotor(jig, deltaTframe, positions, newPositions, force);
}
// LinearMotor handled in preforce above
}
// thermostats
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
if (jig->type == Thermostat) {
jigThermostat(jig, deltaTframe, positions, newPositions);
}
}
// grounds
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
if (jig->type == Ground) {
jigGround(jig, deltaTframe, positions, newPositions, force);
}
}
// measurements
for (j=0;j<part->num_jigs;j++) { /* for each jig */
jig = part->jigs[j];
switch (jig->type) {
case Thermometer:
jigThermometer(jig, deltaTframe, positions, newPositions);
break;
case DihedralMeter:
jigDihedral(jig, newPositions);
break;
case AngleMeter:
jigAngle(jig, newPositions);
break;
case RadiusMeter:
jigRadius(jig, newPositions);
break;
default:
break;
}
}
for (j=0; j<part->num_atoms; j++) {
vadd(averagePositions[j],newPositions[j]);
}
tmp=oldPositions; oldPositions=positions; positions=newPositions; newPositions=tmp;
if (ExcessiveEnergyWarningThisFrame > 0) {
ExcessiveEnergyWarning = 1;
}
}
for (j=0; j<part->num_atoms; j++) {
vmulc(averagePositions[j],deltaTframe);
}
*pOldPositions = oldPositions;
*pNewPositions = newPositions;
*pPositions = positions;
}
