path: root/sim/src/minstructure.c

// Copyright 2005-2006 Nanorex, Inc.  See LICENSE file for details. 

#include "simulator.h"

static char const rcsid[] = "$Id$";

#define COARSE_TOLERANCE 1e-8
#define FINE_TOLERANCE 1e-10

static struct part *Part;

static void
findRMSandMaxForce(struct configuration *p, double *pRMS, double *pMaxForce)
{
    struct xyz f;
    int i;
    double forceSquared;
    double sum_forceSquared = 0.0;
    double max_forceSquared = -1.0;

    // wware 060109  python exception handling
    NULLPTR(p);
    NULLPTR(pRMS);
    NULLPTR(pMaxForce);
    for (i=0; i<Part->num_atoms; i++) {
        if (Part->atoms[i]->isGrounded) {
            continue;
        }
	f = ((struct xyz *)p->gradient)[i];
	forceSquared = vdot(f,f);
	sum_forceSquared += forceSquared;
	if (forceSquared > max_forceSquared) {
	    max_forceSquared = forceSquared;
	}
    }
    *pRMS = sqrt(sum_forceSquared / Part->num_atoms);
    *pMaxForce = sqrt(max_forceSquared);
}

static FILE *minimizeCountFile;

static void
countMinimizeEvaulations(char which)
{
    if (minimizeCountFile == NULL) {
        minimizeCountFile = fopen("/tmp/minimizecounts", "a");
        if (minimizeCountFile == NULL) {
            perror("/tmp/minimizecounts");
            exit(1);
        }
    }
    fputc(which, minimizeCountFile);
    fflush(minimizeCountFile);
}

// This is the potential function which is being minimized.
static void
minimizeStructurePotential(struct configuration *p)
{
    int i;
    struct jig *jig;
    
    updateVanDerWaals(Part, p, (struct xyz *)p->coordinate);
    p->functionValue = calculatePotential(Part, (struct xyz *)p->coordinate);
    for (i=0; i<Part->num_jigs; i++) {
        jig = Part->jigs[i];
        switch (jig->type) {
        case RotaryMotor:
            p->functionValue +=
                jigMinimizePotentialRotaryMotor(Part, jig,
                                                (struct xyz *)p->coordinate,
                                                p->coordinate + jig->coordinateIndex);
            break;
        case LinearMotor:
            p->functionValue +=
                jigMinimizePotentialLinearMotor(Part, jig,
                                                (struct xyz *)p->coordinate,
                                                p->coordinate + jig->coordinateIndex);
            break;
        default:
            break;
        }
    }
    //writeMinimizeMovieFrame(OutputFile, Part, 0, (struct xyz *)p->coordinate, p->functionValue, p->parameter,
    //                        Iteration++, "potential", p->functionDefinition->message);
    if (DEBUG(D_MINIMIZE_POTENTIAL_MOVIE)) { // -D3
	writeSimpleMovieFrame(Part, (struct xyz *)p->coordinate, NULL, "potential %e %e", p->functionValue, p->parameter);
    }
    if (DEBUG(D_MINIMIZE_PARAMETER_GUESS)) {
        countMinimizeEvaulations('p');
    }
}

static double
clamp(double min, double max, double value)
{
    if (value > max) return max;
    if (value < min) return min;
    return value;
}

static double last_rms_force = 0.0;
static double last_max_force = 0.0;
static FILE *parameterGuessFile = NULL;

// A rotary motor should turn no farther than this during a single
// linear minimization.
#define MAX_RADIANS_PER_STEP 0.4

//#define PLOT_LINEAR_MINIMIZATION

// This is the gradient of the potential function which is being minimized.
static void
minimizeStructureGradient(struct configuration *p)
{
    int i;
    double rms_force;
    double max_force;
    double parameterLimit;
    double motorGradient;
    double plimit;
    struct xyz *forces;
    struct jig *jig;
    struct functionDefinition *fd = p->functionDefinition;

#ifdef PLOT_LINEAR_MINIMIZATION
    double parameter;
    double potential;
    struct xyz *position;
    struct configuration *newLocation;
    int j;
    struct stretch *stretch;
    struct bond *bond;
    double r;
    struct xyz rv;
    double rSquared;
#endif

    updateVanDerWaals(Part, p, (struct xyz *)p->coordinate); BAIL();
    if (DEBUG(D_GRADIENT_FROM_POTENTIAL) || DEBUG(D_GRADIENT_COMPARISON)) { // -D10 || -D18
        fd->gradient_delta = 1e-12; // pm
	evaluateGradientFromPotential(p); BAIL();
        for (i=fd->dimension-1; i>=0; i--) {
            p->gradient[i] *= 1e6; // convert uN to pN
        }
        if (DEBUG(D_MINIMIZE_GRADIENT_MOVIE) && DEBUG(D_GRADIENT_COMPARISON)) { // -D4
            struct xyz offset = { 0.0, 10.0, 0.0 };
            
            forces = (struct xyz *)p->gradient;
            for (i=0; i<Part->num_atoms; i++) {
                writeSimpleForceVectorOffset((struct xyz *)p->coordinate, i, &forces[i], 6, 1.0, offset); // yellow
            }
        }
    }
    if (!DEBUG(D_GRADIENT_FROM_POTENTIAL)) { // ! -D10
	calculateGradient(Part, (struct xyz *)p->coordinate, (struct xyz *)p->gradient);
	BAIL();
    }

    parameterLimit = MAXDOUBLE;
    for (i=0; i<Part->num_jigs; i++) {
        jig = Part->jigs[i];
        switch (jig->type) {
        case RotaryMotor:
            jigMinimizeGradientRotaryMotor(Part, jig,
                                           (struct xyz *)p->coordinate,
                                           (struct xyz *)p->gradient,
                                           p->coordinate + jig->coordinateIndex,
                                           p->gradient + jig->coordinateIndex);
            motorGradient = fabs(*(p->gradient + jig->coordinateIndex));
	    CHECKNAN(motorGradient);
            if (motorGradient < 1e-8) {
                motorGradient = 1e-8;
            }
            plimit = MAX_RADIANS_PER_STEP / motorGradient;
            if (plimit < parameterLimit) {
                parameterLimit = plimit;
            }
            break;
        case LinearMotor:
            jigMinimizeGradientLinearMotor(Part, jig,
                                           (struct xyz *)p->coordinate,
                                           (struct xyz *)p->gradient,
                                           p->coordinate + jig->coordinateIndex,
                                           p->gradient + jig->coordinateIndex);
            break;
        default:
            break;
        }
    }
    fd->parameter_limit = parameterLimit;

    // dynamics wants gradient pointing downhill, we want it uphill
    //for (i=0; i<3*Part->num_atoms; i++) {
    //  p->gradient[i] = -p->gradient[i];
    //}
    findRMSandMaxForce(p, &rms_force, &max_force); BAIL();

    // The initial parameter guess function is empirically determined.
    // The regression tests were run with D_MINIMIZE_PARAMETER_GUESS
    // enabled (compiled on in simulator.c).  Plots of the max_force
    // vs minimum parameter value columns were examined with gnuplot.
    // A functional form was determined which stayed within the main
    // body of the data points.  Final determination was based on the
    // evaluation counts also output with that debugging flag on.
    // Given that max_force is non-negative, the current form doesn't
    // need the upper range limit in the clamp.
    fd->initial_parameter_guess = clamp(1e-20, 1e3,
                                        0.7 / (max_force + 1000.0) +
                                        0.1 / (max_force + 20.0));

#ifdef PLOT_LINEAR_MINIMIZATION
    for (parameter = -fd->initial_parameter_guess;
         parameter < fd->initial_parameter_guess;
         parameter += fd->initial_parameter_guess / 500) {
        newLocation = gradientOffset(p, parameter);
        potential = evaluate(newLocation);
        position = (struct xyz *)newLocation->coordinate;
        printf("%e %e ", parameter, potential);
        for (j=0; j<Part->num_stretches; j++) {
            stretch = &Part->stretches[j];
            bond = stretch->b;
            vsub2(rv, position[bond->a2->index], position[bond->a1->index]);
            rSquared = vdot(rv, rv);
            r = sqrt(rSquared);
            potential = stretchPotential(Part, stretch, stretch->stretchType, r);
            printf("%f %f ", r, potential);
        }
        printf("\n");
        SetConfiguration(&newLocation, NULL);
    }
    printf("\n\n");
#endif
    
    writeMinimizeMovieFrame(OutputFile, Part, 0, (struct xyz *)p->coordinate, rms_force, max_force, Iteration++, 0,
			    fd->tolerance == COARSE_TOLERANCE ? "gradient" : "gradient fine", fd->message, evaluate(p));
    if (DEBUG(D_MINIMIZE_GRADIENT_MOVIE)) { // -D4
	writeSimpleMovieFrame(Part, (struct xyz *)p->coordinate, (struct xyz *)p->gradient, "gradient %e %e", rms_force, max_force);
    }
    if (DEBUG(D_MINIMIZE_PARAMETER_GUESS)) {
        countMinimizeEvaulations('g');
        if (parameterGuessFile == NULL) {
            parameterGuessFile = fopen("/tmp/parameterguesses", "a");
            if (parameterGuessFile == NULL) {
                perror("/tmp/parameterguesses");
                exit(1);
            }
        } else {
            fprintf(parameterGuessFile, "%e %e %e\n", last_rms_force, last_max_force, p->parameter);
            fflush(parameterGuessFile);
        }
        last_rms_force = rms_force;
        last_max_force = max_force;
    }
}

static int
minimizeStructureTermination(struct functionDefinition *fd,
                             struct configuration *previous,
                             struct configuration *current)
{
    double fp;
    double fq;
    double rms_force;
    double max_force;
    double tolerance = fd->tolerance;

    fp = evaluate(previous); BAILR(0);
    fq = evaluate(current); BAILR(0);

    evaluateGradient(current); BAILR(0);
    findRMSandMaxForce(current, &rms_force, &max_force); BAILR(0);
    if (tolerance == COARSE_TOLERANCE &&
        rms_force < MinimizeThresholdCutoverRMS &&
        max_force < MinimizeThresholdCutoverMax) {
      fd->tolerance = FINE_TOLERANCE;
      fd->algorithm = PolakRibiereConjugateGradient;
      fd->linear_algorithm = LinearMinimize;
    }
    if (tolerance == FINE_TOLERANCE &&
        (rms_force > MinimizeThresholdCutoverRMS * 1.5 ||
         max_force > MinimizeThresholdCutoverMax * 1.5)) {
      fd->tolerance = COARSE_TOLERANCE;
      fd->algorithm = SteepestDescent;
      fd->linear_algorithm = LinearBracket;
    }
    if (rms_force < MinimizeThresholdEndRMS &&
        max_force < MinimizeThresholdEndMax) {
      return 1;
    }

    return defaultTermination(fd, previous, current);
}

static void
minimizeStructureConstraints(struct configuration *p) 
{
    int i;
    int j;
    double dist;
    struct jig *jig;
    struct xyz *positions = (struct xyz *)p->coordinate;
    struct xyz delta;
    struct atom *a;
    int index;
    
    for (i=0; i<Part->num_jigs; i++) {
        jig = Part->jigs[i];
        switch (jig->type) {
        case Ground:
            for (j=0; j<jig->num_atoms; j++) {
                a = jig->atoms[j];
                index = a->index;
                positions[index] = Part->positions[index];
            }
            break;
        case LinearMotor:
            for (j=0; j<jig->num_atoms; j++) {
                a = jig->atoms[j];
                index = a->index;
                // restrict motion of atom to lay along axis from initial position
                // dist = (positions[index] - Part->positions[index]) dot jig->j.lmotor.axis
                // positions[index] = Part->positions[index] + jig->j.lmotor.axis * dist
                vsub2(delta, positions[index], Part->positions[index]);
                dist = vdot(delta, jig->j.lmotor.axis);
                vmul2c(delta, jig->j.lmotor.axis, dist);
                vadd2(positions[index], Part->positions[index], delta);
            }
            break;
        default:
            break;
        }
    }
}

static struct functionDefinition minimizeStructureFunctions;

void
minimizeStructure(struct part *part)
{
    int iter;
    struct configuration *initial;
    struct configuration *final;
    int i;
    int j;
    int jigDegreesOfFreedom;
    int coordinateCount;
    double rms_force;
    double max_force;
    double model_energy;
    struct jig *jig;

    NULLPTR(part);
    Part = part;

    jigDegreesOfFreedom = 0;
    coordinateCount = part->num_atoms * 3;
    for (i=0; i<Part->num_jigs; i++) {
        jig = Part->jigs[i];
        jig->coordinateIndex = coordinateCount + jigDegreesOfFreedom;
        jigDegreesOfFreedom += jig->degreesOfFreedom;
    }

    initializeFunctionDefinition(&minimizeStructureFunctions,
                                 minimizeStructurePotential,
                                 coordinateCount + jigDegreesOfFreedom,
                                 1024);
    BAIL();
    
    minimizeStructureFunctions.dfunc = minimizeStructureGradient;
    minimizeStructureFunctions.termination = minimizeStructureTermination;
    minimizeStructureFunctions.constraints = minimizeStructureConstraints;
    minimizeStructureFunctions.tolerance = COARSE_TOLERANCE;
    minimizeStructureFunctions.algorithm = SteepestDescent;
    minimizeStructureFunctions.linear_algorithm = LinearBracket;
    
    initial = makeConfiguration(&minimizeStructureFunctions);
    for (i=0, j=0; i<part->num_atoms; i++) {
	initial->coordinate[j++] = part->positions[i].x;
	initial->coordinate[j++] = part->positions[i].y;
	initial->coordinate[j++] = part->positions[i].z;
    }

    // To compare the torsion gradient code to the results of a
    // numerical differentiation, put the following lines in an .mmp
    // file, uncomment the define TORSION_DEBUG line, and run:
    // simulator -m -x TorsionDebug.mmp
    // Then, run:
    // glviewer < TorsionDebug.xyz
#if 0
atom 1 (6) (400, 0, 0) def
atom 2 (6) (250, 0, 0) def
info atom atomtype = sp2
bond1 1
atom 3 (6) (-250, 0, 0) def
info atom atomtype = sp2
bond2 2
atom 4 (6) (-400, 500, 0) def
bond1 3
#endif
    
    //#define TORSION_DEBUG
#ifdef TORSION_DEBUG
    debug_flags |= D_MINIMIZE_GRADIENT_MOVIE
        | D_GRADIENT_COMPARISON
        | D_SKIP_VDW
        | D_SKIP_BEND
        | D_SKIP_STRETCH;
    double theta;
    for (theta=0.0; theta<Pi; theta+=Pi/180.0) {
        initial->coordinate[1] = 50.0 * cos(theta);
        initial->coordinate[2] = 50.0 * sin(theta);
        evaluateGradient(initial);
        free(initial->gradient);
        initial->gradient = NULL;
    }
    exit(0);
#endif
    
    final = minimize(initial, &iter, NumFrames * 100);

    if (final != NULL) {
	// wware 060109  python exception handling
	evaluateGradient(final); BAIL();
	findRMSandMaxForce(final, &rms_force, &max_force); BAIL();

	writeMinimizeMovieFrame(OutputFile, part, 1, (struct xyz *)final->coordinate, rms_force, max_force,
				Iteration, 1, "final structure", minimizeStructureFunctions.message, evaluate(final));

	if (DEBUG(D_MINIMIZE_FINAL_PRINT)) { // -D 11
	    for (i=0, j=0; i<part->num_atoms; i++) {
		part->positions[i].x = final->coordinate[j++];
		part->positions[i].y = final->coordinate[j++];
		part->positions[i].z = final->coordinate[j++];
	    }
	    printPart(stdout, part);
	}
    }

    model_energy = evaluate(final);
    SetConfiguration(&initial, NULL);
    SetConfiguration(&final, NULL);
    if (model_energy > 0.25) {
	done("Final forces: rms %f pN, high %f pN, model energy: %.3f aJ evals: %d,%d",
	     rms_force,
	     max_force,
	     model_energy,
             minimizeStructureFunctions.functionEvaluationCount,
             minimizeStructureFunctions.gradientEvaluationCount);
    } else {
	done("Final forces: rms %f pN, high %f pN, model energy: %.3e aJ evals: %d,%d",
	     rms_force,
	     max_force,
	     model_energy,
             minimizeStructureFunctions.functionEvaluationCount,
             minimizeStructureFunctions.gradientEvaluationCount);
    }
}

/*
 * Local Variables:
 * c-basic-offset: 4
 * tab-width: 8
 * End:
 */