double
rng_gaussian( const double sigma ) {
return gsl_ran_gaussian( r , sigma ) ;
}
/* Initialize particle positions by assigning them
on a cubic grid, then scaling positions
to achieve a given box size and thereby, volume,
and density */
void init ( double * rx, double * ry, double * rz,
double * vx, double * vy, double * vz,
int * ix, int * iy, int * iz,
int n, double L, gsl_rng * r, double T0,
double * KE, char * icf) {
int i,iix,iiy,iiz;
double cmvx=0.0,cmvy=0.0,cmvz=0.0;
double T, fac;
int n3=2;
int vel_ok=0;
/* If icf has a value, assume it is the name of a file containing
the input configuration in XYZ format */
if (icf) {
FILE * fp = fopen(icf,"r");
if (fp) vel_ok = xyz_in(fp,rx,ry,rz,vx,vy,vz,&n);
else {
fprintf(stderr,"# error: could not read %s\n",icf);
exit(-1);
}
}
/* Assign particles on a cubic lattice */
else {
/* Find the lowest perfect cube, n3, greater than or equal to the
number of particles */
while ((n3*n3*n3)<n) n3++;
iix=iiy=iiz=0;
/* Assign particle positions */
for (i=0;i<n;i++) {
rx[i] = ((double)iix+0.5)*L/n3;
ry[i] = ((double)iiy+0.5)*L/n3;
rz[i] = ((double)iiz+0.5)*L/n3;
iix++;
if (iix==n3) {
iix=0;
iiy++;
if (iiy==n3) {
iiy=0;
iiz++;
}
}
}
}
/* If no velocities yet assigned, randomly pick some */
if (!vel_ok) {
for (i=0;i<n;i++) {
vx[i]=gsl_ran_gaussian(r,1.0);
vy[i]=gsl_ran_gaussian(r,1.0);
vz[i]=gsl_ran_gaussian(r,1.0);
}
}
/* Take away any center-of-mass drift; compute initial KE */
for (i=0;i<n;i++) {
cmvx+=vx[i];
cmvy+=vy[i];
cmvz+=vz[i];
}
(*KE)=0;
for (i=0;i<n;i++) {
vx[i]-=cmvx/n;
vy[i]-=cmvy/n;
vz[i]-=cmvz/n;
(*KE)+=vx[i]*vx[i]+vy[i]*vy[i]+vz[i]*vz[i];
}
(*KE)*=0.5;
/* if T0 is specified, scale velocities */
if (T0>0.0) {
T=(*KE)/n*2./3.;
fac=sqrt(T0/T);
(*KE)=0;
for (i=0;i<n;i++) {
vx[i]*=fac;
vy[i]*=fac;
vz[i]*=fac;
(*KE)+=vx[i]*vx[i]+vy[i]*vy[i]+vz[i]*vz[i];
}
(*KE)*=0.5;
}
/* Initialize periodic boundary crossing counter arrays */
memset(ix,0,n*sizeof(int));
memset(iy,0,n*sizeof(int));
memset(iz,0,n*sizeof(int));
}
int main ( int argc, char * argv[] ) {
double * rx, * ry, * rz;
double * vx, * vy, * vz;
double * fx, * fy, * fz;
int * ix, * iy, * iz;
int N=216,c,a;
double L=0.0;
double rho=0.5, Tb = 1.0, nu=1.0, rc2 = 1.e20;
double vir, vir_sum, pcor, V;
double PE, KE, TE, ecor, ecut, T0=0.0, TE0;
double rr3,dt=0.001, dt2, sigma;
int i,j,s;
int nSteps = 10, fSamp=100;
int short_out=0;
int use_e_corr=0;
int unfold = 0;
char fn[20];
FILE * out;
char * wrt_code_str = "w";
char * init_cfg_file = NULL;
gsl_rng * r = gsl_rng_alloc(gsl_rng_mt19937);
unsigned long int Seed = 23410981;
/* Here we parse the command line arguments; If
you add an option, document it in the usage() function! */
for (i=1;i<argc;i++) {
if (!strcmp(argv[i],"-N")) N=atoi(argv[++i]);
else if (!strcmp(argv[i],"-rho")) rho=atof(argv[++i]);
else if (!strcmp(argv[i],"-nu")) nu=atof(argv[++i]);
else if (!strcmp(argv[i],"-dt")) dt=atof(argv[++i]);
else if (!strcmp(argv[i],"-rc")) rc2=atof(argv[++i]);
else if (!strcmp(argv[i],"-ns")) nSteps = atoi(argv[++i]);
else if (!strcmp(argv[i],"-so")) short_out=1;
else if (!strcmp(argv[i],"-T0")) T0=atof(argv[++i]);
else if (!strcmp(argv[i],"-Tb")) Tb=atof(argv[++i]);
else if (!strcmp(argv[i],"-fs")) fSamp=atoi(argv[++i]);
else if (!strcmp(argv[i],"-sf")) wrt_code_str = argv[++i];
else if (!strcmp(argv[i],"-icf")) init_cfg_file = argv[++i];
else if (!strcmp(argv[i],"-ecorr")) use_e_corr = 1;
else if (!strcmp(argv[i],"-seed")) Seed = (unsigned long)atoi(argv[++i]);
else if (!strcmp(argv[i],"-uf")) unfold = 1;
else if (!strcmp(argv[i],"-h")) {
usage(); exit(0);
}
else {
fprintf(stderr,"Error: Command-line argument '%s' not recognized.\n",
argv[i]);
exit(-1);
}
}
/* Compute the side-length */
L = pow((V=N/rho),0.3333333);
/* Compute the tail-corrections; assumes sigma and epsilon are both 1 */
rr3 = 1.0/(rc2*rc2*rc2);
ecor = use_e_corr?8*M_PI*rho*(rr3*rr3*rr3/9.0-rr3/3.0):0.0;
pcor = use_e_corr?16.0/3.0*M_PI*rho*rho*(2./3.*rr3*rr3*rr3-rr3):0.0;
ecut = 4*(rr3*rr3*rr3*rr3-rr3*rr3);
/* Compute the *squared* cutoff, reusing the variable rc2 */
rc2*=rc2;
/* compute the squared time step */
dt2=dt*dt;
/* Compute sigma */
sigma = sqrt(Tb);
/* Output some initial information */
fprintf(stdout,"# Andersen-Thermostat MD Simulation"
" of a Lennard-Jones fluid\n");
fprintf(stdout,"# L = %.5lf; rho = %.5lf; N = %i; rc = %.5lf\n",
L,rho,N,sqrt(rc2));
fprintf(stdout,"# nSteps %i, seed %d, dt %.5lf, T0 %.5lf, nu %.5lf\n",
nSteps,Seed,dt,T0,nu);
/* Seed the random number generator */
gsl_rng_set(r,Seed);
/* Allocate the position arrays */
rx = (double*)malloc(N*sizeof(double));
ry = (double*)malloc(N*sizeof(double));
rz = (double*)malloc(N*sizeof(double));
/* Allocate the boundary crossing counter arrays */
ix = (int*)malloc(N*sizeof(int));
iy = (int*)malloc(N*sizeof(int));
iz = (int*)malloc(N*sizeof(int));
/* Allocate the velocity arrays */
vx = (double*)malloc(N*sizeof(double));
vy = (double*)malloc(N*sizeof(double));
vz = (double*)malloc(N*sizeof(double));
/* Allocate the force arrays */
fx = (double*)malloc(N*sizeof(double));
fy = (double*)malloc(N*sizeof(double));
fz = (double*)malloc(N*sizeof(double));
/* Generate initial positions on a cubic grid,
and measure initial energy */
init(rx,ry,rz,vx,vy,vz,ix,iy,iz,N,L,r,T0,&KE,init_cfg_file);
sprintf(fn,"%i.xyz",0);
out=fopen(fn,"w");
xyz_out(out,rx,ry,rz,vx,vy,vz,ix,iy,iz,L,N,16,1,unfold);
fclose(out);
PE = total_e(rx,ry,rz,fx,fy,fz,N,L,rc2,ecor,ecut,&vir);
TE0=PE+KE;
fprintf(stdout,"# step PE KE TE drift T P\n");
for (s=0;s<nSteps;s++) {
/* First integration half-step */
for (i=0;i<N;i++) {
rx[i]+=vx[i]*dt+0.5*dt2*fx[i];
ry[i]+=vy[i]*dt+0.5*dt2*fy[i];
rz[i]+=vz[i]*dt+0.5*dt2*fz[i];
vx[i]+=0.5*dt*fx[i];
vy[i]+=0.5*dt*fy[i];
vz[i]+=0.5*dt*fz[i];
/* Apply periodic boundary conditions */
if (rx[i]<0.0) { rx[i]+=L; ix[i]--; }
if (rx[i]>L) { rx[i]-=L; ix[i]++; }
if (ry[i]<0.0) { ry[i]+=L; iy[i]--; }
if (ry[i]>L) { ry[i]-=L; iy[i]++; }
if (rz[i]<0.0) { rz[i]+=L; iz[i]--; }
if (rz[i]>L) { rz[i]-=L; iz[i]++; }
}
/* Calculate forces */
PE = total_e(rx,ry,rz,fx,fy,fz,N,L,rc2,ecor,ecut,&vir);
/* Second integration half-step */
KE = 0.0;
for (i=0;i<N;i++) {
vx[i]+=0.5*dt*fx[i];
vy[i]+=0.5*dt*fy[i];
vz[i]+=0.5*dt*fz[i];
KE+=vx[i]*vx[i]+vy[i]*vy[i]+vz[i]*vz[i];
}
KE*=0.5;
/* Andersen thermostat */
KE = 0.0;
for (i=0;i<N;i++) {
if (gsl_rng_uniform(r) < nu*dt) {
vx[i]=gsl_ran_gaussian(r,sigma);
vy[i]=gsl_ran_gaussian(r,sigma);
vz[i]=gsl_ran_gaussian(r,sigma);
}
KE+=vx[i]*vx[i]+vy[i]*vy[i]+vz[i]*vz[i];
}
KE*=0.5;
TE=PE+KE;
fprintf(stdout,"%i %.5lf %.5lf %.5lf %.5lf %.5le %.5lf %.5lf\n",
s,s*dt,PE,KE,TE,(TE-TE0)/TE0,KE*2/3./N,rho*KE*2./3./N+vir/3.0/V);
if (!(s%fSamp)) {
sprintf(fn,"%i.xyz",!strcmp(wrt_code_str,"a")?0:s);
out=fopen(fn,wrt_code_str);
xyz_out(out,rx,ry,rz,vx,vy,vz,ix,iy,iz,L,N,16,1,unfold);
fclose(out);
}
}
}
void Individual1::calcAdGenVal(Parameters& p,Individual1& s,Individual1& d){
for(unsigned short i=0;i<p.getNumTraits();++i){
mSampling[i]=gsl_ran_gaussian(prand,sqrt((0.5-0.25*(s.getInbreedingCoef()+d.getInbreedingCoef()))*p.getGenAdCov(i,i)));
adGenVal[i]=0.5*(s.getAdGenVal(i)+d.getAdGenVal(i))+mSampling[i];
}
}
void Individual::calcPhenVal(Parameters& p){
for(unsigned short i=0;i<p.getNumTraits();++i){
envDevVal[i] = gsl_ran_gaussian(prand, sqrt(p.getGenAdCov(i,i)*(1/p.getHeritability(i)-1))); //generating environment deviates;
phenVal[i]=p.getTraitMeans(i)+adGenVal[i]+envDevVal[i];
}
}
void Individual1::calcAdGenVal(Parameters& p){
for(unsigned short i=0;i<p.getNumTraits();++i){
adGenVal[i]=gsl_ran_gaussian(prand,sqrt(p.getGenAdCov(i,i)));
}
}
int
main()
{
const size_t n = N;
const size_t p = 2;
size_t i;
gsl_rng *r = gsl_rng_alloc(gsl_rng_default);
gsl_matrix *X = gsl_matrix_alloc(n, p);
gsl_vector *y = gsl_vector_alloc(n);
for (i = 0; i < n; ++i)
{
/* generate first random variable u */
double ui = gsl_ran_gaussian(r, 1.0);
/* set v = u + noise */
double vi = ui + gsl_ran_gaussian(r, 0.001);
/* set y = u + v + noise */
double yi = ui + vi + gsl_ran_gaussian(r, 1.0);
/* since u =~ v, the matrix X is ill-conditioned */
gsl_matrix_set(X, i, 0, ui);
gsl_matrix_set(X, i, 1, vi);
/* rhs vector */
gsl_vector_set(y, i, yi);
}
{
gsl_multifit_linear_workspace *w =
gsl_multifit_linear_alloc(n, p);
gsl_vector *c = gsl_vector_alloc(p);
gsl_vector *c_ridge = gsl_vector_alloc(p);
gsl_matrix *cov = gsl_matrix_alloc(p, p);
double chisq;
/* unregularized (standard) least squares fit, lambda = 0 */
gsl_multifit_linear_ridge(0.0, X, y, c, cov, &chisq, w);
fprintf(stderr, "=== Unregularized fit ===\n");
fprintf(stderr, "best fit: y = %g u + %g v\n",
gsl_vector_get(c, 0), gsl_vector_get(c, 1));
fprintf(stderr, "chisq/dof = %g\n", chisq / (n - p));
/* regularize with lambda = 1 */
gsl_multifit_linear_ridge(1.0, X, y, c_ridge, cov, &chisq, w);
fprintf(stderr, "=== Regularized fit ===\n");
fprintf(stderr, "best fit: y = %g u + %g v\n",
gsl_vector_get(c_ridge, 0), gsl_vector_get(c_ridge, 1));
fprintf(stderr, "chisq/dof = %g\n", chisq / (n - p));
gsl_multifit_linear_free(w);
gsl_matrix_free(cov);
gsl_vector_free(c);
gsl_vector_free(c_ridge);
}
gsl_rng_free(r);
gsl_matrix_free(X);
gsl_vector_free(y);
return 0;
}
void ParticleFilter::predict_with_simple_model()
{
float x, y, s;
float TRANS_X_STD = mParams.TRANS_X_STD;
float TRANS_Y_STD = mParams.TRANS_Y_STD;
float TRANS_SCALE_STD = mParams.TRANS_SCALE_STD;
float A1 = mParams.DYNAMICS_A1;
float A2 = mParams.DYNAMICS_A2;
float B0 = mParams.DYNAMICS_B0;
if(mReinit)
{
TRANS_X_STD=200.0;
TRANS_Y_STD=200.0;
TRANS_SCALE_STD=1.0;
mReinit=false;
}
static Particle p;
for(int i=0; i<mParams.NUMBER_OF_PARTICLES; ++i)
{
// x = A1 * ( mParticles[i].x - mParticles[i].x0 ) + A2 * ( mParticles[i].xp - mParticles[i].x0 ) +
// B0 * gsl_ran_gaussian( rng, TRANS_X_STD ) + mParticles[i].x0;
// p.x = MAX( 0.0, MIN( (float) 640 , x ) );
// y = A1 * ( mParticles[i].y - mParticles[i].y0 ) + A2 * ( mParticles[i].yp - mParticles[i].y0 ) +
// B0 * gsl_ran_gaussian( rng, TRANS_Y_STD ) + mParticles[i].y0;
// p.y = MAX( 0.0, MIN( (float) 480 , y ) );
// s = A1 * ( mParticles[i].s - mParticles[i].s0 ) + A2 * ( mParticles[i].sp - mParticles[i].s0 ) +
// B0 * gsl_ran_gaussian( rng, TRANS_SCALE_STD ) + mParticles[i].s0;
// p.s = 1.0;//MAX( 0.0, MIN( (float)1.0 - 1.0, s ) );
//std::cout << "Rand TRANS_X_STD " << TRANS_X_STD << " " << gsl_ran_gaussian( rng, TRANS_X_STD ) << std::endl;
x= mParticles[i].x + gsl_ran_gaussian( rng, TRANS_X_STD );
p.x = MAX( 0.0, MIN( (float) 640 , x ) );
y = mParticles[i].y + gsl_ran_gaussian( rng, TRANS_Y_STD );
p.y = MAX( 0.0, MIN( (float) 480 , y ) );
s = A1 * ( mParticles[i].s - mParticles[i].s0 ) + A2 * ( mParticles[i].sp - mParticles[i].s0 ) +
B0 * gsl_ran_gaussian( rng, TRANS_SCALE_STD ) + mParticles[i].s0;
p.s = 1.0;//MAX( 0.0, MIN( (float)1.0 - 1.0, s ) );
p.xp = mParticles[i].x;
p.yp = mParticles[i].y;
p.sp = mParticles[i].s;
p.x0 = mParticles[i].x0;
p.y0 = mParticles[i].y0;
p.s0 = mParticles[i].s0;
p.w = 0;
mParticles[i].x = p.x;
mParticles[i].y = p.y;
mParticles[i].s = p.s;
mParticles[i].xp = p.xp;
mParticles[i].yp = p.yp;
mParticles[i].sp = p.sp;
mParticles[i].x0 = p.x0;
mParticles[i].y0 = p.y0;
mParticles[i].s0 = p.s0;
mParticles[i].x_velocity = mParticles[i].x - mParticles[i].xp;
mParticles[i].y_velocity = mParticles[i].y - mParticles[i].yp;
mParticles[i].s_velocity = mParticles[i].s - mParticles[i].sp;
mParticles[i].w = p.w;
//std::cout << "particle " << i << " " << mParticles[i].x << " " << mParticles[i].y << " " << mParticles[i].s << std::endl;
}
}
scalar sasfit_ff_RNDMultiLamellarVesicle2(scalar q, sasfit_param * param)
{
scalar sum, sumt;
scalar Delta_s, DRi, Fi, Fj, rij;
scalar xc, yc, zc;
scalar t_sh, s_tsh, R_c, s_Rc, n, s_n, t_sol, s_tsol, Dt_sol, Delta_eta;
int i, j, N, p, Nav = 200;
static int idum = -1;
static gsl_rng * r;
static const gsl_rng_type * T;
// static float o_R_c=-1., o_t_sh=-1., o_t_sol=-1., o_Dt_sol=-1.,o_n=-1.;
static scalar r_i[100][3], R_i[100], tsh_i[100];
sasfit_param subParam;
SASFIT_ASSERT_PTR(param);
sasfit_get_param(param, 10, &t_sh, &s_tsh, &R_c, &s_Rc, &n, &s_n, &t_sol, &s_tsol, &Dt_sol, &Delta_eta);
SASFIT_CHECK_COND1((q < 0.0), param, "q(%lg) < 0",q);
SASFIT_CHECK_COND1((R_c <= 0.0), param, "R_c(%lg) <= 0",R_c);
SASFIT_CHECK_COND1((s_Rc < 0.0), param, "s_Rc(%lg) < 0",s_Rc);
SASFIT_CHECK_COND1((t_sol < 0.0), param, "t_sol(%lg) < 0",t_sol);
SASFIT_CHECK_COND1((s_tsol < 0.0), param, "s_tsol(%lg) < 0",s_tsol);
SASFIT_CHECK_COND1((t_sh < 0.0), param, "t_sh(%lg) < 0",t_sh);
SASFIT_CHECK_COND1((s_tsh < 0.0), param, "s_tsh(%lg) < 0",s_tsh);
SASFIT_CHECK_COND1((n < 1.0), param, "n(%lg) < 1",n);
SASFIT_CHECK_COND1((n > 100), param, "n(%lg) > 100",n);
SASFIT_CHECK_COND1((s_n < 0.0), param, "s_n(%lg) < 0",s_n);
if (idum < 0)
{
idum = 1;
gsl_rng_env_setup();
T = gsl_rng_default;
r = gsl_rng_alloc(T);
}
if (20 < sasfit_eps_get_iter_4_mc())
{
Nav = sasfit_eps_get_iter_4_mc();
} else {
Nav =20;
}
sasfit_init_param( &subParam );
sumt = 0.0;
for (p=0; p < Nav ;p++)
{
// do {
// N = (int) (gsl_ran_gaussian (r,s_n)+n);
// } while ((N>n+3*s_n) || (N<1));
if (s_n== 0.0) {
N = (int) n;
} else {
do {
N = (int) gsl_ran_lognormal(r,log(n),s_n);
}
while ((N>200) || (N<1));
}
r_i[0][0] = 0.0;
r_i[0][1] = 0.0;
r_i[0][2] = 0.0;
for (i=0; i < N ;i++)
{
if (s_tsh == 0.0) {
tsh_i[i] = t_sh;
} else {
do {
tsh_i[i] = gsl_ran_gaussian(r,s_tsh)+t_sh;
}
while (tsh_i[i] <= 0);
}
}
// do {
// R_i[0] = gsl_ran_gaussian(r,s_Rc)+R_c;
// } while (R_i[0] <= 0);
if (s_Rc == 0.0) {
R_i[0] = R_c;
} else {
do {
R_i[0] = gsl_ran_lognormal(r,log(R_c),s_Rc);
}
while (R_i[0] <= 0);
}
for (i=1; i < N ;i++)
{
gsl_ran_dir_3d(r,&xc,&yc,&zc);
if (s_tsol == 0.0) {
DRi = t_sol;
} else {
do {
DRi = gsl_ran_gaussian(r,s_tsol)+t_sol;
}
while (DRi < 0);
}
R_i[i] = R_i[i-1]+tsh_i[i-1]+DRi;
if (Dt_sol <= 0) {
Delta_s = Dt_sol*DRi;
} else {
do {
Delta_s = Dt_sol*DRi*gsl_rng_uniform(r);
}
while (Delta_s < 0);
}
r_i[i][0] = r_i[i-1][0] + Delta_s*xc;
r_i[i][1] = r_i[i-1][1] + Delta_s*yc;
r_i[i][2] = r_i[i-1][2] + Delta_s*zc;
}
sum=0.0;
for (i=0; i < N ;i++)
{
/*
Fi = K(interp,q,R_i[i] ,-Delta_eta,error)
+ K(interp,q,R_i[i]+tsh_i[i], Delta_eta,error);
*/
subParam.p[0] = R_i[i];
subParam.p[3] = -Delta_eta;
Fi = sasfit_ff_sphere_f(q, &subParam);
subParam.p[0] = R_i[i] + tsh_i[i];
subParam.p[3] = Delta_eta;
Fi += sasfit_ff_sphere_f(q, &subParam);
sum = sum + Fi*Fi;
for (j=i+1; j < N ;j++)
{
/*
Fj = K(interp,q,R_i[j] ,-Delta_eta,error)
+ K(interp,q,R_i[j]+tsh_i[j], Delta_eta,error);
*/
subParam.p[0] = R_i[j];
subParam.p[3] = -Delta_eta;
Fj = sasfit_ff_sphere_f(q, &subParam);
subParam.p[0] = R_i[j] + tsh_i[j];
subParam.p[3] = Delta_eta;
Fj += sasfit_ff_sphere_f(q, &subParam);
rij = sqrt( pow(r_i[i][0]-r_i[j][0],2)
+pow(r_i[i][1]-r_i[j][1],2)
+pow(r_i[i][2]-r_i[j][2],2)
);
if (rij == 0)
{
sum = sum + 2.0*Fi*Fj;
} else
{
sum = sum + 2.0*Fi*Fj*sin(q*rij)/(q*rij);
}
}
}
sumt = sumt+sum;
}
SASFIT_CHECK_SUB_ERR(param, subParam);
return sumt/Nav;
}
double
test_gaussian (void)
{
return gsl_ran_gaussian (r_global, 3.0);
}
