From: hackbard <hackbard>
Date: Mon, 3 Apr 2006 15:48:42 +0000 (+0000)
Subject: added harmonic potntial + bugfixes + boundings
X-Git-Url: https://hackdaworld.org/cgi-bin/gitweb.cgi?a=commitdiff_plain;h=45b27e01673a6cc5bebecb49c51d7f587917483e;p=physik%2Fposic.git

added harmonic potntial + bugfixes + boundings
---

diff --git a/clean b/clean
index 2e1cd0e..34c2b3c 100755
--- a/clean
+++ b/clean
@@ -1,3 +1 @@
-#!/bin/bash
-
 rm -f saves/* video/*
diff --git a/moldyn.c b/moldyn.c
index 3d669d2..72a672a 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -177,6 +177,19 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 	return p_total;
 }
 
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t) {
+
+	double tau;
+
+	tau=0.05*nn_dist/(sqrt(3.0*K_BOLTZMANN*t/moldyn->atom[0].mass));
+	tau*=1.0E-9;
+	if(tau<moldyn->tau)
+		printf("[moldyn] warning: time step  (%f > %.15f)\n",
+		       moldyn->tau,tau);
+
+	return tau;	
+}
+
 
 /*
  *
@@ -189,6 +202,9 @@ t_3dvec get_total_p(t_atom *atom, int count) {
 int moldyn_integrate(t_moldyn *moldyn) {
 
 	int i;
+	int write;
+
+	write=moldyn->write;
 
 	/* calculate initial forces */
 	moldyn->force(moldyn);
@@ -198,8 +214,7 @@ int moldyn_integrate(t_moldyn *moldyn) {
 		moldyn->integrate(moldyn);
 
 		/* check for visualiziation */
-		// to be continued ...
-		if(!(i%1)) {
+		if(!(i%write)) {
 			visual_atoms(moldyn->visual,i*moldyn->tau,
 			             moldyn->atom,moldyn->count);
 		}
@@ -233,7 +248,7 @@ int velocity_verlet(t_moldyn *moldyn) {
 
 		/* velocities */
 		v3_scale(&delta,&(atom[i].f),0.5*tau/atom[i].mass);
-		v3_add(&(atom[i].r),&(atom[i].r),&delta);
+		v3_add(&(atom[i].v),&(atom[i].v),&delta);
 	}
 
 	/* forces depending on chosen potential */
@@ -255,6 +270,72 @@ int velocity_verlet(t_moldyn *moldyn) {
  * 
  */
 
+/* harmonic oscillator potential and force */
+
+double potential_harmonic_oscillator(t_moldyn *moldyn) {
+
+	t_ho_params *params;
+	t_atom *atom;
+	int i,j;
+	int count;
+	t_3dvec distance;
+	double d,u;
+	double sc,equi_dist;
+
+	params=moldyn->pot_params;
+	atom=moldyn->atom;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
+	count=moldyn->count;
+
+	u=0.0;
+	for(i=0;i<count;i++) {
+		for(j=0;j<i;j++) {
+			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
+			d=v3_norm(&distance);
+			u+=(0.5*sc*(d-equi_dist)*(d-equi_dist));
+		}
+	}
+
+	return u;
+}
+
+int force_harmonic_oscillator(t_moldyn *moldyn) {
+
+	t_ho_params *params;
+	int i,j,count;
+	t_atom *atom;
+	t_3dvec distance;
+	t_3dvec force;
+	double d;
+	double sc,equi_dist;
+
+	atom=moldyn->atom;	
+	count=moldyn->count;
+	params=moldyn->pot_params;
+	sc=params->spring_constant;
+	equi_dist=params->equilibrium_distance;
+
+	for(i=0;i<count;i++) v3_zero(&(atom[i].f));
+
+	for(i=0;i<count;i++) {
+		for(j=0;j<i;j++) {
+			v3_sub(&distance,&(atom[i].r),&(atom[j].r));
+			v3_per_bound(&distance,&(moldyn->dim));
+			d=v3_norm(&distance);
+			if(d<=moldyn->cutoff) {
+				v3_scale(&force,&distance,
+				         (-sc*(1.0-(equi_dist/d))));
+				v3_add(&(atom[i].f),&(atom[i].f),&force);
+				v3_sub(&(atom[j].f),&(atom[j].f),&force);
+			}
+		}
+	}
+
+	return 0;
+}
+
+
 /* lennard jones potential & force for one sort of atoms */
  
 double potential_lennard_jones(t_moldyn *moldyn) {
diff --git a/moldyn.h b/moldyn.h
index d94e193..a2633ba 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -20,6 +20,7 @@ typedef struct s_atom {
 	t_3dvec f;	/* forces */
 	int element;	/* number of element in pse */
 	double mass;	/* atom mass */
+	//t_list vicinity	/* verlet neighbour list */
 } t_atom;
 
 typedef struct s_moldyn {
@@ -28,15 +29,22 @@ typedef struct s_moldyn {
 	double (*potential)(struct s_moldyn *moldyn);
 	void *pot_params;
 	int (*force)(struct s_moldyn *moldyn);
+	double cutoff;
 	double cutoff_square;
 	t_3dvec dim;
 	int (*integrate)(struct s_moldyn *moldyn);
 	int time_steps;
 	double tau;
 	void *visual;
+	int write;
 	unsigned char status;
 } t_moldyn;
 
+typedef struct s_ho_params {
+	double spring_constant;
+	double equilibrium_distance;
+} t_ho_params;
+
 typedef struct s_lj_params {
 	double sigma6;
 	double sigma12;
@@ -54,18 +62,20 @@ typedef struct s_lj_params {
 
 /* phsical values */
 
-//#define K_BOLTZMANN		1.3807E-23
-#define K_BOLTZMANN		1.0
+#define K_BOLTZMANN		1.3807e-27			/* Nm/K */
+#define AMU			1.660540e-27			/* kg */
 
 #define FCC			0x01
 #define DIAMOND			0x02
 
 #define C			0x06
-#define M_C			6.0
+#define M_C			(12.011*AMU)
 
-#define Si			0x0e
-#define M_SI			14.0
-#define LC_SI			5.43105
+#define SI			0x0e
+#define LC_SI			0.543105e-9				/* m */
+#define M_SI			(28.085*AMU)				/* kg */
+#define LJ_SIGMA_SI		((0.25*sqrt(3.0)*LC_SI)/1.122462)	/* m */
+#define LJ_EPSILON_SI		(2.1678*1.60e-19)			/* Nm */
 
 /* function prototypes */
 
@@ -79,9 +89,13 @@ double get_e_pot(t_moldyn *moldyn);
 double get_total_energy(t_moldyn *moldyn);
 t_3dvec get_total_p(t_atom *atom,int count);
 
+double estimate_time_step(t_moldyn *moldyn,double nn_dist,double t);
+
 int moldyn_integrate(t_moldyn *moldyn);
 int velocity_verlet(t_moldyn *moldyn);
 
+double potential_harmonic_oscillator(t_moldyn *moldyn);
+int force_harmonic_oscillator(t_moldyn *moldyn);
 double potential_lennard_jones(t_moldyn *moldyn);
 int force_lennard_jones(t_moldyn *moldyn);
 
diff --git a/perms b/perms
index d1f5e41..5693501 100755
--- a/perms
+++ b/perms
@@ -1,3 +1 @@
-#!/bin/bash
-
 chmod 640 saves/*
diff --git a/posic.c b/posic.c
index 926e20c..5ff3bc1 100644
--- a/posic.c
+++ b/posic.c
@@ -1,9 +1,11 @@
 /*
  * posic.c - precipitation process of silicon carbide in silicon
  *
- * author: Frank Zirkelbach <hackbard@hackdaworld.org>
+ * author: Frank Zirkelbach <frank.zirkelbach@physik.uni-augsburg.de>
  *
  */
+
+#include <math.h>
  
 #include "moldyn.h"
 #include "math/math.h"
@@ -29,8 +31,9 @@ int main(int argc,char **argv) {
 	int count;
 
 	t_lj_params lj;
+	t_ho_params ho;
 
-	char fb[32]="saves/fcc_test";
+	char fb[32]="saves/lj_test";
 
 	/* init */
 
@@ -48,6 +51,10 @@ int main(int argc,char **argv) {
 	b=LEN_Y;
 	c=LEN_Z;
 
+	vis.dim.x=a*LC_SI;
+	vis.dim.y=b*LC_SI;
+	vis.dim.z=c*LC_SI;
+
 	t=TEMPERATURE;
 
 	printf("placing silicon atoms ... ");
@@ -55,16 +62,16 @@ int main(int argc,char **argv) {
 	//printf("(%d) ok!\n",count);
 	count=2;
 	si=malloc(2*sizeof(t_atom));
-	si[0].r.x=2.0;
+	si[0].r.x=0.16e-9;
 	si[0].r.y=0;
 	si[0].r.z=0;
-	si[0].element=Si;
-	si[0].mass=14.0;
-	si[1].r.x=-2.0;
+	si[0].element=SI;
+	si[0].mass=M_SI;
+	si[1].r.x=-0.16e-9;
 	si[1].r.y=0;
 	si[1].r.z=0;
-	si[1].element=Si;
-	si[1].mass=14.0;
+	si[1].element=SI;
+	si[1].mass=M_SI;
 
 	printf("setting thermal fluctuations\n");
 	//thermal_init(si,&random,count,t);
@@ -74,56 +81,65 @@ int main(int argc,char **argv) {
 	/* check kinetic energy */
 
 	e=get_e_kin(si,count);
-	printf("kinetic energy: %f\n",e);
-	printf("3/2 N k T = %f\n",1.5*count*K_BOLTZMANN*t);
+	printf("kinetic energy: %.40f [J]\n",e);
+	printf("3/2 N k T = %.40f [J]\n",1.5*count*K_BOLTZMANN*t);
 
 	/* check total momentum */
 	p=get_total_p(si,count);
-	printf("total momentum: %f\n",v3_norm(&p));
+	printf("total momentum: %.30f [Ns]\n",v3_norm(&p));
 
 	/* check potential energy */
 	md.count=count;
 	md.atom=si;
 	md.potential=potential_lennard_jones;
+	//md.potential=potential_harmonic_oscillator;
 	md.force=force_lennard_jones;
+	//md.force=force_harmonic_oscillator;
 	//md.cutoff_square=((LC_SI/4.0)*(LC_SI/4.0));
-	md.cutoff_square=36.0;
+	md.cutoff=(0.4e-9);
+	md.cutoff_square=(0.6e-9*0.6e-9);
 	md.pot_params=&lj;
+	//md.pot_params=&ho;
 	md.integrate=velocity_verlet;
 	md.time_steps=RUNS;
 	md.tau=TAU;
 	md.status=0;
 	md.visual=&vis;
+	md.write=WRITE_FILE;
 
-	lj.sigma6=3.0/16.0*LC_SI*LC_SI;
+	lj.sigma6=LJ_SIGMA_SI*LJ_SIGMA_SI;
 	help=lj.sigma6*lj.sigma6;
 	lj.sigma6*=help;
 	lj.sigma12=lj.sigma6*lj.sigma6;
-	lj.epsilon=10000;
+	lj.epsilon=LJ_EPSILON_SI;
+
+	ho.equilibrium_distance=0.3e-9;
+	ho.spring_constant=1.0e-9;
 
 	u=get_e_pot(&md);
 
-	printf("potential energy: %f\n",u);
-	printf("total energy (1): %f\n",e+u);
-	printf("total energy (2): %f\n",get_total_energy(&md));
+	printf("potential energy: %.40f [J]\n",u);
+	printf("total energy (1): %.40f [J]\n",e+u);
+	printf("total energy (2): %.40f [J]\n",get_total_energy(&md));
 
 	md.dim.x=a*LC_SI;
 	md.dim.y=b*LC_SI;
 	md.dim.z=c*LC_SI;
 
+	printf("estimated accurate time step: %.30f [s]\n",
+	       estimate_time_step(&md,3.0,t));
+
+
 	/*
 	 * let's do the actual md algorithm now
 	 *
 	 * integration of newtons equations
 	 */
 
-	/* visualize */
-	//visual_atoms(&vis,0.0,si,count);
-	
-
 	moldyn_integrate(&md);
 
-	printf("total energy (after integration): %f\n",get_total_energy(&md));
+	printf("total energy (after integration): %.40f [J]\n",
+	       get_total_energy(&md));
 
 	/* close */
 
diff --git a/posic.h b/posic.h
index 6a8131d..d31331f 100644
--- a/posic.h
+++ b/posic.h
@@ -17,15 +17,16 @@
 #ifndef POSIC_H
 #define POSIC_H
 
-#define RUNS 200
-#define TAU 0.001
+#define RUNS 10000000
+#define TAU 0.000000000000001
+#define WRITE_FILE 100000
 
 #define TEMPERATURE 273.0 
 
-#define LEN_X 15
-#define LEN_Y 15
-#define LEN_Z 15
+#define LEN_X 3
+#define LEN_Y 3
+#define LEN_Z 3
 
-#define R_CUTOFF 20
+#define R_CUTOFF (0.25*LEN_Z)
 
 #endif
diff --git a/visual/visual.c b/visual/visual.c
index 9d0f5a2..38ff0b0 100644
--- a/visual/visual.c
+++ b/visual/visual.c
@@ -31,6 +31,8 @@ int visual_init(t_visual *v,char *filebase) {
 		return -1;
 	}
 
+	memset(&(v->dim),0,sizeof(t_3dvec));
+
 	return 0;
 }
 
@@ -45,9 +47,14 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
 
 	int i,fd;
  	char file[128+64];
+	t_3dvec dim;
+
+	dim.x=10e9*v->dim.x;
+	dim.y=10e9*v->dim.y;
+	dim.z=10e9*v->dim.z;
 
 	char pse[19][4]={
-		"foo",
+		"*",
 		"H",
 		"He",
 		"Li",
@@ -77,9 +84,9 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
 
 	/* script file update */
 	dprintf(v->fd,"load xyz %s\n",file);
-	dprintf(v->fd,"spacefill 200\n");
-	//dprintf(v->fd,"rotate x 100\n");
-	//dprintf(v->fd,"rotate y 10\n");
+	dprintf(v->fd,"spacefill 300\n");
+	dprintf(v->fd,"rotate x 100\n");
+	dprintf(v->fd,"rotate y 10\n");
 	dprintf(v->fd,"set ambient 20\n");
 	dprintf(v->fd,"set specular on\n");
 	sprintf(file,"%s-%.15f.ppm",v->fb,time);
@@ -87,11 +94,23 @@ int visual_atoms(t_visual *v,double time,t_atom *atom,int n) {
 	dprintf(v->fd,"zap\n");
 
 	/* write the actual data file */
-	dprintf(fd,"%d\n",n);
+	dprintf(fd,"%d\n",(dim.x==0)?n:n+8);
 	dprintf(fd,"atoms at time %.15f\n",time);
 	for(i=0;i<n;i++)
 		dprintf(fd,"%s %f %f %f\n",pse[atom[i].element],
-		                           atom[i].r.x,atom[i].r.y,atom[i].r.z);
+		                           10e9*atom[i].r.x,
+		                           10e9*atom[i].r.y,
+		                           10e9*atom[i].r.z);
+	if(dim.x) {
+		dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,dim.y/2,dim.z/2);
+		dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,dim.y/2,dim.z/2);
+		dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,-dim.y/2,dim.z/2);
+		dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,dim.y/2,-dim.z/2);
+		dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,-dim.y/2,dim.z/2);
+		dprintf(fd,"%s %f %f %f\n",pse[0],dim.x/2,-dim.y/2,-dim.z/2);
+		dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,dim.y/2,-dim.z/2);
+		dprintf(fd,"%s %f %f %f\n",pse[0],-dim.x/2,-dim.y/2,-dim.z/2);
+	}
 	close(fd);
 
 	return 0;
diff --git a/visual/visual.h b/visual/visual.h
index 092af84..e2681d9 100644
--- a/visual/visual.h
+++ b/visual/visual.h
@@ -9,10 +9,12 @@
 #define VISUAL_H
 
 #include "../moldyn.h"
+#include "../math/math.h"
 
 typedef struct s_visual {
 	int fd;			/* rasmol script file descriptor */
 	char fb[128];		/* basename of the save files */
+	t_3dvec dim;		/* dimensions of the simulation cell */
 } t_visual;