From cba0d347201db1c99dc23736658ed78ed12ad5bd Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Fri, 11 Sep 2009 18:31:39 +0200
Subject: [PATCH] added msd calc + 11x constraints as ifdef

---
 moldyn.c   | 151 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 moldyn.h   |   1 +
 msd_calc.c |  54 +++++++++++++++++++
 3 files changed, 206 insertions(+)
 create mode 100644 msd_calc.c

diff --git a/moldyn.c b/moldyn.c
index 15dcede..bd29afc 100644
--- a/moldyn.c
+++ b/moldyn.c
@@ -81,6 +81,10 @@ int moldyn_init(t_moldyn *moldyn,int argc,char **argv) {
 #ifdef CONSTRAINT_110_5832
 	printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
 	printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
+#endif
+#ifdef CONSTRAINT_11X_5832
+	printf("\n\n\nWARNING! WARNING! WARNING!\n\n\n");
+	printf("\n\n\n!! -- constraints enabled -- !!\n\n\n");
 #endif
 	return 0;
 }
@@ -2264,6 +2268,10 @@ int velocity_verlet(t_moldyn *moldyn) {
 	double tau,tau_square,h;
 	t_3dvec delta;
 	t_atom *atom;
+#ifdef CONSTRAINT_11X_5832
+	double xt,yt,zt;
+	double xtt,ytt,ztt;
+#endif
 
 	atom=moldyn->atom;
 	count=moldyn->count;
@@ -2275,6 +2283,28 @@ int velocity_verlet(t_moldyn *moldyn) {
 		atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
 		atom[5832].f.y=-atom[5832].f.x;
 	}
+#endif
+#ifdef CONSTRAINT_11X_5832
+	if(count==5833) {
+		// second trafo
+		xt=atom[5832].f.x;
+		yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129);
+		zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		atom[5832].f.x=xt;
+		atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
 #endif
 	for(i=0;i<count;i++) {
 		/* check whether fixed atom */
@@ -2288,6 +2318,30 @@ int velocity_verlet(t_moldyn *moldyn) {
 			delta.y=-delta.x;
 		}
 #endif
+#ifdef JHDVHJDV
+#ifdef CONSTRAINT_11X_5832
+	if(i==5833) {
+		// second trafo
+		xt=delta.x;
+		yt=delta.y*cos(-0.16935129)-delta.z*sin(-0.16935129);
+		zt=delta.y*sin(-0.16935129)+delta.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		delta.x=xt;
+		delta.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		delta.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
+#endif
+#endif
 #ifndef QUENCH
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 #endif
@@ -2296,6 +2350,30 @@ int velocity_verlet(t_moldyn *moldyn) {
 		if(i==5832) {
 			delta.y=-delta.x;
 		}
+#endif
+#ifdef GHDJHBSJBSD
+#ifdef CONSTRAINT_11X_5832
+	if(i==5833) {
+		// second trafo
+		xt=delta.x;
+		yt=delta.y*cos(-0.16935129)-delta.z*sin(-0.16935129);
+		zt=delta.y*sin(-0.16935129)+delta.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		delta.x=xt;
+		delta.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		delta.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
+#endif
 #endif
 		v3_add(&(atom[i].r),&(atom[i].r),&delta);
 		//check_per_bound_and_care_for_pbc(moldyn,&(atom[i]));
@@ -2328,6 +2406,28 @@ int velocity_verlet(t_moldyn *moldyn) {
 		atom[5832].f.x=0.5*(atom[5832].f.x-atom[5832].f.y);
 		atom[5832].f.y=-atom[5832].f.x;
 	}
+#endif
+#ifdef CONSTRAINT_11X_5832
+	if(count==5833) {
+		// second trafo
+		xt=atom[5832].f.x;
+		yt=atom[5832].f.y*cos(-0.16935129)-atom[5832].f.z*sin(-0.16935129);
+		zt=atom[5832].f.y*sin(-0.16935129)+atom[5832].f.z*cos(-0.16935129);
+		// first trafo
+		xtt=xt*cos(M_PI/4.0)-yt*sin(M_PI/4.0);
+		ytt=xt*sin(M_PI/4.0)+yt*sin(M_PI/4.0);
+		ztt=zt;
+		// apply constraints
+		ytt=0.0;
+		// first trafo backwards
+		xt=xtt*cos(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		yt=-xtt*sin(M_PI/4.0)+ytt*sin(M_PI/4.0);
+		zt=ztt;
+		// second trafo backwards
+		atom[5832].f.x=xt;
+		atom[5832].f.y=yt*cos(-0.16935129)+zt*sin(-0.16935129);
+		atom[5832].f.z=-yt*sin(-0.16935129)+zt*cos(-0.16935129);
+	}
 #endif
 	for(i=0;i<count;i++) {
 		/* check whether fixed atom */
@@ -3197,6 +3297,57 @@ int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc) {
 	return 0;
 }
 
+int calculate_msd(t_moldyn *moldyn,double *msd) {
+
+	int i;
+	t_atom *atom;
+	t_3dvec dist;
+	t_3dvec final_r;
+	double d2;
+	int a_cnt;
+	int b_cnt;
+
+	atom=moldyn->atom;
+	msd[0]=0;
+	msd[1]=0;
+	msd[2]=0;
+	a_cnt=0;
+	b_cnt=0;
+
+	for(i=0;i<moldyn->count;i++) {
+
+		/* care for pb crossing */
+		if(atom[i].pbc[0]|atom[i].pbc[1]|atom[i].pbc[2]) {
+			printf("[moldyn] msd pb crossings for atom %d\n",i);
+			printf("  x: %d y: %d z: %d\n",
+			       atom[i].pbc[0],atom[i].pbc[1],atom[i].pbc[2]);
+		}
+		final_r.x=atom[i].r.x+atom[i].pbc[0]*moldyn->dim.x;
+		final_r.y=atom[i].r.y+atom[i].pbc[1]*moldyn->dim.y;
+		final_r.z=atom[i].r.z+atom[i].pbc[2]*moldyn->dim.z;
+		/* calculate distance */
+		v3_sub(&dist,&final_r,&(atom[i].r_0));
+		d2=v3_absolute_square(&dist);
+
+		if(atom[i].brand) {
+			b_cnt+=1;
+			msd[1]+=d2;
+		}
+		else {
+			a_cnt+=1;
+			msd[0]+=d2;
+		}
+
+		msd[2]+=d2;
+	}
+
+	msd[0]/=a_cnt;
+	msd[1]/=b_cnt;
+	msd[2]/=moldyn->count;
+		
+	return 0;
+}
+
 int bonding_analyze(t_moldyn *moldyn,double *cnt) {
 
 	return 0;
diff --git a/moldyn.h b/moldyn.h
index bdb3758..a1866a9 100644
--- a/moldyn.h
+++ b/moldyn.h
@@ -523,6 +523,7 @@ int get_line(int fd,char *line,int max);
 
 int pair_correlation_init(t_moldyn *moldyn,double dr);
 int calculate_diffusion_coefficient(t_moldyn *moldyn,double *dc);
+int calculate_msd(t_moldyn *moldyn,double *msd);
 int calculate_pair_correlation_process(t_moldyn *moldyn,t_atom *itom,
                                        t_atom *jtom,void *data,u8 bc);
 int calculate_pair_correlation(t_moldyn *moldyn,double dr,void *ptr);
diff --git a/msd_calc.c b/msd_calc.c
new file mode 100644
index 0000000..80388d8
--- /dev/null
+++ b/msd_calc.c
@@ -0,0 +1,54 @@
+/*
+ * calculation of mean square displacement
+ *
+ * author: frank.zirkelbach@physik.uni-augsburg.de
+ *
+ */
+
+#define _GNU_SOURCE
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+#include <string.h>
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+
+#include "moldyn.h"
+
+int usage(char *prog) {
+
+	printf("\nusage:\n");
+	printf("  %s <save file>\n\n",prog);
+
+	return -1;
+}
+
+int main(int argc,char **argv) {
+
+	t_moldyn moldyn;
+	int ret;
+	double msd[3];
+
+	if(argc!=2) {
+		usage(argv[0]);
+		return -1;
+	}
+
+	memset(&moldyn,0,sizeof(t_moldyn));
+
+	printf("[msd calc] reading save file ...\n");
+	ret=moldyn_read_save_file(&moldyn,argv[1]);
+	if(ret) {
+		printf("[msd calc] exit!\n");
+		return ret;
+	}
+
+	calculate_msd(&moldyn,msd);
+	
+	printf("MSD - %f ps: %.10f %.10f %.10f\n",moldyn.time,
+	       msd[0],msd[1],msd[2]);
+
+	return 0;
+}
+
-- 
2.39.2