tempory debug. (f28561b6) · Commits · DeAn Wei / prodata

include/MD.h

+0 −1

Original line number	Diff line number	Diff line
		@@ -28,7 +28,6 @@ typedef struct{

		typedef struct {
		int timestep;
		int atoms;
		real8 box[6];

		vector<string> bounds;

include/Util.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -41,5 +41,5 @@ real8 LinearInterpolation(const Curve_t &curve, real8 x, real8 min = -1, real8 m
		void SwapTable(Table_t &table);
		void SwapLineList(LineList_t &list);
		void CleanMgData(MgData_t &mg);

		void NormalizeVec(real8 vec[3]);
		#endif

src/HandleExtendedDislocation.cpp

+156 −8

Original line number	Diff line number	Diff line
		@@ -197,17 +197,32 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		return;
		}

		typedef struct {
		real8 x,y,z;
		vector<Atom_t *> nbr;
		}Probe_t;

		bool com(Atom_t p, Atom_t q){
		if(fabs(p.y - q.y) < 0.1){
		if(fabs(p.z - q.z)< 0.1){
		return(p.x<q.x);
		}else{
		return(p.z < q.z);
		}
		}else{
		return(p.y < q.y);
		}
		}
		void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		{
		int i, j, file, index;
		int i, j, file, index, lastIndex, firstNbr, indexVar;
		double cutofflen = 2.556;
		MgData_t mg;
		LineList_t list;
		string cutoffName("cutoff"), dvarName("dvar"), dvar("c_vcna");
		double dir[3] = {0, 1, 0}, p0[3], dval=5;
		string cutoffName("cutoff"), dvarName("dvar"), dvar("c_vcna"), p0Name("p0"), dirName("dir");

		vector<Atom_t>::iterator it;

		if((index = GetValID(inArgs->priVars, cutoffName)) < inArgs->priVars.size()){
		cutofflen = atof(inArgs->priVars[index].vals[0].c_str());
		@@ -216,18 +231,45 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)

		if((index = GetValID(inArgs->priVars, dvarName)) < inArgs->priVars.size()){
		dvar = inArgs->priVars[index].vals[0];
		if(inArgs->priVars[index].vals.size() == 2){
		dval = atof(inArgs->priVars[index].vals[1].c_str());
		}
		}
		printf("The determined var (dvar) is %s, value is %f\n", dvar.c_str(), dval);

		if((index = GetValID(inArgs->priVars, p0Name)) < inArgs->priVars.size()){
		if(inArgs->priVars[index].vals.size() != 3){
		Fatal("You have to determine the initial point by -dp0 x y z");
		}
		p0[0] = atof(inArgs->priVars[index].vals[0].c_str());
		p0[1] = atof(inArgs->priVars[index].vals[1].c_str());
		p0[2] = atof(inArgs->priVars[index].vals[2].c_str());
		}else{
		Fatal("You have to determine the initial point by -dp0 x y z");

		}
		printf("The initial probe point (p0) is %f %f %f\n", p0[0], p0[1], p0[2]);

		if((index = GetValID(inArgs->priVars, dirName)) < inArgs->priVars.size()){
		if(inArgs->priVars[index].vals.size() != 3){
		Fatal("at least 3 vals for %s", dirName.c_str());
		}
		dir[0] = atof(inArgs->priVars[index].vals[0].c_str());
		dir[1] = atof(inArgs->priVars[index].vals[1].c_str());
		dir[2] = atof(inArgs->priVars[index].vals[2].c_str());
		NormalizeVec(dir);
		}
		printf("The determined var (dvar) is %s\n", dvar.c_str());
		printf("The direction of probe moving is along %f, %f, %f\n", dir[0], dir[1], dir[2]);

		ReadDataFromMDLogFile(inArgs->auxFiles, list);

		for(file=0; file<inArgs->inpFiles.size(); file++){
		printf("1\n");
		ReadMGDataFile(inArgs->inpFiles[file], mg);
		sort(mg.atom.begin(), mg.atom.end(), com);
		printf("2\n");

		#if 0
		printf("Timestep %d, Atoms %d, Bouds %s %s %s, ",
		mg.timestep, mg.atoms, mg.bounds[0].c_str(),
		mg.timestep, (int)mg.atom.size(), mg.bounds[0].c_str(),
		mg.bounds[1].c_str(), mg.bounds[2].c_str());
		printf("Box %e %e %e %e %e %e\n", mg.box[0], mg.box[1],
		mg.box[2], mg.box[3], mg.box[4], mg.box[5]);
		@@ -237,6 +279,112 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		printf("%s(%d) ", mg.variables[i].c_str(), (int)mg.atom.size());
		}
		printf("\n");

		for(i=0; i<mg.variables.size(); i++){
		if(dvar == mg.variables[i])break;
		}
		if((i=indexVar) == mg.variables.size()){
		Fatal("There is no %s in the mg file %s", dvar.c_str(),
		inArgs->inpFiles[file].c_str());
		}

		printf("2.1 %d\n", indexVar);
		for(it = mg.atom.end(), i=mg.atom.size()-1; it != mg.atom.begin(); it--, i--){
		printf("2.1.0 %f %f %f %d\n", (it).x, (it).y, (*it).z, (int)mg.atom[i].vars.size());
		if((it).x < mg.box[0] + (mg.box[1]-mg.box[0])0.05 \|\|
		(it).y < mg.box[2] + (mg.box[3]-mg.box[2])0.05 \|\|
		(it).z < mg.box[4] + (mg.box[5]-mg.box[4])0.05 \|\|
		(it).x > mg.box[0] + (mg.box[1]-mg.box[0])0.95 \|\|
		(it).y > mg.box[2] + (mg.box[3]-mg.box[2])0.95 \|\|
		(it).z > mg.box[4] + (mg.box[5]-mg.box[4])0.95){

		printf("2.1.00 %f\n", dval);
		if(mg.atom[i].vars[indexVar] == dval){
		printf("2.1.1 %f\n", dval);
		// vector<double>().swap(mg.atom[i].vars);
		printf("2.1.2\n");
		mg.atom.erase(it);
		printf("2.1.3\n");
		}
		}
		}

		printf("3\n");
		sort(mg.atom.begin(), mg.atom.end(), com);
		printf("4 %d\n", mg.atom.size());

		for(i=0; i<mg.atom.size(); i++){
		if(mg.atom[i].vars.size()!=3){
		Fatal("%d i vars size 0");
		}
		}

		vector<Probe_t> probes;
		Probe_t probe;
		double d = 0.0;

		probe.y = p0[1];
		probe.z = p0[2];

		lastIndex = 0;
		while(1){
		printf("4.1\n");
		vector<Atom_t *>().swap(probe.nbr);
		probe.x += (dir[0]dcutofflen*0.8);
		probe.y += (dir[1]dcutofflen*0.8);
		probe.z += (dir[2]dcutofflen*0.8);

		firstNbr = 1;
		printf("4.2 %d\n", (int)mg.atom.size());
		for(i=lastIndex; i<mg.atom.size(); i++){
		printf("4.3.1 %d, %d, %d\n", i, indexVar, (int)mg.atom[i].vars.size());
		if((pow((mg.atom[i].y-probe.y), 2) +
		pow((mg.atom[i].z-probe.z), 2) < cutofflen*cutofflen)
		&& mg.atom[i].vars[indexVar] == dval){
		printf("4.3.1.1 %d\n", i);
		if(firstNbr){
		lastIndex = i;
		firstNbr = 0;
		}
		probe.nbr.push_back(&mg.atom[i]);
		printf("4.3.1.2 %d\n", i);
		}
		printf("4.3.2 %d\n", i);
		}
		printf("4.4\n");
		if(probe.nbr.size()>0){
		printf("4.5.1\n");
		probes.push_back(probe);
		printf("4.5.2\n");
		vector<Atom_t *>().swap(probe.nbr);
		printf("4.5.3\n");
		}
		printf("4.6\n");
		if(probe.y > mg.atom.back().y \|\|
		probe.z > mg.atom.back().z)break;
		d++;
		}

		printf("probes:\n");
		for(i=0; i<probes.size(); i++){
		probes[i].x = 0.0;
		probes[i].y = 0.0;
		probes[i].z = 0.0;
		for(j=0; j<probes[i].nbr.size(); j++){
		probes[i].x += probes[i].nbr[j]->x;
		probes[i].y += probes[i].nbr[j]->y;
		probes[i].z += probes[i].nbr[j]->z;
		}
		probes[i].x /= (double)probes[i].nbr.size();
		probes[i].y /= (double)probes[i].nbr.size();
		probes[i].z /= (double)probes[i].nbr.size();

		printf("probe %d, (%f,%f,%f) has nbr %d\n", i, probes[i].x, probes[i].y,
		probes[i].z, (int)probes[i].nbr.size());
		}


		#if 0
		#endif

		}

src/ReadData.cpp

+3 −3

Original line number	Diff line number	Diff line
		@@ -56,7 +56,7 @@ int ReadTecplotNormalData(string &file, Table_t &table, string &secLine)

		int ReadMGDataFile(const string &file, MgData_t &mgdata)
		{
		int i, j;
		int i, j, atoms;
		int idCol = 0, typeCol = 0;
		int xCol = 0, yCol = 0, zCol = 0;
		ifstream infile;
		@@ -87,7 +87,7 @@ int ReadMGDataFile(const string &file, MgData_t &mgdata)
		if(words.size()==4){
		if(words[2] == "OF" && words[3] == "ATOMS"){
		getline(infile,str);
		mgdata.atoms = atoi(str.c_str());
		atoms = atoi(str.c_str());
		}
		}
		}else if(words[1] == "BOX"){
		@@ -126,7 +126,7 @@ int ReadMGDataFile(const string &file, MgData_t &mgdata)
		j++;
		}

		mgdata.atom.resize(mgdata.atoms);
		mgdata.atom.resize(atoms);
		for(i=0; i<mgdata.atom.size(); i++){
		vector<string>().swap(subwords);
		getline(infile,str);

src/Util.cpp

+15 −1

Original line number	Diff line number	Diff line
		@@ -197,7 +197,6 @@ void CleanMgData(MgData_t &mg)
		{
		int i;
		mg.timestep = 0;
		mg.atoms = 0;
		for(i=0; i<6; i++){
		mg.box[i] = 0.0;
		}
		@@ -214,6 +213,21 @@ void CleanMgData(MgData_t &mg)
		}


		void NormalizeVec(real8 vec[3])
		{
		real8 a2, a;

		a2 = (vec[0]vec[0] + vec[1]vec[1] + vec[2]*vec[2]);

		if (a2 > 0.0) {
		a = sqrt(a2);
		vec[0] /= a;
		vec[1] /= a;
		vec[2] /= a;
		}

		return;
		}