1. use command -help to stop program and check private parameters. (4aaf4092) · Commits · DeAn Wei / prodata

include/Home.h

+1 −0

Original line number	Diff line number	Diff line
		@@ -33,6 +33,7 @@ typedef struct {
		double burgMag;
		int seed;
		int type;
		bool help;

		vector<string> inpFiles, outFiles;
		vector<string> auxFiles;

src/HandleExtendedDislocation.cpp

+11 −7

Original line number	Diff line number	Diff line
		@@ -84,6 +84,7 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		remeshSize = atof(inArgs->priVars[index].vals[0].c_str());
		}
		printf("The remesh size is %f\n", remeshSize);
		if(inArgs->help)return;

		for(file=0; file<inArgs->inpFiles.size(); file++){

		@@ -296,7 +297,7 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		int nums[2] = {18, 24}, logfile;
		int stepID;
		double cutofflen = 2.556, alpha = 0.005, beta = 1.0;
		double position[3], separation;
		double position[3], separation, dis, maxDis;
		MgData_t mg;
		LineList_t list;
		double dir[3] = {0, 1, 0}, p0[3], dval=5;
		@@ -347,7 +348,7 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		dir[2] = atof(inArgs->priVars[index].vals[2].c_str());
		NormalizeVec(dir);
		}
		printf("The moving direction of probe is along %f, %f, %f\n", dir[0], dir[1], dir[2]);
		printf("The moving direction of probe (dir) is along %f, %f, %f\n", dir[0], dir[1], dir[2]);

		if((index = GetValID(inArgs->priVars, numsName)) < inArgs->priVars.size()){
		if(inArgs->priVars[index].vals.size() == 2){
		@@ -355,7 +356,9 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		nums[1] = atoi(inArgs->priVars[index].vals[1].c_str());
		}
		}
		printf("The parameters (para): cut-off length %f and resolution value %f\n", cutofflen, alpha);
		printf("The range of effective atoms of a paritial (nums) is [%d,%d]\n", nums[0], nums[1]);

		if(inArgs->help)return;
		logfile = ReadDataFromMDLogFile(inArgs->auxFiles, list);

		for(file=0; file<inArgs->inpFiles.size(); file++){
		@@ -378,7 +381,6 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		(it).z > mg.box[4] + (mg.box[5]-mg.box[4])0.95){

		if(mg.atom[i].vars[indexVar] == dval){
		// vector<double>().swap(mg.atom[i].vars);
		mg.atom.erase(it);
		}
		}
		@@ -413,15 +415,17 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		lastIndex = 0;
		while(1){
		vector<Atom_t *>().swap(probe.nbr);

		probe.x += (dir[0]dcutofflen*alpha);
		probe.y += (dir[1]dcutofflen*alpha);
		probe.z += (dir[2]dcutofflen*alpha);

		firstNbr = 1;
		maxDis = -1E10;
		for(i=lastIndex; i<mg.atom.size(); i++){
		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){
		dis = sqrt(pow((mg.atom[i].y-probe.y), 2) +
		pow((mg.atom[i].z-probe.z), 2) );
		if(dis < cutofflen && mg.atom[i].vars[indexVar] == dval){
		if(firstNbr){
		lastIndex = i;
		firstNbr = 0;

src/Main.cpp

+5 −10

Original line number	Diff line number	Diff line
		@@ -65,11 +65,6 @@ Option_t optList[OPT_MAX] = {
		-------------------------------------------------------------------------/
		static void Usage(char *program)
		{
		printf("\n");
		printf("Usage:\n");
		printf("\n");
		printf("\n");

		return;
		}

		@@ -93,11 +88,8 @@ static void PrintHelp(char *program)
		printf(" Options may be abbreviated to the shortest non-ambiguous\n");
		printf("\n");


		exit(0);
		}


		/*---------------------------------------------------------------------------
		*
		* Function: InitDefaultValues
		@@ -110,6 +102,7 @@ static void InitDefaultValues(InArgs_t *inArgs)
		inArgs->outFiles.push_back((char*)"output");
		inArgs->seed = time(0) + getpid();
		inArgs->type = 0;
		inArgs->help = 0;

		return;
		}
		@@ -235,7 +228,8 @@ static void GetInArgs(int argc, char argv[], InArgs_t inArgs)
		switch (j) {
		case OPT_HELP:
		PrintHelp(argv[0]);
		exit(0);
		inArgs->help = 1;
		break;
		case OPT_INPFILE:
		swap(inArgs->inpFiles, argValues);
		break;
		@@ -263,6 +257,7 @@ static void GetInArgs(int argc, char argv[], InArgs_t inArgs)

		}

		#if 0
		if(inArgs->priVars.size()>0){
		printf("Private vars for type %d:\n", inArgs->type);
		for(i=0; i<inArgs->priVars.size(); i++){
		@@ -273,7 +268,7 @@ static void GetInArgs(int argc, char argv[], InArgs_t inArgs)
		printf("\n");
		}
		}

		#endif

		strs.resize(inArgs->inpFiles.size());
		for(i=0; i<inArgs->inpFiles.size(); i++){

src/Math.cpp

+76 −56

Original line number	Diff line number	Diff line
		@@ -11,15 +11,17 @@ using namespace std;
		void AverageLines(InArgs_t *inArgs)
		{
		int index, i, j, k, colX, colY;
		int record = 0, readState;
		real8 rsize = 20, min, max;
		string rsizeName("rsize"), varsName("vars"), recordName("record");
		string xName("X"), yName("Y"), str("Ave_"), secLine;
		int readState;
		bool firstFile = 1;
		real8 rsize = 20, min, max, effNums;
		string rsizeName("rsize"), varsName("vars");
		string str("Ave_"), secLine;

		LineList_t list;
		Curve_t curve;

		vector<real8> seq, yVals, aveVals;
		vector<int> varID;
		vector<real8> seq;
		vector<Table_t> tables(inArgs->inpFiles.size());
		vector<string> s1, s2;

		@@ -29,18 +31,22 @@ void AverageLines(InArgs_t *inArgs)
		printf("The remesh size (rsize) is %f\n", rsize);

		if((index = GetValID(inArgs->priVars, varsName)) < inArgs->priVars.size()){
		if(inArgs->priVars[index].vals.size() == 2){
		xName = inArgs->priVars[index].vals[0];
		yName = inArgs->priVars[index].vals[1];
		if(inArgs->priVars[index].vals.size() < 2){
		Fatal("variables is not enough for aveage line");
		}
		}
		str += yName;
		printf("The variables (vars) are %s %s\n", xName.c_str(), yName.c_str());

		if((index = GetValID(inArgs->priVars, recordName)) < inArgs->priVars.size()){
		record = atoi(inArgs->priVars[index].vals[0].c_str());
		list.variables.resize(inArgs->priVars[index].vals.size());
		varID.resize(inArgs->priVars[index].vals.size());

		printf("The variables (vars) are ");
		for(i=0; i<inArgs->priVars[index].vals.size(); i++){
		list.variables[i] = inArgs->priVars[index].vals[i];
		printf("%s ", list.variables[i].c_str());
		}
		printf("The Record (record) state is %d\n", record);
		printf("\n");
		}

		if(inArgs->help)return;

		if(inArgs->inpFiles.size() == 0){
		Fatal("There is no input file.");
		@@ -49,67 +55,81 @@ void AverageLines(InArgs_t *inArgs)
		for(i=0; i<inArgs->inpFiles.size(); i++){
		readState = ReadTecplotNormalData(inArgs->inpFiles[i], tables[i], secLine);
		if(!readState)continue;
		if(i == 0){
		colX = GetColIDFromTable(tables[i], xName);
		colY = GetColIDFromTable(tables[i], yName);

		effNums++;
		if(tables[i].data.size() < 2){
		Fatal("The size of file %s is wrong", inArgs->inpFiles[i].c_str());
		}

		if(firstFile){
		if(list.variables.size()==0){
		list.variables.resize(tables[i].variables.size());
		varID.resize(list.variables.size());

		printf("The average variables (vars) are: ");
		for(j=0; j<tables[i].variables.size(); j++){
		list.variables[j] = tables[i].variables[j];
		printf("%s ",list.variables[j].c_str());
		}
		printf("\n");
		}
		min = tables[i].data[0][colX];
		max = tables[i].data[tables[i].data.size()-1][colX];
		firstFile = 0;
		}else{
		if(colX != GetColIDFromTable(tables[i], xName) \|\|
		colY != GetColIDFromTable(tables[i], yName)){
		Fatal("The format of file %s is not same as the first one",
		inArgs->inpFiles[i].c_str());
		}

		if(min < tables[i].data[0][colX]) min = tables[i].data[0][colX];
		if(max > tables[i].data[tables[i].data.size()-1][colX]){
		max = tables[i].data[tables[i].data.size()-1][colX];
		}
		}
		if(tables[i].data.size() < 2){
		Fatal("The size of file %s is wrong", inArgs->inpFiles[i].c_str());
		}
		}

		printf("The effective range of %s is [%f,%f]\n", list.variables[0].c_str(), min, max);
		seq = GenerateSequence(min, max, rsize);
		yVals.resize(seq.size());
		aveVals.resize(seq.size());
		list.data.resize(list.variables.size());
		for(i=0; i<list.data.size(); i++){
		list.data[i].resize(seq.size());
		for(j=0; j<list.data[i].size(); j++)list.data[i][j] = 0.0;
		}

		for(i=0; i<seq.size(); i++){
		aveVals[i] = 0.0;
		list.data[0][i] = seq[i];
		}

		list.variables.push_back(xName);
		list.data.push_back(seq);
		for(i=0; i<tables.size(); i++){
		if(tables[i].data.size()==0)continue;

		for(i=0; i<inArgs->inpFiles.size(); i++){
		for(j=0; j<varID.size(); j++){
		varID[j] = GetColIDFromTable(tables[i], list.variables[j]);
		if(varID[j] == tables[i].variables.size()){
		Fatal("there is no %s in the file %s ", list.variables[j].c_str(),
		inArgs->inpFiles[i].c_str());
		}

		if(j==0){
		curve.ax.resize(tables[i].data.size());
		curve.ay.resize(tables[i].data.size());

		for(j=0; j<curve.ax.size(); j++){
		curve.ax[j] = tables[i].data[j][colX];
		curve.ay[j] = tables[i].data[j][colY];
		for(k=0; k<curve.ax.size(); k++){
		curve.ax[k] = tables[i].data[k][varID[j]];
		}
		}else{
		for(k=0; k<curve.ax.size(); k++){
		curve.ay[k] = tables[i].data[k][varID[j]];
		}

		for(j=0; j<seq.size(); j++){
		yVals[j] = LinearInterpolation(curve, seq[j], min, max);
		aveVals[j] += yVals[j];
		for(k=0; k<seq.size(); k++){
		list.data[j][k] += LinearInterpolation(curve, seq[k], min, max);
		}
		}
		list.data.push_back(yVals);

		if(record){
		s1 = split(inArgs->inpFiles[i], "/");
		s2 = split(s1.back(), ".");
		list.variables.push_back(s2.front());
		list.data.push_back(yVals);
		}
		}

		list.variables.push_back(str);
		for(j=0; j<seq.size(); j++){
		aveVals[j] /= ((double)inArgs->inpFiles.size());
		for(i=1; i<list.data.size(); i++){
		for(j=0; j<list.data[i].size(); j++){
		list.data[i][j] /= effNums;
		}
		}
		list.data.push_back(aveVals);

		WriteTecplotNormalData(list, inArgs->outFiles[0], 10);

src/ReadData.cpp

+1 −1

Original line number	Diff line number	Diff line
		@@ -53,7 +53,7 @@ int ReadTecplotNormalData(string &file, Table_t &table, string &secLine)
		j++;
		}
		infile.close();
		printf("Finsish reading input file %s\n", file.c_str());
		// printf("Finsish reading input file %s\n", file.c_str());
		return 1;
		}