add type 2 (e392bfae) · Commits · DeAn Wei / prodata

include/MD.h

0 → 100644

+41 −0

Original line number	Diff line number	Diff line
		#ifndef _MD_h
		#define _MD_h

		#include <stdio.h>
		#include <stdarg.h>
		#include <unistd.h>
		#include <errno.h>
		#include <time.h>
		#include <vector>
		#include <string>
		#include <cstring>
		#include <vector>
		#include <iostream>
		#include <fstream>
		#include <math.h>
		#include <sstream>

		#include <stdlib.h>
		#include <algorithm>
		#include <numeric>

		typedef struct{
		int id, type;
		double x, y, z;

		vector<double> vars;
		}Atom_t;

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

		vector<string> bounds;
		vector<string> variables;
		vector<Atom_t> atom;
		}MgData_t;

		void HandleExtendedDislocation_MD(InArgs_t *inArgs);

		#endif

include/ProDataIO.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -23,7 +23,7 @@
		#include "MD.h"


		int ReadTecplotNormalData(string &file, Table_t &table);
		int ReadTecplotNormalData(string &file, Table_t &table, string &secLine);
		void WriteTecplotNormalData(const LineList_t &list, const string &file,
		double precision = 6);
		int ReadMGDataFile(const string &file, MgData_t &mgdata);

src/HandleExtendedDislocation.cpp

+120 −75

Original line number	Diff line number	Diff line
		@@ -21,16 +21,17 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		real8 cubel = 20000, boundMin[3], boundMax[3];
		real8 remeshSize = 20.0, burgID1 = 7, burgID2 = 12;
		real8 rd, yi1, yj1, yk2, yk3, s;
		int index, i, j, k;
		int index, i, j, k, file, iPos;
		int colX, colY, colBurgID;
		string cubelName = "cubel", burgIDName = "burgID", remeshSizeName = "rsize";
		string fileName;
		real8 separation = 0.0;
		string fileName, secLine, fdir, curDir("./"), fname, aveFile;
		real8 separation = 0.0, position = 0.0;
		Point_t p;
		vector<Point_t> points1, points2;
		Curve_t curve1, curve2;
		LineList_t list;

		vector<string> words;
		vector<real8> seq;
		vector<vector<double> > data(7);

		@@ -47,6 +48,15 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		}
		printf("The cubel size is %f\n", cubel);

		if(inArgs->outFiles.size() < 2){
		aveFile = "Ave.plt";
		}else{
		aveFile = inArgs->outFiles[1];
		}
		ofstream out;
		out.open(aveFile.c_str(), ios::out);
		out << "variables = timeNow, separation, position" << endl;

		boundMin[0] = -0.5*cubel;
		boundMin[1] = -0.5*cubel;
		boundMin[2] = -0.5*cubel;
		@@ -68,7 +78,13 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		}
		printf("The remesh size is %f\n", remeshSize);

		ReadTecplotNormalData(inArgs->inpFiles[0], table);
		for(file=0; file<inArgs->inpFiles.size(); file++){

		vector<string>().swap(table.variables);

		ReadTecplotNormalData(inArgs->inpFiles[file], table, secLine);
		vector<string>().swap(words);
		words = split(secLine, "\"");

		if(table.data.size() < 2)Fatal("the data size is %d", table.data.size());

		@@ -76,6 +92,8 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		colY = GetColIDFromTable(table, "Y");
		colBurgID = GetColIDFromTable(table, "burgID");

		vector<Point_t>().swap(points1);
		vector<Point_t>().swap(points2);
		p.x = 1.0E10; p.y = 1.0E10;
		for(i=0; i<table.data.size(); i++){
		if(p.x == table.data[i][colX] &&
		@@ -110,18 +128,26 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		curve2.ay[i] = points2[i].y;
		}

		vector<double>().swap(seq);
		seq = GenerateSequence(boundMin[0], boundMax[0], remeshSize);

		data[0].assign(seq.begin(), seq.end());
		for(i=1; i<data.size(); i++) data[i].resize(data[0].size());
		data.resize(7);
		for(i=0; i<data.size(); i++) data[i].resize(seq.size());
		for(i=0; i<seq.size(); i++){
		data[0][i] = seq[i];
		}

		separation = 0.0;
		position = 0.0;
		for(i=0; i<seq.size(); i++){
		data[1][i] = LinearInterpolation(curve1, seq[i], boundMin[0], boundMax[0]);
		data[2][i] = LinearInterpolation(curve2, seq[i], boundMin[0], boundMax[0]);
		data[3][i] = 0.5 * (data[1][i] + data[2][i]);
		separation += fabs(data[1][i] - data[2][i]);
		position += data[3][i];
		}
		separation /= ((double)seq.size());
		position /= ((double)seq.size());

		for(i=0; i<seq.size(); i++){
		data[4][i] = 0.0;
		@@ -147,7 +173,26 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)

		swap(list.data, data);
		fileName = inArgs->outFiles[0];

		iPos = inArgs->inpFiles[file].find_last_of('/');
		if(iPos == string::npos){
		fdir = curDir;
		fname = inArgs->inpFiles[file];
		}else{
		fdir = curDir + inArgs->inpFiles[file].substr(0,iPos);
		fname = inArgs->inpFiles[file].substr(iPos+1);
		}

		fileName += "-";
		fileName += fname;

		WriteTecplotNormalData(list, fileName, 10);
		vector<vector<double> >().swap(list.data);

		out << words[1] << " ";
		out << setprecision(10) << separation << " ";
		out << setprecision(10) << position << endl;
		}

		return;
		}

src/Main.cpp

+2 −0

Original line number	Diff line number	Diff line
		@@ -282,6 +282,8 @@ static void GetInArgs(int argc, char argv[], InArgs_t inArgs)
		}
		}
		swap(bakInps, inArgs->inpFiles);

		sort(inArgs->inpFiles.begin(), inArgs->inpFiles.end());
		if(inArgs->inpFiles.size()>1){
		printf("Input files are:\n");
		for(i=0; i<inArgs->inpFiles.size(); i++){

src/Math.cpp

+2 −2

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@ void AverageLines(InArgs_t *inArgs)
		int record = 0;
		real8 rsize = 20, min, max;
		string rsizeName("rsize"), varsName("vars"), recordName("record");
		string xName("X"), yName("Y"), str("Ave_");
		string xName("X"), yName("Y"), str("Ave_"), secLine;

		LineList_t list;
		Curve_t curve;
		@@ -43,7 +43,7 @@ void AverageLines(InArgs_t *inArgs)
		printf("The Record (record) state is %d\n", record);

		for(i=0; i<inArgs->inpFiles.size(); i++){
		ReadTecplotNormalData(inArgs->inpFiles[i], tables[i]);
		ReadTecplotNormalData(inArgs->inpFiles[i], tables[i], secLine);
		if(i == 0){
		colX = GetColIDFromTable(tables[i], xName);
		colY = GetColIDFromTable(tables[i], yName);