1. add openmp for HandleExtendedDislocation_MD. (ef182913) · Commits · DeAn Wei / prodata

CMakeLists.txt

+1 −1

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ Set(CMAKE_CXX_COMPILER "g++")
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")

		#FIND_PACKAGE( OpenMP REQUIRED)
		FIND_PACKAGE( OpenMP REQUIRED)
		if(OPENMP_FOUND)
		set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
		message(STATUS "OpenMP_C_FLAGS = " ${OpenMP_C_FLAGS})

include/Home.h

+21 −1

Original line number	Diff line number	Diff line
		@@ -15,6 +15,25 @@
		#include <vector>
		#include <list>

		#ifdef _OPENMP

		#include <omp.h>

		#define INIT_LOCK(a) omp_init_lock((a))
		#define LOCK(a) omp_set_lock((a))
		#define UNLOCK(a) omp_unset_lock((a))
		#define DESTROY_LOCK(a) omp_destroy_lock((a))

		#else /* _OPENMP not defined */

		#define INIT_LOCK(a)
		#define LOCK(a)
		#define UNLOCK(a)
		#define DESTROY_LOCK(a)

		#endif /* end ifdef _OPENMP */


		#define real8 double
		using namespace std;

		@@ -32,7 +51,7 @@ typedef struct {
		typedef struct {
		double burgMag;
		int seed;
		int type;
		int type, nThreads;
		bool help;

		vector<string> inpFiles, outFiles;
		@@ -67,6 +86,7 @@ typedef enum{
		OPT_TYPE,
		OPT_PRIVATEVALS,
		OPT_AUXFILE,
		OPT_THREADS,
		OPT_MAX
		}OPT_t;

include/MD.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -28,8 +28,8 @@ typedef struct{

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

		vector<vector<real8> > box;
		vector<string> bounds;
		vector<string> variables;
		vector<Atom_t> atom;

src/CMakeLists.txt

+6 −2

Original line number	Diff line number	Diff line
		Set (SRCS
		Main.cpp ReadData.cpp Util.cpp Math.cpp HandleExtendedDislocation.cpp
		WriteData.cpp Parse.cpp)
		WriteData.cpp Parse.cpp Custom.cpp)

		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -Wno-unknown-pragmas -DPARALLEL=1 " )
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 " )
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ")

		if(OPENMP_FOUND)
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -openmp")
		endif(OPENMP_FOUND)

		add_executable(prodata ${SRCS})
		add_definitions( -DPARALLEL=1)

src/HandleExtendedDislocation.cpp

+89 −78

Original line number	Diff line number	Diff line
		@@ -127,9 +127,14 @@ void HandleExtendedDislocation_DDD(InArgs_t *inArgs)
		vector<string>().swap(table.variables);

		if(!ReadTecplotNormalData(inArgs->inpFiles[file], table, secLine))continue;

		vector<string>().swap(words);
		words = split(secLine, "\"");

		if(words.size() == 0){
		Fatal("can not find the timesolution in file %s", inArgs->inpFiles[file].c_str());
		}

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

		colX = GetColIDFromTable(table, "X");
		@@ -385,15 +390,15 @@ typedef struct {
		}Probe_t;

		typedef struct {
		int timestep;
		long int timestep;
		double x,y,z;
		double separation;
		vector<double> vars;
		}EDState_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){
		if(fabs(p.y - q.y) < 1.0E-20){
		if(fabs(p.z - q.z)< 1.0E-20){
		return(p.x<q.x);
		}else{
		return(p.z < q.z);
		@@ -414,21 +419,22 @@ bool com3(EDState_t p, EDState_t q)

		void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		{
		int i, j, file, index, lastIndex, firstNbr, indexVar;
		int i, j, file, index, firstNbr, indexVar;
		int nums[2] = {18, 24}, logfile;
		int stepID;
		double cutofflen = 2.556, alpha = 0.005, beta = 1.0;
		double position[3], separation, dis, maxDis;
		double cutofflen = 2.556, alpha = 0.1, beta = 1.0;
		double position[3];
		MgData_t mg;
		LineList_t list;
		double dir[3] = {0, 1, 0}, p0[3], dval=5;
		double dir[3] = {0, 1, 0}, p0[3], dval=5, effeSepRange[2] = {1.0,40.0};
		bool noP0 = 1;
		string paraName("para"), dvarName("dvar"), dvar("c_vcna"), p0Name("p0"), dirName("dir");
		string numsName("nums");
		string numsName("nums"), ppstring("pp"), separationName("separation");
		int lastIndex = 0;
		double dis, minDis;

		vector<Atom_t>::iterator it;
		vector<EDState_t> states;
		EDState_t state;

		ofstream out;
		out.open(inArgs->outFiles[0].c_str(), ios::out);
		@@ -477,76 +483,88 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		nums[1] = atoi(inArgs->priVars[index].vals[1].c_str());
		}
		}
		printf("The range of effective atoms of a paritial (nums) is [%d,%d]\n", nums[0], nums[1]);
		printf("The range of effective number of a paritial (nums) is [%d,%d]\n", nums[0], nums[1]);

		if((index = GetValID(inArgs->priVars, separationName)) < inArgs->priVars.size()){
		if(inArgs->priVars[index].vals.size() == 2){
		effeSepRange[0] = atof(inArgs->priVars[index].vals[0].c_str());
		effeSepRange[1] = atof(inArgs->priVars[index].vals[1].c_str());
		}
		}
		printf("The range of effective separtion of the extended dislocation (separation) is [%f,%f]\n", effeSepRange[0], effeSepRange[1]);

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

		states.resize(inArgs->inpFiles.size());
		for(file=0; file<inArgs->inpFiles.size(); file++){
		states[file].timestep = 1E10;
		}

		#pragma omp parallel for private(mg, it, i, j, indexVar, firstNbr, lastIndex, dis, minDis) shared(states)
		for(file=0; file<inArgs->inpFiles.size(); file++){
		#pragma omp critical
		{
		ReadMGDataFile(inArgs->inpFiles[file], mg);
		}

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

		for(it = mg.atom.end(), i=mg.atom.size()-1; it != mg.atom.begin(); it--, i--){
		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){
		for(i=0; i<mg.atom.size(); ){
		if(mg.atom[i].vars[indexVar] != dval){
		mg.atom.erase(mg.atom.begin()+i);
		continue;
		}

		if(mg.atom[i].vars[indexVar] == dval){
		mg.atom.erase(it);
		if(mg.atom[i].x < mg.box[0][0] + 2 \|\|
		mg.atom[i].y < mg.box[1][0] + 2 \|\|
		mg.atom[i].z < mg.box[2][0] + 2 \|\|
		mg.atom[i].x > mg.box[0][1] - 2 \|\|
		mg.atom[i].y > mg.box[1][1] - 2 \|\|
		mg.atom[i].z > mg.box[2][1] - 2){
		mg.atom.erase(mg.atom.begin()+i);
		continue;
		}

		i++;
		}

		if(mg.atom.size() == 0){
		continue;
		}

		if(noP0 ==1 && file == 0){
		j = 0;
		for(i=0; i<mg.atom.size(); i++){
		if(mg.atom[i].vars[indexVar] != dval)continue;
		j++;
		p0[0] += mg.atom[i].x;
		p0[2] += mg.atom[i].z;
		}
		if(j==0){
		Fatal("The");
		}
		p0[1] = mg.box[2];
		p0[0] /= ((double)j);
		p0[2] /= ((double)j);
		printf("The initial probe point (p0) is %f %f %f\n", p0[0], p0[1], p0[2]);
		Fatal("The initial probe point (p0) is %f %f %f\n", p0[0], p0[1], p0[2]);
		}

		sort(mg.atom.begin(), mg.atom.end(), com);

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

		probe.y = p0[1];
		probe.y = mg.atom[0].y;
		probe.z = p0[2];

		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;
		minDis = 1E10;
		for(i=lastIndex; i<mg.atom.size(); i++){
		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(dis < minDis){
		minDis = dis;
		}

		if(dis < cutofflen){
		if(firstNbr){
		lastIndex = i;
		firstNbr = 0;
		@@ -558,24 +576,19 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		probes.push_back(probe);
		vector<Atom_t *>().swap(probe.nbr);
		}
		if(probe.y > mg.atom.back().y \|\|
		probe.z > mg.atom.back().z)break;
		d++;
		}

		#if 0
		printf("Timestep %d, Atoms %d, Bouds %s %s %s, ",
		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]);
		if(probe.y > mg.atom.back().y)break;

		printf("variables are ");
		for(i=0; i<mg.variables.size(); i++){
		printf("%s(%d) ", mg.variables[i].c_str(), (int)mg.atom.size());
		if(minDis < alpha){
		probe.x += (dir[0]*alpha);
		probe.y += (dir[1]*alpha);
		probe.z += (dir[2]*alpha);
		}else{
		probe.x += (dir[0]*minDis);
		probe.y += (dir[1]*minDis);
		probe.z += (dir[2]*minDis);
		}
		}
		printf("\n");
		#endif

		for(i=0; i<probes.size(); i++){
		probes[i].x = 0.0;
		probes[i].y = 0.0;
		@@ -592,35 +605,31 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		}
		sort(probes.begin(), probes.end(), com2);

		separation = 0;
		double separation = 0;

		if(probes.size() > 0){
		separation = fabs(probes[0].y-probes.back().y);
		if(separation > 0.1 && separation < 20){
		state.x = (probes[0].x+probes.back().x)*0.5;
		state.y = (probes[0].y+probes.back().y)*0.5;
		state.z = (probes[0].z+probes.back().z)*0.5;
		state.timestep = mg.timestep;
		state.separation = separation;
		if(separation > effeSepRange[0] && separation < effeSepRange[1]){
		states[file].x = (probes[0].x+probes.back().x)*0.5;
		states[file].y = (probes[0].y+probes.back().y)*0.5;
		states[file].z = (probes[0].z+probes.back().z)*0.5;
		states[file].timestep = mg.timestep;
		states[file].separation = separation;

		if(logfile ==1){
		state.vars.resize(list.variables.size()-1);
		states[file].vars.resize(list.variables.size()-1);
		for(i=0; i<list.data[0].size(); i++){
		if(state.timestep == ((int)list.data[0][i]))break;
		if(states[file].timestep == ((int)list.data[0][i]))break;
		}
		for(j=0; j<state.vars.size(); j++){
		state.vars[j] = list.data[j+1][i];
		for(j=0; j<states[file].vars.size(); j++){
		states[file].vars[j] = list.data[j+1][i];
		}
		}
		states.push_back(state);
		}
		}

		}

		if(states.size() == 0){
		Fatal("No out data can be dumped, please check parameters");
		}

		sort(states.begin(), states.end(), com3);

		out << "variables = timestep, separation, y";
		@@ -632,6 +641,8 @@ void HandleExtendedDislocation_MD(InArgs_t *inArgs)
		out << endl;

		for(i=0; i<states.size(); i++){
		if(states[i].timestep > 1E9)break;

		out << states[i].timestep << " ";
		out << states[i].separation << " ";
		out << states[i].y << " ";