replace variable length arrays in fix gle with new/delete (6dcee30b) · Commits · 郑智淋 / lammps

src/USER-MISC/fix_gle.cpp

+47 −38

Original line number	Diff line number	Diff line
		@@ -44,6 +44,7 @@ using namespace FixConst;

		enum{NOBIAS,BIAS};
		enum{CONSTANT,EQUAL,ATOM};

		//#define GLE_DEBUG 1

		#define MAXLINE 1024
		@@ -62,17 +63,16 @@ namespace GLE {
		//"stabilized" cholesky decomposition. does a LDL^t decomposition, then sets to zero the negative diagonal elements and gets MM^t
		void StabCholesky(int n, const double* MMt, double* M)
		{
		double L[n*n], D[n];
		double L = new double[nn];
		double *D = new double[n];

		int i,j,k;
		for(i=0; i<n; ++i) D[i]=0.;
		for(i=0; i<n*n; ++i) L[i]=0.;
		for (i=0; i<n; ++i) D[i]=0.0;
		for (i=0; i<n*n; ++i) L[i]=0.0;

		for(i=0; i<n; ++i)
		{
		L[midx(n,i,i)]=1.;
		for (j=0; j<i; j++)
		{
		for (i=0; i<n; ++i) {
		L[midx(n,i,i)]=1.0;
		for (j=0; j<i; j++) {
		L[midx(n,i,j)]=MMt[midx(n,i,j)];
		for (k=0; k<j; ++k) L[midx(n,i,j)]-=L[midx(n,i,k)]L[midx(n,j,k)]D[k];
		if (D[j]!=0.) L[midx(n,i,j)]/=D[j];
		@@ -82,15 +82,18 @@ void StabCholesky(int n, const double* MMt, double* M)
		for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]L[midx(n,i,k)]D[k];
		}

		for(i=0; i<n; ++i)
		{
		for (i=0; i<n; ++i) {
		#ifdef GLE_DEBUG
		if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);
		#endif
		D[i]=(D[i]>0.?sqrt(D[i]):0.);
		D[i]=(D[i]>0.0) ? sqrt(D[i]):0.0;
		}

		for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
		for (i=0; i<n; ++i)
		for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];

		delete[] D;
		delete[] L;
		}

		void MyMult(int n, int m, int r, const double* A, const double* B, double* C, double cf=0.0)
		@@ -162,7 +165,9 @@ void MyPrint(int n, const double* A)
		//matrix exponential by scaling and squaring.
		void MatrixExp(int n, const double* M, double* EM, int j=8, int k=8)
		{
		double tc[j+1], SM[nn], TMP[nn];
		double *tc = new double[j+1];
		double SM = new double[nn];
		double TMP = new double[nn];
		double onetotwok=pow(0.5,1.0*k);


		@@ -174,14 +179,18 @@ void MatrixExp(int n, const double* M, double* EM, int j=8, int k=8)
		for (int i=0; i<n; ++i) EM[midx(n,i,i)]=tc[j];

		//taylor exp of scaled matrix
		for (int p=j-1; p>=0; p--)
		{
		for (int p=j-1; p>=0; p--) {
		MyMult(n, n, n, SM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
		for (int i=0; i<n; ++i) EM[midx(n,i,i)]+=tc[p];
		}

		for (int p=0; p<k; p++)
		{ MyMult(n, n, n, EM, EM, TMP); for (int i=0; i<n*n; ++i) EM[i]=TMP[i]; }
		for (int p=0; p<k; p++) {
		MyMult(n, n, n, EM, EM, TMP);
		for (int i=0; i<n*n; ++i) EM[i]=TMP[i];
		}
		delete[] tc;
		delete[] SM;
		delete[] TMP;
		}
		}

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