update colvars abf integrate tool from git repo (a42b0b7d) · Commits · 郑智淋 / lammps

tools/colvars/abf_data.cpp

+4 −4

Original line number	Diff line number	Diff line
		@@ -12,7 +12,6 @@ ABFdata::ABFdata(const char *gradFileName)

		std::ifstream gradFile;
		std::ifstream countFile;
		int n;
		char hash;
		double xi;
		char *countFileName;
		@@ -153,6 +152,7 @@ ABFdata::ABFdata(const char *gradFileName)
		// Could check for end-of-file string here
		countFile.close();
		delete[] countFileName;
		delete[] pos;

		// for metadynamics
		bias = new double[scalar_dim];

tools/colvars/abf_integrate.cpp

+11 −14

Original line number	Diff line number	Diff line
		@@ -22,10 +22,7 @@ int main(int argc, char *argv[])
		char *out_file;
		unsigned int step, nsteps, total, out_freq;
		int pos, dpos, *newpos;
		unsigned int *histogram;
		const double grad, newgrad;
		unsigned int offset, newoffset;
		int not_accepted;
		double dA;
		double temp;
		double mbeta;
		@@ -47,7 +44,7 @@ int main(int argc, char *argv[])

		if (!(data_file = parse_cl(argc, argv, &nsteps, &temp, &meta, &hill, &hill_fact))) {
		std::cerr << "\nabf_integrate: MC-based integration of multidimensional free energy gradient\n";
		std::cerr << "Version 20110511\n\n";
		std::cerr << "Version 20160420\n\n";
		std::cerr << "Syntax: " << argv[0] <<
		" <filename> [-n <nsteps>] [-t <temp>] [-m [0\|1] (metadynamics)]"
		" [-h <hill_height>] [-f <variable_hill_factor>]\n\n";
		@@ -91,6 +88,10 @@ int main(int argc, char *argv[])
		dpos = new int[data.Nvars];
		newpos = new int[data.Nvars];

		// TODO: this will be an infinite loop if there is no sampling
		// it would be more robust to build a list of non-empty bins, and
		// pick from there (or just treat the special case of no sampling
		// and output a null PMF)
		do {
		for (int i = 0; i < data.Nvars; i++) {
		pos[i] = rand() % data.sizes[i];
		@@ -128,9 +129,9 @@ int main(int argc, char *argv[])
		data.bias[offset] += hill;
		}

		grad = data.gradients + offset * data.Nvars;
		const double grad = data.gradients + offset data.Nvars;

		not_accepted = 1;
		int not_accepted = 1;
		while (not_accepted) {
		dA = 0.0;
		total++;
		@@ -206,7 +207,7 @@ double compute_deviation(ABFdata * data, bool meta, double kT)
		double *dev = data->deviation;
		double *est = data->estimate;
		const double *grad = data->gradients;
		int pos, dpos, *newpos;
		int pos, newpos;
		double rmsd = 0.0;
		unsigned int offset, newoffset;
		double sum;
		@@ -215,7 +216,6 @@ double compute_deviation(ABFdata * data, bool meta, double kT)
		unsigned int norm = 0; // number of data points summmed

		pos = new int[data->Nvars];
		dpos = new int[data->Nvars];
		newpos = new int[data->Nvars];

		for (int i = 0; i < data->Nvars; i++)
		@@ -287,7 +287,6 @@ double compute_deviation(ABFdata * data, bool meta, double kT)

		delete [] pos;
		delete [] newpos;
		delete [] dpos;

		return sqrt(rmsd / norm);
		}
		@@ -296,8 +295,6 @@ double compute_deviation(ABFdata * data, bool meta, double kT)
		char parse_cl(int argc, char argv[], unsigned int nsteps, double temp,
		bool * meta, double hill, double hill_fact)
		{
		char *filename = NULL;
		float f_temp, f_hill;
		int meta_int;

		// getting default value for the integer

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