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Update Colvars library to version 2019-04-26

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The following is list of relevant issues fixed and improvements:

Fix forces and missing output of runtime histogram for histogramRestraint
https://github.com/Colvars/colvars/pull/246

Use fix_modify to add configuration to Colvars:
https://github.com/Colvars/colvars/pull/216

Fix componentCoeff and name not working with orientationAngle components:
https://github.com/Colvars/colvars/issues/213

Fix 1-timestep offset with extendedLagrangian:
https://github.com/Colvars/colvars/pull/210

Changes to improve compiler support:
https://github.com/Colvars/colvars/pull/203

Fix ignored anisotropic cutoff3 for groupCoordNum:
https://github.com/Colvars/colvars/pull/202

New dipoleMagnitude variable:
https://github.com/Colvars/colvars/pull/198

Parser improvements:
https://github.com/Colvars/colvars/pull/196
This commit is contained in:
Giacomo Fiorin
2019-04-30 09:50:12 -04:00
parent 0005ee3e93
commit 7e00acce53
45 changed files with 2378 additions and 1328 deletions
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93
lib/colvars/colvar_UIestimator.h
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@ -33,24 +33,24 @@ namespace UIestimator {
public:
n_matrix() {}
n_matrix(const std::vector<double> & lowerboundary, // lowerboundary of x
const std::vector<double> & upperboundary, // upperboundary of
const std::vector<double> & width, // width of x
const int y_size) { // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
n_matrix(const std::vector<double> & lowerboundary_input, // lowerboundary of x
const std::vector<double> & upperboundary_input, // upperboundary of
const std::vector<double> & width_input, // width of x
const int y_size_input) { // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
int i;
this->lowerboundary = lowerboundary;
this->upperboundary = upperboundary;
this->width = width;
this->dimension = lowerboundary.size();
this->y_size = y_size; // keep in mind the internal (spare) matrix is stored in diagonal form
this->y_total_size = int(std::pow(double(y_size), double(dimension)) + EPSILON);
this->lowerboundary = lowerboundary_input;
this->upperboundary = upperboundary_input;
this->width = width_input;
this->dimension = lowerboundary_input.size();
this->y_size = y_size_input; // keep in mind the internal (spare) matrix is stored in diagonal form
this->y_total_size = int(cvm::pow(double(y_size_input), double(dimension)) + EPSILON);
// the range of the matrix is [lowerboundary, upperboundary]
x_total_size = 1;
for (i = 0; i < dimension; i++) {
x_size.push_back(int((upperboundary[i] - lowerboundary[i]) / width[i] + EPSILON));
x_size.push_back(int((upperboundary_input[i] - lowerboundary_input[i]) / width_input[i] + EPSILON));
x_total_size *= x_size[i];
}
@ -89,9 +89,10 @@ namespace UIestimator {
std::vector<int> temp; // this vector is used in convert_x and convert_y to save computational resource
int i, j;
int convert_x(const std::vector<double> & x) { // convert real x value to its interal index
int i, j;
for (i = 0; i < dimension; i++) {
temp[i] = int((x[i] - lowerboundary[i]) / width[i] + EPSILON);
}
@ -121,7 +122,7 @@ namespace UIestimator {
int index = 0;
for (i = 0; i < dimension; i++) {
if (i + 1 < dimension)
index += temp[i] * int(std::pow(double(y_size), double(dimension - i - 1)) + EPSILON);
index += temp[i] * int(cvm::pow(double(y_size), double(dimension - i - 1)) + EPSILON);
else
index += temp[i];
}
@ -139,19 +140,19 @@ namespace UIestimator {
public:
n_vector() {}
n_vector(const std::vector<double> & lowerboundary, // lowerboundary of x
const std::vector<double> & upperboundary, // upperboundary of
const std::vector<double> & width, // width of x
const int y_size, // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
n_vector(const std::vector<double> & lowerboundary_input, // lowerboundary of x
const std::vector<double> & upperboundary_input, // upperboundary of
const std::vector<double> & width_input, // width of x
const int y_size_input, // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered
const T & default_value) { // the default value of T
this->width = width;
this->dimension = lowerboundary.size();
this->width = width_input;
this->dimension = lowerboundary_input.size();
x_total_size = 1;
for (int i = 0; i < dimension; i++) {
this->lowerboundary.push_back(lowerboundary[i] - (y_size - 1) / 2 * width[i] - EPSILON);
this->upperboundary.push_back(upperboundary[i] + (y_size - 1) / 2 * width[i] + EPSILON);
this->lowerboundary.push_back(lowerboundary_input[i] - (y_size_input - 1) / 2 * width_input[i] - EPSILON);
this->upperboundary.push_back(upperboundary_input[i] + (y_size_input - 1) / 2 * width_input[i] + EPSILON);
x_size.push_back(int((this->upperboundary[i] - this->lowerboundary[i]) / this->width[i] + EPSILON));
x_total_size *= x_size[i];
@ -215,26 +216,26 @@ namespace UIestimator {
UIestimator() {}
//called when (re)start an eabf simulation
UIestimator(const std::vector<double> & lowerboundary,
const std::vector<double> & upperboundary,
const std::vector<double> & width,
const std::vector<double> & krestr, // force constant in eABF
const std::string & output_filename, // the prefix of output files
const int output_freq,
const bool restart, // whether restart from a .count and a .grad file
const std::vector<std::string> & input_filename, // the prefixes of input files
const double temperature) {
UIestimator(const std::vector<double> & lowerboundary_input,
const std::vector<double> & upperboundary_input,
const std::vector<double> & width_input,
const std::vector<double> & krestr_input, // force constant in eABF
const std::string & output_filename_input, // the prefix of output files
const int output_freq_input,
const bool restart_input, // whether restart from a .count and a .grad file
const std::vector<std::string> & input_filename_input, // the prefixes of input files
const double temperature_input) {
// initialize variables
this->lowerboundary = lowerboundary;
this->upperboundary = upperboundary;
this->width = width;
this->krestr = krestr;
this->output_filename = output_filename;
this->output_freq = output_freq;
this->restart = restart;
this->input_filename = input_filename;
this->temperature = temperature;
this->lowerboundary = lowerboundary_input;
this->upperboundary = upperboundary_input;
this->width = width_input;
this->krestr = krestr_input;
this->output_filename = output_filename_input;
this->output_freq = output_freq_input;
this->restart = restart_input;
this->input_filename = input_filename_input;
this->temperature = temperature_input;
int i, j;
@ -300,7 +301,7 @@ namespace UIestimator {
~UIestimator() {}
// called from MD engine every step
bool update(const int step, std::vector<double> x, std::vector<double> y) {
bool update(cvm::step_number step, std::vector<double> x, std::vector<double> y) {
int i;
@ -431,7 +432,7 @@ namespace UIestimator {
loop_flag_y[k] = loop_flag_x[k] - HALF_Y_SIZE * width[k];
}
int j = 0;
j = 0;
while (j >= 0) {
norm += distribution_x_y.get_value(loop_flag_x, loop_flag_y);
for (k = 0; k < dimension; k++) {
@ -672,7 +673,7 @@ namespace UIestimator {
}
// read input files
void read_inputfiles(const std::vector<std::string> input_filename)
void read_inputfiles(const std::vector<std::string> filename)
{
char sharp;
double nothing;
@ -683,11 +684,11 @@ namespace UIestimator {
std::vector<double> position_temp(dimension, 0);
std::vector<double> grad_temp(dimension, 0);
int count_temp = 0;
for (i = 0; i < int(input_filename.size()); i++) {
for (i = 0; i < int(filename.size()); i++) {
int size = 1 , size_temp = 0;
std::string count_filename = input_filename[i] + ".UI.count";
std::string grad_filename = input_filename[i] + ".UI.grad";
std::string count_filename = filename[i] + ".UI.count";
std::string grad_filename = filename[i] + ".UI.grad";
std::ifstream count_file(count_filename.c_str(), std::ios::in);
std::ifstream grad_file(grad_filename.c_str(), std::ios::in);