update colvars library to version 2016-09-30
This commit is contained in:
Axel Kohlmeyer
@ -612,3 +612,250 @@ cvm::real colvarbias_restraint_linear::restraint_convert_k(cvm::real k,
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colvarbias_restraint_histogram::colvarbias_restraint_histogram(char const *key)
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: colvarbias(key)
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{
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lower_boundary = 0.0;
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upper_boundary = 0.0;
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width = 0.0;
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gaussian_width = 0.0;
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}
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int colvarbias_restraint_histogram::init(std::string const &conf)
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{
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colvarbias::init(conf);
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get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary);
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get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary);
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get_keyval(conf, "width", width, width);
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if (width <= 0.0) {
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cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
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}
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get_keyval(conf, "gaussianWidth", gaussian_width, 2.0 * width, colvarparse::parse_silent);
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get_keyval(conf, "gaussianSigma", gaussian_width, 2.0 * width);
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if (lower_boundary >= upper_boundary) {
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cvm::error("Error: the upper boundary, "+
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cvm::to_str(upper_boundary)+
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", is not higher than the lower boundary, "+
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cvm::to_str(lower_boundary)+".\n",
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INPUT_ERROR);
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}
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cvm::real const nbins = (upper_boundary - lower_boundary) / width;
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int const nbins_round = (int)(nbins);
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if (std::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) {
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cvm::log("Warning: grid interval ("+
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cvm::to_str(lower_boundary, cvm::cv_width, cvm::cv_prec)+" - "+
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cvm::to_str(upper_boundary, cvm::cv_width, cvm::cv_prec)+
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") is not commensurate to its bin width ("+
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cvm::to_str(width, cvm::cv_width, cvm::cv_prec)+").\n");
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}
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p.resize(nbins_round);
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ref_p.resize(nbins_round);
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p_diff.resize(nbins_round);
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bool const inline_ref_p =
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get_keyval(conf, "refHistogram", ref_p.data_array(), ref_p.data_array());
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std::string ref_p_file;
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get_keyval(conf, "refHistogramFile", ref_p_file, std::string(""));
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if (ref_p_file.size()) {
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if (inline_ref_p) {
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cvm::error("Error: cannot specify both refHistogram and refHistogramFile at the same time.\n",
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INPUT_ERROR);
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} else {
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std::ifstream is(ref_p_file.c_str());
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std::string data_s = "";
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std::string line;
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while (getline_nocomments(is, line)) {
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data_s.append(line+"\n");
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}
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if (data_s.size() == 0) {
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cvm::error("Error: file \""+ref_p_file+"\" empty or unreadable.\n", FILE_ERROR);
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}
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is.close();
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cvm::vector1d<cvm::real> data;
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if (data.from_simple_string(data_s) != 0) {
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cvm::error("Error: could not read histogram from file \""+ref_p_file+"\".\n");
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}
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if (data.size() == 2*ref_p.size()) {
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// file contains both x and p(x)
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size_t i;
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for (i = 0; i < ref_p.size(); i++) {
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ref_p[i] = data[2*i+1];
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}
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} else if (data.size() == ref_p.size()) {
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ref_p = data;
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} else {
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cvm::error("Error: file \""+ref_p_file+"\" contains a histogram of different length.\n",
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INPUT_ERROR);
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}
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}
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}
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cvm::real const ref_integral = ref_p.sum() * width;
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if (std::fabs(ref_integral - 1.0) > 1.0e-03) {
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cvm::log("Reference distribution not normalized, normalizing to unity.\n");
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ref_p /= ref_integral;
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}
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get_keyval(conf, "writeHistogram", b_write_histogram, false);
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get_keyval(conf, "forceConstant", force_k, 1.0);
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return COLVARS_OK;
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}
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colvarbias_restraint_histogram::~colvarbias_restraint_histogram()
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{
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p.resize(0);
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ref_p.resize(0);
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p_diff.resize(0);
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}
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int colvarbias_restraint_histogram::update()
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{
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if (cvm::debug())
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cvm::log("Updating the histogram restraint bias \""+this->name+"\".\n");
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size_t vector_size = 0;
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size_t icv;
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for (icv = 0; icv < colvars.size(); icv++) {
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vector_size += colvars[icv]->value().size();
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}
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cvm::real const norm = 1.0/(std::sqrt(2.0*PI)*gaussian_width*vector_size);
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// calculate the histogram
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p.reset();
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for (icv = 0; icv < colvars.size(); icv++) {
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colvarvalue const &cv = colvars[icv]->value();
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if (cv.type() == colvarvalue::type_scalar) {
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cvm::real const cv_value = cv.real_value;
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size_t igrid;
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for (igrid = 0; igrid < p.size(); igrid++) {
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cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
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p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
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(2.0 * gaussian_width * gaussian_width));
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}
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} else if (cv.type() == colvarvalue::type_vector) {
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size_t idim;
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for (idim = 0; idim < cv.vector1d_value.size(); idim++) {
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cvm::real const cv_value = cv.vector1d_value[idim];
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size_t igrid;
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for (igrid = 0; igrid < p.size(); igrid++) {
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cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
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p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
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(2.0 * gaussian_width * gaussian_width));
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}
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}
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} else {
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// TODO
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}
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}
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cvm::real const force_k_cv = force_k * vector_size;
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// calculate the difference between current and reference
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p_diff = p - ref_p;
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bias_energy = 0.5 * force_k_cv * p_diff * p_diff;
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// calculate the forces
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for (icv = 0; icv < colvars.size(); icv++) {
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colvarvalue const &cv = colvars[icv]->value();
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colvarvalue &cv_force = colvar_forces[icv];
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cv_force.type(cv);
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cv_force.reset();
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if (cv.type() == colvarvalue::type_scalar) {
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cvm::real const cv_value = cv.real_value;
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cvm::real &force = cv_force.real_value;
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size_t igrid;
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for (igrid = 0; igrid < p.size(); igrid++) {
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cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
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force += force_k_cv * p_diff[igrid] *
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norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
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(2.0 * gaussian_width * gaussian_width)) *
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(-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
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}
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} else if (cv.type() == colvarvalue::type_vector) {
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size_t idim;
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for (idim = 0; idim < cv.vector1d_value.size(); idim++) {
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cvm::real const cv_value = cv.vector1d_value[idim];
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cvm::real &force = cv_force.vector1d_value[idim];
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size_t igrid;
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for (igrid = 0; igrid < p.size(); igrid++) {
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cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
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force += force_k_cv * p_diff[igrid] *
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norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
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(2.0 * gaussian_width * gaussian_width)) *
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(-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
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}
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}
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} else {
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// TODO
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}
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}
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return COLVARS_OK;
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}
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std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os)
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{
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if (b_write_histogram) {
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std::string file_name(cvm::output_prefix+"."+this->name+".hist.dat");
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std::ofstream os(file_name.c_str());
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os << "# " << cvm::wrap_string(colvars[0]->name, cvm::cv_width)
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<< " " << "p(" << cvm::wrap_string(colvars[0]->name, cvm::cv_width-3)
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<< ")\n";
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size_t igrid;
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for (igrid = 0; igrid < p.size(); igrid++) {
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cvm::real const x_grid = (lower_boundary + (igrid+1)*width);
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os << " "
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<< std::setprecision(cvm::cv_prec)
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<< std::setw(cvm::cv_width)
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<< x_grid
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<< " "
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<< std::setprecision(cvm::cv_prec)
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<< std::setw(cvm::cv_width)
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<< p[igrid] << "\n";
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}
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os.close();
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}
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return os;
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}
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std::istream & colvarbias_restraint_histogram::read_restart(std::istream &is)
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{
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return is;
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}
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std::ostream & colvarbias_restraint_histogram::write_traj_label(std::ostream &os)
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{
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os << " ";
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if (b_output_energy) {
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os << " E_"
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<< cvm::wrap_string(this->name, cvm::en_width-2);
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}
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return os;
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}
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std::ostream & colvarbias_restraint_histogram::write_traj(std::ostream &os)
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{
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os << " ";
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if (b_output_energy) {
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os << " "
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<< std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
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<< bias_energy;
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}
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return os;
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}
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