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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13670 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2015-07-22 14:36:59 +00:00
parent f9b7502079
commit 6e40300d26
15 changed files with 246 additions and 56 deletions
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46
lib/colvars/colvar.cpp
View File

@ -845,6 +845,7 @@ void colvar::calc()
// prepare atom groups for calculation
if (cvm::debug())
cvm::log("Collecting data from atom groups.\n");
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
cvm::atom_group &atoms = *(cvcs[i]->atom_groups[ig]);
@ -856,6 +857,7 @@ void colvar::calc()
// each atom group will take care of its own ref_pos_group, if defined
}
}
//// Don't try to get atom velocities, as no back-end currently implements it
// if (tasks[task_output_velocity] && !tasks[task_fdiff_velocity]) {
// for (i = 0; i < cvcs.size(); i++) {
@ -864,6 +866,7 @@ void colvar::calc()
// }
// }
// }
if (tasks[task_system_force]) {
for (i = 0; i < cvcs.size(); i++) {
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
@ -880,6 +883,7 @@ void colvar::calc()
// First, update component values
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
(cvcs[i])->calc_value();
cvm::decrease_depth();
@ -905,6 +909,7 @@ void colvar::calc()
} else if (x.type() == colvarvalue::type_scalar) {
// polynomial combination allowed
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
x += (cvcs[i])->sup_coeff *
( ((cvcs[i])->sup_np != 1) ?
std::pow((cvcs[i])->value().real_value, (cvcs[i])->sup_np) :
@ -913,6 +918,7 @@ void colvar::calc()
} else {
// only linear combination allowed
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
x += (cvcs[i])->sup_coeff * (cvcs[i])->value();
}
}
@ -928,17 +934,15 @@ void colvar::calc()
for (i = 0; i < cvcs.size(); i++) {
// calculate the gradients of each component
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
(cvcs[i])->calc_gradients();
// if requested, propagate (via chain rule) the gradients above
// to the atoms used to define the roto-translation
for (ig = 0; ig < cvcs[i]->atom_groups.size(); ig++) {
if (cvcs[i]->atom_groups[ig]->b_fit_gradients)
cvcs[i]->atom_groups[ig]->calc_fit_gradients();
}
cvm::decrease_depth();
}
@ -958,6 +962,7 @@ void colvar::calc()
atomic_gradients[a].reset();
}
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
// Coefficient: d(a * x^n) = a * n * x^(n-1) * dx
cvm::real coeff = (cvcs[i])->sup_coeff * cvm::real((cvcs[i])->sup_np) *
std::pow((cvcs[i])->value().real_value, (cvcs[i])->sup_np-1);
@ -1123,19 +1128,23 @@ cvm::real colvar::update()
if (tasks[task_Jacobian_force]) {
size_t i;
cvm::increase_depth();
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
(cvcs[i])->calc_Jacobian_derivative();
}
cvm::decrease_depth();
}
size_t ncvc = 0;
fj.reset();
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
// linear combination is assumed
fj += 1.0 / ( cvm::real(cvcs.size()) * cvm::real((cvcs[i])->sup_coeff) ) *
fj += 1.0 / cvm::real((cvcs[i])->sup_coeff) *
(cvcs[i])->Jacobian_derivative();
ncvc++;
}
fj *= cvm::boltzmann() * cvm::temperature();
fj *= (1.0/cvm::real(ncvc)) * cvm::boltzmann() * cvm::temperature();
// the instantaneous Jacobian force was not included in the reported system force;
// instead, it is subtracted from the applied force (silent Jacobian correction)
@ -1196,6 +1205,7 @@ void colvar::communicate_forces()
if (tasks[task_scripted]) {
std::vector<cvm::matrix2d<cvm::real> > func_grads;
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
func_grads.push_back(cvm::matrix2d<cvm::real> (x.size(),
cvcs[i]->value().size()));
}
@ -1211,6 +1221,7 @@ void colvar::communicate_forces()
}
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
// cvc force is colvar force times colvar/cvc Jacobian
// (vector-matrix product)
@ -1221,6 +1232,7 @@ void colvar::communicate_forces()
} else if (x.type() == colvarvalue::type_scalar) {
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
(cvcs[i])->apply_force(f * (cvcs[i])->sup_coeff *
cvm::real((cvcs[i])->sup_np) *
@ -1232,6 +1244,7 @@ void colvar::communicate_forces()
} else {
for (i = 0; i < cvcs.size(); i++) {
if (!cvcs[i]->b_enabled) continue;
cvm::increase_depth();
(cvcs[i])->apply_force(f * (cvcs[i])->sup_coeff);
cvm::decrease_depth();
@ -1243,6 +1256,25 @@ void colvar::communicate_forces()
}
int colvar::set_cvc_flags(std::vector<bool> const &flags) {
size_t i;
if (flags.size() != cvcs.size()) {
cvm::error("ERROR: Wrong number of CVC flags provided.");
return COLVARS_ERROR;
}
bool e = false;
for (i = 0; i < cvcs.size(); i++) {
cvcs[i]->b_enabled = flags[i];
e = e || flags[i];
}
if (!e) {
cvm::error("ERROR: All CVCs are disabled for this colvar.");
return COLVARS_ERROR;
}
return COLVARS_OK;
}
// ******************** METRIC FUNCTIONS ********************
// Use the metrics defined by \link cvc \endlink objects

2
lib/colvars/colvar.h
View File

@ -329,6 +329,8 @@ public:
/// colvar::update()) to the external degrees of freedom
void communicate_forces();
/// \brief Enables and disables individual CVCs based on flags
int set_cvc_flags(std::vector<bool> const &flags);
/// \brief Use the internal metrics (as from \link cvc
/// \endlink objects) to calculate square distances and gradients

7
lib/colvars/colvarbias.cpp
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@ -100,6 +100,13 @@ void colvarbias::add_colvar(std::string const &cv_name)
}
cvm::real colvarbias::update()
{
has_data = true;
return 0.0;
}
void colvarbias::communicate_forces()
{
for (size_t i = 0; i < colvars.size(); i++) {

2
lib/colvars/colvarbias.h
View File

@ -19,7 +19,7 @@ public:
/// Retrieve colvar values and calculate their biasing forces
/// Return bias energy
virtual cvm::real update() = 0;
virtual cvm::real update();
// TODO: move update_bias here (share with metadynamics)

37
lib/colvars/colvarbias_histogram.cpp
View File

@ -11,7 +11,9 @@ colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *
grid(NULL), out_name("")
{
get_keyval(conf, "outputFile", out_name, std::string(""));
get_keyval(conf, "outputFileDX", out_name_dx, std::string(""));
get_keyval(conf, "outputFreq", output_freq, cvm::restart_out_freq);
/// with VMD, this may not be an error
// if ( output_freq == 0 ) {
// cvm::error("User required histogram with zero output frequency");
@ -74,9 +76,6 @@ colvarbias_histogram::colvarbias_histogram(std::string const &conf, char const *
/// Destructor
colvarbias_histogram::~colvarbias_histogram()
{
if (grid_os.is_open())
grid_os.close();
if (grid) {
delete grid;
grid = NULL;
@ -89,6 +88,9 @@ colvarbias_histogram::~colvarbias_histogram()
/// Update the grid
cvm::real colvarbias_histogram::update()
{
// update base class
colvarbias::update();
if (cvm::debug()) {
cvm::log("Updating histogram bias " + this->name);
}
@ -105,6 +107,13 @@ cvm::real colvarbias_histogram::update()
}
}
if (out_name_dx.size() == 0) {
if (cvm::step_relative() == 0) {
out_name_dx = cvm::output_prefix + "." + this->name + ".dx";
cvm::log("Histogram " + this->name + " will be written to file \"" + out_name_dx + "\"");
}
}
if (colvar_array_size == 0) {
// update indices for scalar values
size_t i;
@ -132,23 +141,39 @@ cvm::real colvarbias_histogram::update()
if (output_freq && (cvm::step_absolute() % output_freq) == 0) {
write_output_files();
}
return 0.0; // no bias energy for histogram
}
int colvarbias_histogram::write_output_files()
{
if (!has_data) {
// nothing to write
return COLVARS_OK;
}
if (out_name.size()) {
cvm::log("Writing the histogram file \""+out_name+"\".\n");
grid_os.open(out_name.c_str());
cvm::ofstream grid_os(out_name.c_str());
if (!grid_os.is_open()) {
cvm::error("Error opening histogram file " + out_name + " for writing");
cvm::error("Error opening histogram file " + out_name + " for writing.\n", FILE_ERROR);
}
// TODO add return code here
grid->write_multicol(grid_os);
grid_os.close();
}
if (out_name_dx.size()) {
cvm::log("Writing the histogram file \""+out_name_dx+"\".\n");
cvm::ofstream grid_os(out_name_dx.c_str());
if (!grid_os.is_open()) {
cvm::error("Error opening histogram file " + out_name_dx + " for writing.\n", FILE_ERROR);
}
// TODO add return code here
grid->write_opendx(grid_os);
grid_os.close();
}
return COLVARS_OK;
}

6
lib/colvars/colvarbias_histogram.h
View File

@ -28,8 +28,7 @@ protected:
/// n-dim histogram
colvar_grid_scalar *grid;
std::vector<int> bin;
std::string out_name;
std::string out_name, out_name_dx;
size_t output_freq;
/// If one or more of the variables are \link type_vector \endlink, treat them as arrays of this length
@ -37,9 +36,6 @@ protected:
/// If colvar_array_size is larger than 1, weigh each one by this number before accumulating the histogram
std::vector<cvm::real> weights;
void write_grid();
cvm::ofstream grid_os; /// Stream for writing grid to disk
std::istream& read_restart(std::istream&);
std::ostream& write_restart(std::ostream&);
};

8
lib/colvars/colvarcomp.cpp
View File

@ -8,7 +8,9 @@
colvar::cvc::cvc()
: sup_coeff(1.0), sup_np(1),
: sup_coeff(1.0),
sup_np(1),
b_enabled(true),
b_periodic(false),
b_inverse_gradients(false),
b_Jacobian_derivative(false),
@ -17,7 +19,9 @@ colvar::cvc::cvc()
colvar::cvc::cvc(std::string const &conf)
: sup_coeff(1.0), sup_np(1),
: sup_coeff(1.0),
sup_np(1),
b_enabled(true),
b_periodic(false),
b_inverse_gradients(false),
b_Jacobian_derivative(false),

9
lib/colvars/colvarcomp.h
View File

@ -84,14 +84,19 @@ public:
/// \brief Exponent in the polynomial combination (default: 1)
int sup_np;
/// \brief This defaults to true; setting it to false disables
/// update of this cvc to save compute time (useful with scriptedFunction)
bool b_enabled;
/// \brief Is this a periodic component?
bool b_periodic;
/// \brief Period of this cvc value, (default: 0.0, non periodic)
cvm::real period;
/// \brief If the component is periodic, wrap around this value (default: 0.0)
cvm::real wrap_center;
bool b_periodic;
/// \brief Constructor
///
/// At least one constructor which reads a string should be defined

47
lib/colvars/colvargrid.cpp
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@ -103,6 +103,53 @@ std::ostream & colvar_grid_scalar::write_restart(std::ostream &os)
}
cvm::real colvar_grid_scalar::maximum_value() const
{
cvm::real max = data[0];
for (size_t i = 0; i < nt; i++) {
if (data[i] > max) max = data[i];
}
return max;
}
cvm::real colvar_grid_scalar::minimum_value() const
{
cvm::real min = data[0];
for (size_t i = 0; i < nt; i++) {
if (data[i] < min) min = data[i];
}
return min;
}
cvm::real colvar_grid_scalar::integral() const
{
cvm::real sum = 0.0;
for (size_t i = 0; i < nt; i++) {
sum += data[i];
}
cvm::real bin_volume = 1.0;
for (size_t id = 0; id < widths.size(); id++) {
bin_volume *= widths[id];
}
return bin_volume * sum;
}
cvm::real colvar_grid_scalar::entropy() const
{
cvm::real sum = 0.0;
for (size_t i = 0; i < nt; i++) {
sum += -1.0 * data[i] * std::log(data[i]);
}
cvm::real bin_volume = 1.0;
for (size_t id = 0; id < widths.size(); id++) {
bin_volume *= widths[id];
}
return bin_volume * sum;
}
colvar_grid_gradient::colvar_grid_gradient()
: colvar_grid<cvm::real>(), samples(NULL)

73
lib/colvars/colvargrid.h
View File

@ -1025,6 +1025,49 @@ public:
has_data = true;
return is;
}
/// \brief Write the grid data without labels, as they are
/// represented in memory
/// \param buf_size Number of values per line
std::ostream & write_opendx(std::ostream &os)
{
// write the header
os << "object 1 class gridpositions counts";
int icv;
for (icv = 0; icv < number_of_colvars(); icv++) {
os << " " << number_of_points(icv);
}
os << "\n";
os << "origin";
for (icv = 0; icv < number_of_colvars(); icv++) {
os << " " << (lower_boundaries[icv].real_value + 0.5 * widths[icv]);
}
os << "\n";
for (icv = 0; icv < number_of_colvars(); icv++) {
os << "delta";
for (size_t icv2 = 0; icv2 < number_of_colvars(); icv2++) {
if (icv == icv2) os << " " << widths[icv];
else os << " " << 0.0;
}
os << "\n";
}
os << "object 2 class gridconnections counts";
for (icv = 0; icv < number_of_colvars(); icv++) {
os << " " << number_of_points(icv);
}
os << "\n";
os << "object 3 class array type double rank 0 items "
<< number_of_points() << " data follows\n";
write_raw(os);
os << "object \"collective variables scalar field\" class field\n";
return os;
}
};
@ -1161,13 +1204,14 @@ public:
"larger than 1 in a scalar data grid.\n");
return 0.;
}
if (samples)
if (samples) {
return (samples->value(ix) > 0) ?
(data[address(ix)] / cvm::real(samples->value(ix))) :
0.0;
else
} else {
return data[address(ix)];
}
}
/// \brief Get the value from a formatted output and transform it
/// into the internal representation (it may have been rescaled or
@ -1203,24 +1247,17 @@ public:
std::ostream & write_restart(std::ostream &os);
/// \brief Return the highest value
inline cvm::real maximum_value()
{
cvm::real max = data[0];
for (size_t i = 0; i < nt; i++) {
if (data[i] > max) max = data[i];
}
return max;
}
cvm::real maximum_value() const;
/// \brief Return the lowest value
inline cvm::real minimum_value()
{
cvm::real min = data[0];
for (size_t i = 0; i < nt; i++) {
if (data[i] < min) min = data[i];
}
return min;
}
cvm::real minimum_value() const;
/// \brief Calculates the integral of the map (uses widths if they are defined)
cvm::real integral() const;
/// \brief Assuming that the map is a normalized probability density,
/// calculates the entropy (uses widths if they are defined)
cvm::real entropy() const;
private:
// gradient

1
lib/colvars/colvarmodule.cpp
View File

@ -782,6 +782,7 @@ std::istream & colvarmodule::read_restart(std::istream &is)
}
}
is.clear();
parse->clear_keyword_registry();
}
// colvars restart

2
lib/colvars/colvarmodule.h
View File

@ -4,7 +4,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2015-04-22"
#define COLVARS_VERSION "2015-07-21"
#endif
#ifndef COLVARS_DEBUG

14
lib/colvars/colvarparse.cpp
View File

@ -355,6 +355,14 @@ void colvarparse::strip_values(std::string &conf)
}
void colvarparse::clear_keyword_registry()
{
allowed_keywords.clear();
data_begin_pos.clear();
data_end_pos.clear();
}
int colvarparse::check_keywords(std::string &conf, char const *key)
{
if (cvm::debug())
@ -396,9 +404,9 @@ int colvarparse::check_keywords(std::string &conf, char const *key)
return COLVARS_ERROR;
}
}
allowed_keywords.clear();
data_begin_pos.clear();
data_end_pos.clear();
clear_keyword_registry();
return COLVARS_OK;
}

5
lib/colvars/colvarparse.h
View File

@ -37,7 +37,7 @@ protected:
/// \brief Whether or not to accumulate data_begin_pos and
/// data_end_pos in key_lookup(); it may be useful to disable
/// this after the constructor is called, because other files may be
/// read (e.g. restart) that would mess up with the registry; in any
/// read (e.g. restart) that would mess up the registry; in any
/// case, nothing serious happens until check_keywords() is invoked
/// (which should happen only right after construction)
bool save_delimiters;
@ -144,6 +144,9 @@ public:
/// then loop over all words
int check_keywords(std::string &conf, char const *key);
/// \brief Use this after parsing a config string (note that check_keywords() calls it already)
void clear_keyword_registry();
/// \brief Return a lowercased copy of the string
static inline std::string to_lower_cppstr(std::string const &in)

23
lib/colvars/colvarscript.cpp
View File

@ -256,6 +256,29 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
return COLVARSCRIPT_OK;
}
if (subcmd == "cvcflags") {
if (argc < 4) {
result = "cvcflags: missing parameter: vector of flags";
return COLVARSCRIPT_ERROR;
}
std::string flags_str = argv[3];
std::istringstream is(flags_str);
std::vector<bool> flags;
int flag;
while (is >> flag) {
flags.push_back(flag != 0);
}
int res = cv->set_cvc_flags(flags);
if (res != COLVARS_OK) {
result = "Error setting CVC flags";
return COLVARSCRIPT_ERROR;
}
result = "0";
return COLVARSCRIPT_OK;
}
result = "Syntax error\n" + help_string();
return COLVARSCRIPT_ERROR;
}