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update colvars library to version 2016-08-19 

(cherry picked from commit c67326be6d)
This commit is contained in:
Axel Kohlmeyer 2016-08-23 05:53:05 -04:00
parent 3b476d914f
commit 16607a0132
16 changed files with 88 additions and 100 deletions
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doc/src/PDF/colvars-refman-lammps.pdf
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8
lib/colvars/Makefile.fermi
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@ -93,8 +93,8 @@ colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvarscript.h colvarbias.h
colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvardeps.h
colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
colvarproxy.h colvarvalue.h colvarparse.h
colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvargrid.h
@ -104,12 +104,12 @@ colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
colvarscript.h
colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
colvarparse.h colvardeps.h
colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

8
lib/colvars/Makefile.g++
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@ -92,8 +92,8 @@ colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvarscript.h colvarbias.h
colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvardeps.h
colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
colvarproxy.h colvarvalue.h colvarparse.h
colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvargrid.h
@ -103,12 +103,12 @@ colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
colvarscript.h
colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
colvarparse.h colvardeps.h
colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

8
lib/colvars/Makefile.mingw32-cross
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@ -100,8 +100,8 @@ $(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvarscript.h colvarbias.h
$(DIR)colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvardeps.h
$(DIR)colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
colvarproxy.h colvarvalue.h colvarparse.h
$(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvargrid.h
@ -111,12 +111,12 @@ $(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
colvarscript.h
$(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
$(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
colvarparse.h colvardeps.h
$(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
$(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

8
lib/colvars/Makefile.mingw64-cross
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@ -100,8 +100,8 @@ $(DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \
$(DIR)colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvarscript.h colvarbias.h
$(DIR)colvardeps.o: colvardeps.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvardeps.h
$(DIR)colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \
colvarproxy.h colvarvalue.h colvarparse.h
$(DIR)colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \
colvaratoms.h colvargrid.h
@ -111,12 +111,12 @@ $(DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \
colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \
colvarscript.h
$(DIR)colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
$(DIR)colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \
colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \
colvarparse.h colvardeps.h
$(DIR)colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h colvarparse.h colvardeps.h
colvarvalue.h colvarparse.h
$(DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \
colvarvalue.h

44
lib/colvars/colvar.cpp
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@ -771,7 +771,7 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)
error_code |= calc_cvc_values(first_cvc, num_cvcs);
error_code |= calc_cvc_gradients(first_cvc, num_cvcs);
error_code |= calc_cvc_sys_forces(first_cvc, num_cvcs);
error_code |= calc_cvc_total_force(first_cvc, num_cvcs);
error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);
if (cvm::debug())
@ -790,7 +790,7 @@ int colvar::collect_cvc_data()
error_code |= collect_cvc_values();
error_code |= collect_cvc_gradients();
error_code |= collect_cvc_sys_forces();
error_code |= collect_cvc_total_forces();
error_code |= collect_cvc_Jacobians();
error_code |= calc_colvar_properties();
@ -889,21 +889,22 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
size_t i, cvc_count;
if (is_enabled(f_cv_gradient)) {
if (cvm::debug())
cvm::log("Calculating gradients of colvar \""+this->name+"\".\n");
if (cvm::debug())
cvm::log("Calculating gradients of colvar \""+this->name+"\".\n");
// calculate the gradients of each component
cvm::increase_depth();
for (i = first_cvc, cvc_count = 0;
(i < cvcs.size()) && (cvc_count < cvc_max_count);
i++) {
if (!cvcs[i]->is_enabled()) continue;
cvc_count++;
// calculate the gradients of each component
cvm::increase_depth();
for (i = first_cvc, cvc_count = 0;
(i < cvcs.size()) && (cvc_count < cvc_max_count);
i++) {
if (!cvcs[i]->is_enabled()) continue;
cvc_count++;
if ((cvcs[i])->is_enabled(f_cvc_gradient)) {
(cvcs[i])->calc_gradients();
// if requested, propagate (via chain rule) the gradients above
// to the atoms used to define the roto-translation
// This could be integrated in the CVC base class
for (size_t 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();
@ -914,6 +915,7 @@ int colvar::calc_cvc_gradients(int first_cvc, size_t num_cvcs)
}
}
}
cvm::decrease_depth();
if (cvm::debug())
@ -976,7 +978,7 @@ int colvar::collect_cvc_gradients()
}
int colvar::calc_cvc_sys_forces(int first_cvc, size_t num_cvcs)
int colvar::calc_cvc_total_force(int first_cvc, size_t num_cvcs)
{
size_t const cvc_max_count = num_cvcs ? num_cvcs : num_active_cvcs();
size_t i, cvc_count;
@ -1010,7 +1012,7 @@ int colvar::calc_cvc_sys_forces(int first_cvc, size_t num_cvcs)
}
int colvar::collect_cvc_sys_forces()
int colvar::collect_cvc_total_forces()
{
if (is_enabled(f_cv_total_force_calc)) {
ft.reset();
@ -1097,10 +1099,8 @@ int colvar::calc_colvar_properties()
// report the restraint center as "value"
x_reported = xr;
v_reported = vr;
// the "total force" with the extended Lagrangian is just the
// harmonic term acting on the extended coordinate
// Note: this is the force for current timestep
ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
// the "total force" with the extended Lagrangian is
// calculated in update_forces_energy() below
} else {
@ -1175,14 +1175,18 @@ cvm::real colvar::update_forces_energy()
// the total force is applied to the fictitious mass, while the
// atoms only feel the harmonic force
// fr: bias force on extended coordinate (without harmonic spring), for output in trajectory
// f_ext: total force on extended coordinate (including harmonic spring)
// fr: bias force on extended variable (without harmonic spring), for output in trajectory
// f_ext: total force on extended variable (including harmonic spring)
// f: - initially, external biasing force
// - after this code block, colvar force to be applied to atomic coordinates, ie. spring force
fr = f;
f_ext = f + (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);
f = (-0.5 * ext_force_k) * this->dist2_rgrad(xr, x);
// The total force acting on the extended variable is f_ext
// This will be used in the next timestep
ft_reported = f_ext;
// leapfrog: starting from x_i, f_i, v_(i-1/2)
vr += (0.5 * dt) * f_ext / ext_mass;
// Because of leapfrog, kinetic energy at time i is approximate

4
lib/colvars/colvar.h
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@ -254,7 +254,7 @@ public:
/// \brief Same as \link colvar::calc_cvc_values \endlink but for gradients
int calc_cvc_gradients(int first, size_t num_cvcs);
/// \brief Same as \link colvar::calc_cvc_values \endlink but for total forces
int calc_cvc_sys_forces(int first, size_t num_cvcs);
int calc_cvc_total_force(int first, size_t num_cvcs);
/// \brief Same as \link colvar::calc_cvc_values \endlink but for Jacobian derivatives/forces
int calc_cvc_Jacobians(int first, size_t num_cvcs);
@ -266,7 +266,7 @@ public:
/// \brief Same as \link colvar::collect_cvc_values \endlink but for gradients
int collect_cvc_gradients();
/// \brief Same as \link colvar::collect_cvc_values \endlink but for total forces
int collect_cvc_sys_forces();
int collect_cvc_total_forces();
/// \brief Same as \link colvar::collect_cvc_values \endlink but for Jacobian derivatives/forces
int collect_cvc_Jacobians();
/// \brief Calculate the quantities associated to the colvar (but not to the CVCs)

16
lib/colvars/colvarbias_abf.cpp
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@ -31,10 +31,8 @@ int colvarbias_abf::init(std::string const &conf)
// ************* parsing general ABF options ***********************
get_keyval(conf, "applyBias", apply_bias, true);
if (apply_bias) {
enable(f_cvb_apply_force);
} else {
get_keyval_feature((colvarparse *)this, conf, "applyBias", f_cvb_apply_force, true);
if (!is_enabled(f_cvb_apply_force)){
cvm::log("WARNING: ABF biases will *not* be applied!\n");
}
@ -84,9 +82,6 @@ int colvarbias_abf::init(std::string const &conf)
// Request calculation of total force (which also checks for availability)
if(enable(f_cvb_get_total_force)) return cvm::get_error();
}
if (apply_bias) {
if(enable(f_cvb_apply_force)) return cvm::get_error();
}
bool b_extended = false;
for (size_t i = 0; i < colvars.size(); i++) {
@ -249,6 +244,11 @@ int colvarbias_abf::update()
// and subtract previous ABF force
system_force[i] = colvars[i]->total_force().real_value
- colvar_forces[i].real_value;
// if (cvm::debug())
// cvm::log("ABF System force calc: cv " + cvm::to_str(i) +
// " fs " + cvm::to_str(system_force[i]) +
// " = ft " + cvm::to_str(colvars[i]->total_force().real_value) +
// " - fa " + cvm::to_str(colvar_forces[i].real_value));
}
gradients->acc_force(force_bin, system_force);
}
@ -277,7 +277,7 @@ int colvarbias_abf::update()
}
// Compute and apply the new bias, if applicable
if ( apply_bias && samples->index_ok(bin) ) {
if (is_enabled(f_cvb_apply_force) && samples->index_ok(bin)) {
size_t count = samples->value(bin);
cvm::real fact = 1.0;

1
lib/colvars/colvarbias_abf.h
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@ -32,7 +32,6 @@ private:
/// Base filename(s) for reading previous gradient data (replaces data from restart file)
std::vector<std::string> input_prefix;
bool apply_bias;
bool update_bias;
bool hide_Jacobian;
size_t full_samples;

3
lib/colvars/colvarcomp.cpp
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@ -43,7 +43,8 @@ colvar::cvc::cvc(std::string const &conf)
// All cvcs implement this
provide(f_cvc_debug_gradient);
get_keyval(conf, "debugGradients", set_feature(f_cvc_debug_gradient), false, parse_silent);
get_keyval_feature((colvarparse *)this, conf, "debugGradients",
f_cvc_debug_gradient, false, parse_silent);
// Attempt scalable calculations when in parallel? (By default yes, if available)
get_keyval(conf, "scalable", b_try_scalable, true);

29
lib/colvars/colvardeps.cpp
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@ -1,4 +1,3 @@
#include "colvarmodule.h"
#include "colvardeps.h"
@ -30,6 +29,18 @@ void colvardeps::provide(int feature_id) {
}
bool colvardeps::get_keyval_feature(colvarparse *cvp,
std::string const &conf, char const *key,
int feature_id, bool const &def_value,
colvarparse::Parse_Mode const parse_mode)
{
bool value;
bool const found = cvp->get_keyval(conf, key, value, def_value, parse_mode);
if (value) enable(feature_id);
return found;
}
int colvardeps::enable(int feature_id,
bool dry_run /* default: false */,
// dry_run: fail silently, do not enable if available
@ -48,7 +59,7 @@ int colvardeps::enable(int feature_id,
if (cvm::debug()) {
cvm::log("DEPS: " + description +
(dry_run ? " testing " : " requiring ") +
"\"" + f->description);
"\"" + f->description +"\"");
}
if (fs->enabled) {
@ -140,11 +151,7 @@ int colvardeps::enable(int feature_id,
// 4) solve deps in children
for (i=0; i<f->requires_children.size(); i++) {
int g = f->requires_children[i];
if (cvm::debug())
cvm::log("requires children " + features()[g]->description);
// cvm::log("children " + cvm::to_str(g));
for (j=0; j<children.size(); j++) {
// cvm::log("child " + children[j]->description);
cvm::increase_depth();
res = children[j]->enable(g, dry_run, false);
cvm::decrease_depth();
@ -215,7 +222,7 @@ void colvardeps::init_cvb_requires() {
// Initialize feature_states for each instance
feature_states.reserve(f_cvb_ntot);
for (i = 0; i < f_cvb_ntot; i++) {
feature_states.push_back(new feature_state(this, feature_states.size(), true, false));
feature_states.push_back(new feature_state(true, false));
// Most features are available, so we set them so
// and list exceptions below
}
@ -319,7 +326,7 @@ void colvardeps::init_cv_requires() {
// Initialize feature_states for each instance
feature_states.reserve(f_cv_ntot);
for (i = 0; i < f_cv_ntot; i++) {
feature_states.push_back(new feature_state(this, feature_states.size(), true, false));
feature_states.push_back(new feature_state(true, false));
// Most features are available, so we set them so
// and list exceptions below
}
@ -364,7 +371,7 @@ void colvardeps::init_cvc_requires() {
f_description(f_cvc_debug_gradient, "debug gradient");
f_req_self(f_cvc_debug_gradient, f_cvc_gradient);
f_description(f_cvc_Jacobian, "Jacobian");
f_description(f_cvc_Jacobian, "Jacobian derivative");
f_req_self(f_cvc_Jacobian, f_cvc_inv_gradient);
f_description(f_cvc_com_based, "depends on group centers of mass");
@ -385,7 +392,7 @@ void colvardeps::init_cvc_requires() {
// default as unavailable, not enabled
feature_states.reserve(f_cvc_ntot);
for (i = 0; i < colvardeps::f_cvc_ntot; i++) {
feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
feature_states.push_back(new feature_state(false, false));
}
// Features that are implemented by all cvcs by default
@ -429,7 +436,7 @@ void colvardeps::init_ag_requires() {
// default as unavailable, not enabled
feature_states.reserve(f_ag_ntot);
for (i = 0; i < colvardeps::f_ag_ntot; i++) {
feature_states.push_back(new feature_state(this, feature_states.size(), false, false));
feature_states.push_back(new feature_state(false, false));
}
// Features that are implemented (or not) by all atom groups

30
lib/colvars/colvardeps.h
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@ -1,10 +1,11 @@
// -*- c++ -*-
#include "colvarmodule.h"
#ifndef COLVARDEPS_H
#define COLVARDEPS_H
#include "colvarmodule.h"
#include "colvarparse.h"
/// Parent class for a member object of a bias, cv or cvc etc. containing dependencies
/// (features) and handling dependency resolution
@ -27,16 +28,9 @@ public:
std::string description; // reference to object name (cv, cvc etc.)
/// This contains the current state of each feature for each object
class feature_state {
private:
colvardeps *const deps_object;
int const id;
operator int() { return 0; } // never cast as int
public:
inline colvardeps *object() const { return deps_object; }
inline int feature_id() const { return id; }
feature_state(colvardeps *o, int i, bool a, bool e)
: deps_object(o), id(i), available(a), enabled(e) {}
struct feature_state {
feature_state(bool a, bool e)
: available(a), enabled(e) {}
/// Available means: supported, subject to dependencies as listed,
/// MAY BE ENABLED AS A RESULT OF DEPENDENCY SOLVING
@ -55,12 +49,6 @@ public:
/// List of the state of all features
std::vector<feature_state *> feature_states;
/// Allow setting a feature state while parsing its kewyord
inline feature_state * set_feature(int id)
{
return feature_states[id];
}
/// Describes a feature and its dependecies
/// used in a static array within each subclass
class feature {
@ -146,6 +134,12 @@ public:
void provide(int feature_id); // set the feature's flag to available in local object
/// Parse a keyword and enable a feature accordingly
bool get_keyval_feature(colvarparse *cvp,
std::string const &conf, char const *key,
int feature_id, bool const &def_value,
colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal);
int enable(int f, bool dry_run = false, bool toplevel = true); // enable a feature and recursively solve its dependencies
// dry_run is set to true to recursively test if a feature is available, without enabling it
// int disable(int f);

2
lib/colvars/colvarmodule.h
View File

@ -4,7 +4,7 @@
#define COLVARMODULE_H
#ifndef COLVARS_VERSION
#define COLVARS_VERSION "2016-08-10"
#define COLVARS_VERSION "2016-08-19"
#endif
#ifndef COLVARS_DEBUG

15
lib/colvars/colvarparse.cpp
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@ -354,21 +354,6 @@ bool colvarparse::get_keyval(std::string const &conf,
}
bool colvarparse::get_keyval(std::string const &conf,
char const *key,
colvardeps::feature_state *value,
bool const &def_value,
Parse_Mode const parse_mode)
{
bool feature_flag = def_value;
bool const b_found = get_keyval(conf, key, feature_flag, def_value, parse_mode);
if (feature_flag) {
value->object()->enable(value->feature_id());
}
return b_found;
}
// multiple-value keyword parsers
bool colvarparse::get_keyval(std::string const &conf,

7
lib/colvars/colvarparse.h
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@ -8,7 +8,6 @@
#include "colvarmodule.h"
#include "colvarvalue.h"
#include "colvardeps.h"
/// \file colvarparse.h Parsing functions for collective variables
@ -181,12 +180,6 @@ public:
bool &value,
bool const &def_value = false,
Parse_Mode const parse_mode = parse_normal);
bool get_keyval(std::string const &conf,
char const *key,
colvardeps::feature_state *value,
bool const &def_value = false,
Parse_Mode const parse_mode = parse_normal);
bool get_keyval(std::string const &conf,
char const *key,
std::vector<int> &values,

5
lib/colvars/colvarscript.cpp
View File

@ -336,6 +336,11 @@ int colvarscript::proc_bias(int argc, char const *argv[]) {
return COLVARS_OK;
}
if (subcmd == "state") {
b->print_state();
return COLVARS_OK;
}
// Subcommands for MW ABF
if (subcmd == "bin") {
int r = b->current_bin();