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update colvars library to version 2016-09-30

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This commit is contained in:
Axel Kohlmeyer
2016-09-30 08:15:44 -04:00
parent f7b5afee82
commit 6d200061ca
20 changed files with 728 additions and 155 deletions
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doc/src/PDF/colvars-refman-lammps.pdf
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6
doc/src/fix_colvars.txt
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@ -39,8 +39,8 @@ metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
(US) via a flexible harmonic restraint bias. The colvars library is (US) via a flexible harmonic restraint bias. The colvars library is
hosted at "http://colvars.github.io/"_http://colvars.github.io/ hosted at "http://colvars.github.io/"_http://colvars.github.io/
This documentation describes only the fix colvars command itself and This documentation describes only the fix colvars command itself and
LAMMPS specific parts of the code. The full documentation of the LAMMPS specific parts of the code. The full documentation of the
colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf colvars library is available as "this supplementary PDF document"_PDF/colvars-refman-lammps.pdf
A detailed discussion of the implementation of the portable collective A detailed discussion of the implementation of the portable collective
@ -122,7 +122,7 @@ not a limitation of functionality.
[Default:] [Default:]
The default options are input = NULL, output = out, seed = 1966, unwrap yes, The default options are input = NULL, output = out, seed = 1966, unwrap yes,
and tstat = NULL. and tstat = NULL.
:line :line

54
lib/colvars/colvar.cpp
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@ -150,7 +150,7 @@ colvar::colvar(std::string const &conf)
feature_states[f_cv_linear]->enabled = lin; feature_states[f_cv_linear]->enabled = lin;
} }
// Colvar is homogeneous iff: // Colvar is homogeneous if:
// - it is linear (hence not scripted) // - it is linear (hence not scripted)
// - all cvcs have coefficient 1 or -1 // - all cvcs have coefficient 1 or -1
// i.e. sum or difference of cvcs // i.e. sum or difference of cvcs
@ -375,28 +375,16 @@ colvar::colvar(std::string const &conf)
{ {
bool temp; bool temp;
if (get_keyval(conf, "outputSystemForce", temp, false)) { if (get_keyval(conf, "outputSystemForce", temp, false, colvarparse::parse_silent)) {
cvm::error("Colvar option outputSystemForce is deprecated.\n" cvm::error("Option outputSystemForce is deprecated: only outputTotalForce is supported instead.\n"
"Please use outputTotalForce, or outputSystemForce within an ABF bias."); "The two are NOT identical: see http://colvars.github.io/totalforce.html.\n", INPUT_ERROR);
return; return;
} }
} }
{ get_keyval_feature(this, conf, "outputTotalForce", f_cv_output_total_force, false);
bool b_output_total_force; get_keyval_feature(this, conf, "outputAppliedForce", f_cv_output_applied_force, false);
get_keyval(conf, "outputTotalForce", b_output_total_force, false); get_keyval_feature(this, conf, "subtractAppliedForce", f_cv_subtract_applied_force, false);
if (b_output_total_force) {
enable(f_cv_output_total_force);
}
}
{
bool b_output_applied_force;
get_keyval(conf, "outputAppliedForce", b_output_applied_force, false);
if (b_output_applied_force) {
enable(f_cv_output_applied_force);
}
}
// Start in active state by default // Start in active state by default
enable(f_cv_active); enable(f_cv_active);
@ -409,6 +397,8 @@ colvar::colvar(std::string const &conf)
fj.type(value()); fj.type(value());
ft.type(value()); ft.type(value());
ft_reported.type(value()); ft_reported.type(value());
f_old.type(value());
f_old.reset();
if (cvm::b_analysis) if (cvm::b_analysis)
parse_analysis(conf); parse_analysis(conf);
@ -519,6 +509,8 @@ int colvar::init_components(std::string const &conf)
"number", "coordNum"); "number", "coordNum");
error_code |= init_components_type<selfcoordnum>(conf, "self-coordination " error_code |= init_components_type<selfcoordnum>(conf, "self-coordination "
"number", "selfCoordNum"); "number", "selfCoordNum");
error_code |= init_components_type<groupcoordnum>(conf, "group-coordination "
"number", "groupCoord");
error_code |= init_components_type<angle>(conf, "angle", "angle"); error_code |= init_components_type<angle>(conf, "angle", "angle");
error_code |= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle"); error_code |= init_components_type<dipole_angle>(conf, "dipole angle", "dipoleAngle");
error_code |= init_components_type<dihedral>(conf, "dihedral", "dihedral"); error_code |= init_components_type<dihedral>(conf, "dihedral", "dihedral");
@ -1104,6 +1096,14 @@ int colvar::calc_colvar_properties()
} else { } else {
if (is_enabled(f_cv_subtract_applied_force)) {
// correct the total force only if it has been measured
// TODO add a specific test instead of relying on sq norm
if (ft.norm2() > 0.0) {
ft -= f_old;
}
}
x_reported = x; x_reported = x;
ft_reported = ft; ft_reported = ft;
} }
@ -1210,6 +1210,10 @@ cvm::real colvar::update_forces_energy()
x_old = x; x_old = x;
} }
if (is_enabled(f_cv_subtract_applied_force)) {
f_old = f;
}
if (cvm::debug()) if (cvm::debug())
cvm::log("Done updating colvar \""+this->name+"\".\n"); cvm::log("Done updating colvar \""+this->name+"\".\n");
return (potential_energy + kinetic_energy); return (potential_energy + kinetic_energy);
@ -1640,15 +1644,9 @@ std::ostream & colvar::write_traj(std::ostream &os)
} }
if (is_enabled(f_cv_output_applied_force)) { if (is_enabled(f_cv_output_applied_force)) {
if (is_enabled(f_cv_extended_Lagrangian)) { os << " "
os << " " << std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width) << applied_force();
<< fr;
} else {
os << " "
<< std::setprecision(cvm::cv_prec) << std::setw(cvm::cv_width)
<< f;
}
} }
return os; return os;

13
lib/colvars/colvar.h
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@ -175,6 +175,9 @@ public:
/// (if defined) contribute to it /// (if defined) contribute to it
colvarvalue f; colvarvalue f;
/// Applied force at the previous step (to be subtracted from total force if needed)
colvarvalue f_old;
/// \brief Total force, as derived from the atomic trajectory; /// \brief Total force, as derived from the atomic trajectory;
/// should equal the system force plus \link f \endlink /// should equal the system force plus \link f \endlink
colvarvalue ft; colvarvalue ft;
@ -272,10 +275,13 @@ public:
/// \brief Calculate the quantities associated to the colvar (but not to the CVCs) /// \brief Calculate the quantities associated to the colvar (but not to the CVCs)
int calc_colvar_properties(); int calc_colvar_properties();
/// Get the current biasing force /// Get the current applied force
inline colvarvalue bias_force() const inline colvarvalue const applied_force() const
{ {
return fb; if (is_enabled(f_cv_extended_Lagrangian)) {
return fr;
}
return f;
} }
/// Set the total biasing force to zero /// Set the total biasing force to zero
@ -482,6 +488,7 @@ public:
class dihedral; class dihedral;
class coordnum; class coordnum;
class selfcoordnum; class selfcoordnum;
class groupcoordnum;
class h_bond; class h_bond;
class rmsd; class rmsd;
class orientation_angle; class orientation_angle;

4
lib/colvars/colvarbias_histogram.cpp
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@ -67,7 +67,7 @@ int colvarbias_histogram::init(std::string const &conf)
if (colvar_array_size > 0) { if (colvar_array_size > 0) {
weights.assign(colvar_array_size, 1.0); weights.assign(colvar_array_size, 1.0);
get_keyval(conf, "weights", weights, weights, colvarparse::parse_silent); get_keyval(conf, "weights", weights, weights);
} }
for (i = 0; i < colvars.size(); i++) { for (i = 0; i < colvars.size(); i++) {
@ -79,7 +79,7 @@ int colvarbias_histogram::init(std::string const &conf)
{ {
std::string grid_conf; std::string grid_conf;
if (key_lookup(conf, "grid", grid_conf)) { if (key_lookup(conf, "histogramGrid", grid_conf)) {
grid->parse_params(grid_conf); grid->parse_params(grid_conf);
} }
} }

6
lib/colvars/colvarbias_meta.cpp
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@ -92,7 +92,11 @@ int colvarbias_meta::init(std::string const &conf)
get_keyval(conf, "keepHills", keep_hills, false); get_keyval(conf, "keepHills", keep_hills, false);
if (! get_keyval(conf, "writeFreeEnergyFile", dump_fes, true)) if (! get_keyval(conf, "writeFreeEnergyFile", dump_fes, true))
get_keyval(conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent); get_keyval(conf, "dumpFreeEnergyFile", dump_fes, true, colvarparse::parse_silent);
get_keyval(conf, "saveFreeEnergyFile", dump_fes_save, false); if (get_keyval(conf, "saveFreeEnergyFile", dump_fes_save, false, colvarparse::parse_silent)) {
cvm::log("Option \"saveFreeEnergyFile\" is deprecated, "
"please use \"keepFreeEnergyFiles\" instead.");
}
get_keyval(conf, "keepFreeEnergyFiles", dump_fes_save, dump_fes_save);
hills_energy = new colvar_grid_scalar(colvars); hills_energy = new colvar_grid_scalar(colvars);
hills_energy_gradients = new colvar_grid_gradient(colvars); hills_energy_gradients = new colvar_grid_gradient(colvars);

247
lib/colvars/colvarbias_restraint.cpp
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@ -612,3 +612,250 @@ cvm::real colvarbias_restraint_linear::restraint_convert_k(cvm::real k,
colvarbias_restraint_histogram::colvarbias_restraint_histogram(char const *key)
: colvarbias(key)
{
lower_boundary = 0.0;
upper_boundary = 0.0;
width = 0.0;
gaussian_width = 0.0;
}
int colvarbias_restraint_histogram::init(std::string const &conf)
{
colvarbias::init(conf);
get_keyval(conf, "lowerBoundary", lower_boundary, lower_boundary);
get_keyval(conf, "upperBoundary", upper_boundary, upper_boundary);
get_keyval(conf, "width", width, width);
if (width <= 0.0) {
cvm::error("Error: \"width\" must be positive.\n", INPUT_ERROR);
}
get_keyval(conf, "gaussianWidth", gaussian_width, 2.0 * width, colvarparse::parse_silent);
get_keyval(conf, "gaussianSigma", gaussian_width, 2.0 * width);
if (lower_boundary >= upper_boundary) {
cvm::error("Error: the upper boundary, "+
cvm::to_str(upper_boundary)+
", is not higher than the lower boundary, "+
cvm::to_str(lower_boundary)+".\n",
INPUT_ERROR);
}
cvm::real const nbins = (upper_boundary - lower_boundary) / width;
int const nbins_round = (int)(nbins);
if (std::fabs(nbins - cvm::real(nbins_round)) > 1.0E-10) {
cvm::log("Warning: grid interval ("+
cvm::to_str(lower_boundary, cvm::cv_width, cvm::cv_prec)+" - "+
cvm::to_str(upper_boundary, cvm::cv_width, cvm::cv_prec)+
") is not commensurate to its bin width ("+
cvm::to_str(width, cvm::cv_width, cvm::cv_prec)+").\n");
}
p.resize(nbins_round);
ref_p.resize(nbins_round);
p_diff.resize(nbins_round);
bool const inline_ref_p =
get_keyval(conf, "refHistogram", ref_p.data_array(), ref_p.data_array());
std::string ref_p_file;
get_keyval(conf, "refHistogramFile", ref_p_file, std::string(""));
if (ref_p_file.size()) {
if (inline_ref_p) {
cvm::error("Error: cannot specify both refHistogram and refHistogramFile at the same time.\n",
INPUT_ERROR);
} else {
std::ifstream is(ref_p_file.c_str());
std::string data_s = "";
std::string line;
while (getline_nocomments(is, line)) {
data_s.append(line+"\n");
}
if (data_s.size() == 0) {
cvm::error("Error: file \""+ref_p_file+"\" empty or unreadable.\n", FILE_ERROR);
}
is.close();
cvm::vector1d<cvm::real> data;
if (data.from_simple_string(data_s) != 0) {
cvm::error("Error: could not read histogram from file \""+ref_p_file+"\".\n");
}
if (data.size() == 2*ref_p.size()) {
// file contains both x and p(x)
size_t i;
for (i = 0; i < ref_p.size(); i++) {
ref_p[i] = data[2*i+1];
}
} else if (data.size() == ref_p.size()) {
ref_p = data;
} else {
cvm::error("Error: file \""+ref_p_file+"\" contains a histogram of different length.\n",
INPUT_ERROR);
}
}
}
cvm::real const ref_integral = ref_p.sum() * width;
if (std::fabs(ref_integral - 1.0) > 1.0e-03) {
cvm::log("Reference distribution not normalized, normalizing to unity.\n");
ref_p /= ref_integral;
}
get_keyval(conf, "writeHistogram", b_write_histogram, false);
get_keyval(conf, "forceConstant", force_k, 1.0);
return COLVARS_OK;
}
colvarbias_restraint_histogram::~colvarbias_restraint_histogram()
{
p.resize(0);
ref_p.resize(0);
p_diff.resize(0);
}
int colvarbias_restraint_histogram::update()
{
if (cvm::debug())
cvm::log("Updating the histogram restraint bias \""+this->name+"\".\n");
size_t vector_size = 0;
size_t icv;
for (icv = 0; icv < colvars.size(); icv++) {
vector_size += colvars[icv]->value().size();
}
cvm::real const norm = 1.0/(std::sqrt(2.0*PI)*gaussian_width*vector_size);
// calculate the histogram
p.reset();
for (icv = 0; icv < colvars.size(); icv++) {
colvarvalue const &cv = colvars[icv]->value();
if (cv.type() == colvarvalue::type_scalar) {
cvm::real const cv_value = cv.real_value;
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width));
}
} else if (cv.type() == colvarvalue::type_vector) {
size_t idim;
for (idim = 0; idim < cv.vector1d_value.size(); idim++) {
cvm::real const cv_value = cv.vector1d_value[idim];
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
p[igrid] += norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width));
}
}
} else {
// TODO
}
}
cvm::real const force_k_cv = force_k * vector_size;
// calculate the difference between current and reference
p_diff = p - ref_p;
bias_energy = 0.5 * force_k_cv * p_diff * p_diff;
// calculate the forces
for (icv = 0; icv < colvars.size(); icv++) {
colvarvalue const &cv = colvars[icv]->value();
colvarvalue &cv_force = colvar_forces[icv];
cv_force.type(cv);
cv_force.reset();
if (cv.type() == colvarvalue::type_scalar) {
cvm::real const cv_value = cv.real_value;
cvm::real &force = cv_force.real_value;
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
force += force_k_cv * p_diff[igrid] *
norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width)) *
(-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
}
} else if (cv.type() == colvarvalue::type_vector) {
size_t idim;
for (idim = 0; idim < cv.vector1d_value.size(); idim++) {
cvm::real const cv_value = cv.vector1d_value[idim];
cvm::real &force = cv_force.vector1d_value[idim];
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+0.5)*width);
force += force_k_cv * p_diff[igrid] *
norm * std::exp(-1.0 * (x_grid - cv_value) * (x_grid - cv_value) /
(2.0 * gaussian_width * gaussian_width)) *
(-1.0 * (x_grid - cv_value) / (gaussian_width * gaussian_width));
}
}
} else {
// TODO
}
}
return COLVARS_OK;
}
std::ostream & colvarbias_restraint_histogram::write_restart(std::ostream &os)
{
if (b_write_histogram) {
std::string file_name(cvm::output_prefix+"."+this->name+".hist.dat");
std::ofstream os(file_name.c_str());
os << "# " << cvm::wrap_string(colvars[0]->name, cvm::cv_width)
<< " " << "p(" << cvm::wrap_string(colvars[0]->name, cvm::cv_width-3)
<< ")\n";
size_t igrid;
for (igrid = 0; igrid < p.size(); igrid++) {
cvm::real const x_grid = (lower_boundary + (igrid+1)*width);
os << " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< x_grid
<< " "
<< std::setprecision(cvm::cv_prec)
<< std::setw(cvm::cv_width)
<< p[igrid] << "\n";
}
os.close();
}
return os;
}
std::istream & colvarbias_restraint_histogram::read_restart(std::istream &is)
{
return is;
}
std::ostream & colvarbias_restraint_histogram::write_traj_label(std::ostream &os)
{
os << " ";
if (b_output_energy) {
os << " E_"
<< cvm::wrap_string(this->name, cvm::en_width-2);
}
return os;
}
std::ostream & colvarbias_restraint_histogram::write_traj(std::ostream &os)
{
os << " ";
if (b_output_energy) {
os << " "
<< std::setprecision(cvm::en_prec) << std::setw(cvm::en_width)
<< bias_energy;
}
return os;
}

48
lib/colvars/colvarbias_restraint.h
View File

@ -168,4 +168,52 @@ protected:
}; };
/// Restrain the 1D histogram of a set of variables (or of a multidimensional one)
// TODO this could be reimplemented more cleanly as a derived class of both restraint and histogram
class colvarbias_restraint_histogram : public colvarbias {
public:
colvarbias_restraint_histogram(char const *key);
int init(std::string const &conf);
~colvarbias_restraint_histogram();
virtual int update();
virtual std::istream & read_restart(std::istream &is);
virtual std::ostream & write_restart(std::ostream &os);
virtual std::ostream & write_traj_label(std::ostream &os);
virtual std::ostream & write_traj(std::ostream &os);
protected:
/// Probability density
cvm::vector1d<cvm::real> p;
/// Reference probability density
cvm::vector1d<cvm::real> ref_p;
/// Difference between probability density and reference
cvm::vector1d<cvm::real> p_diff;
/// Lower boundary of the grid
cvm::real lower_boundary;
/// Upper boundary of the grid
cvm::real upper_boundary;
/// Resolution of the grid
cvm::real width;
/// Width of the Gaussians
cvm::real gaussian_width;
/// Restraint force constant
cvm::real force_k;
/// Write the histogram to a file
bool b_write_histogram;
};
#endif #endif

17
lib/colvars/colvarcomp.cpp
View File

@ -54,6 +54,21 @@ colvar::cvc::cvc(std::string const &conf)
} }
int colvar::cvc::init_total_force_params(std::string const &conf)
{
if (get_keyval_feature(this, conf, "oneSiteSystemForce",
f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) {
cvm::log("Warning: keyword \"oneSiteSystemForce\" is deprecated: "
"please use \"oneSiteTotalForce\" instead.\n");
}
if (get_keyval_feature(this, conf, "oneSiteTotalForce",
f_cvc_one_site_total_force, is_enabled(f_cvc_one_site_total_force))) {
cvm::log("Computing total force on group 1 only");
}
return COLVARS_OK;
}
cvm::atom_group *colvar::cvc::parse_group(std::string const &conf, cvm::atom_group *colvar::cvc::parse_group(std::string const &conf,
char const *group_key, char const *group_key,
bool optional) bool optional)
@ -77,8 +92,6 @@ cvm::atom_group *colvar::cvc::parse_group(std::string const &conf,
if (is_enabled(f_cvc_scalable)) { if (is_enabled(f_cvc_scalable)) {
cvm::log("Will enable scalable calculation for group \""+group->key+"\".\n"); cvm::log("Will enable scalable calculation for group \""+group->key+"\".\n");
} else {
cvm::log("Scalable calculation is not available for group \""+group->key+"\" with the current configuration.\n");
} }
} }

65
lib/colvars/colvarcomp.h
View File

@ -108,6 +108,9 @@ public:
char const *group_key, char const *group_key,
bool optional = false); bool optional = false);
/// \brief Parse options pertaining to total force calculation
virtual int init_total_force_params(std::string const &conf);
/// \brief After construction, set data related to dependency handling /// \brief After construction, set data related to dependency handling
int setup(); int setup();
@ -306,9 +309,6 @@ protected:
cvm::rvector dist_v; cvm::rvector dist_v;
/// Use absolute positions, ignoring PBCs when present /// Use absolute positions, ignoring PBCs when present
bool b_no_PBC; bool b_no_PBC;
/// Compute total force on first site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
bool b_1site_force;
public: public:
distance(std::string const &conf); distance(std::string const &conf);
distance(); distance();
@ -388,9 +388,6 @@ protected:
cvm::atom_group *ref2; cvm::atom_group *ref2;
/// Use absolute positions, ignoring PBCs when present /// Use absolute positions, ignoring PBCs when present
bool b_no_PBC; bool b_no_PBC;
/// Compute total force on one site only to avoid unwanted
/// coupling to other colvars (see e.g. Ciccotti et al., 2005)
bool b_1site_force;
/// Vector on which the distance vector is projected /// Vector on which the distance vector is projected
cvm::rvector axis; cvm::rvector axis;
/// Norm of the axis /// Norm of the axis
@ -854,6 +851,62 @@ public:
colvarvalue const &x2) const; colvarvalue const &x2) const;
}; };
/// \brief Colvar component: coordination number between two groups
/// (colvarvalue::type_scalar type, range [0:N1*N2])
class colvar::groupcoordnum
: public colvar::distance
{
protected:
/// \brief "Cutoff" for isotropic calculation (default)
cvm::real r0;
/// \brief "Cutoff vector" for anisotropic calculation
cvm::rvector r0_vec;
/// \brief Wheter dist/r0 or \vec{dist}*\vec{1/r0_vec} should ne be
/// used
bool b_anisotropic;
/// Integer exponent of the function numerator
int en;
/// Integer exponent of the function denominator
int ed;
public:
/// Constructor
groupcoordnum(std::string const &conf);
groupcoordnum();
virtual inline ~groupcoordnum() {}
virtual void calc_value();
virtual void calc_gradients();
virtual void apply_force(colvarvalue const &force);
template<bool b_gradients>
/// \brief Calculate a coordination number through the function
/// (1-x**n)/(1-x**m), x = |A1-A2|/r0 \param r0 "cutoff" for the
/// coordination number \param exp_num \i n exponent \param exp_den
/// \i m exponent \param A1 atom \param A2 atom
static cvm::real switching_function(cvm::real const &r0,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
/*
template<bool b_gradients>
/// \brief Calculate a coordination number through the function
/// (1-x**n)/(1-x**m), x = |(A1-A2)*(r0_vec)^-|1 \param r0_vec
/// vector of different cutoffs in the three directions \param
/// exp_num \i n exponent \param exp_den \i m exponent \param A1
/// atom \param A2 atom
static cvm::real switching_function(cvm::rvector const &r0_vec,
int const &exp_num, int const &exp_den,
cvm::atom &A1, cvm::atom &A2);
virtual cvm::real dist2(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_lgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
virtual colvarvalue dist2_rgrad(colvarvalue const &x1,
colvarvalue const &x2) const;
*/
};
/// \brief Colvar component: hydrogen bond, defined as the product of /// \brief Colvar component: hydrogen bond, defined as the product of
/// a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) /// a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol))
/// (colvarvalue::type_scalar type, range [0:1]) /// (colvarvalue::type_scalar type, range [0:1])

22
lib/colvars/colvarcomp_angles.cpp
View File

@ -18,9 +18,9 @@ colvar::angle::angle(std::string const &conf)
group1 = parse_group(conf, "group1"); group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2"); group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3"); group3 = parse_group(conf, "group3");
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing total force on group 1 only"); init_total_force_params(conf);
}
x.type(colvarvalue::type_scalar); x.type(colvarvalue::type_scalar);
} }
@ -33,7 +33,6 @@ colvar::angle::angle(cvm::atom const &a1,
provide(f_cvc_inv_gradient); provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian); provide(f_cvc_Jacobian);
provide(f_cvc_com_based); provide(f_cvc_com_based);
b_1site_force = false;
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1)); group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2)); group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
@ -94,7 +93,7 @@ void colvar::angle::calc_force_invgrads()
// centered on group2, which means group2 is kept fixed // centered on group2, which means group2 is kept fixed
// when propagating changes in the angle) // when propagating changes in the angle)
if (b_1site_force) { if (is_enabled(f_cvc_one_site_total_force)) {
group1->read_total_forces(); group1->read_total_forces();
cvm::real norm_fact = 1.0 / dxdr1.norm2(); cvm::real norm_fact = 1.0 / dxdr1.norm2();
ft.real_value = norm_fact * dxdr1 * group1->total_force(); ft.real_value = norm_fact * dxdr1 * group1->total_force();
@ -140,9 +139,8 @@ colvar::dipole_angle::dipole_angle(std::string const &conf)
group2 = parse_group(conf, "group2"); group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3"); group3 = parse_group(conf, "group3");
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) { init_total_force_params(conf);
cvm::log("Computing total force on group 1 only");
}
x.type(colvarvalue::type_scalar); x.type(colvarvalue::type_scalar);
} }
@ -152,7 +150,6 @@ colvar::dipole_angle::dipole_angle(cvm::atom const &a1,
cvm::atom const &a3) cvm::atom const &a3)
{ {
function_type = "dipole_angle"; function_type = "dipole_angle";
b_1site_force = false;
group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1)); group1 = new cvm::atom_group(std::vector<cvm::atom>(1, a1));
group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2)); group2 = new cvm::atom_group(std::vector<cvm::atom>(1, a2));
@ -250,14 +247,13 @@ colvar::dihedral::dihedral(std::string const &conf)
provide(f_cvc_Jacobian); provide(f_cvc_Jacobian);
provide(f_cvc_com_based); provide(f_cvc_com_based);
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing total force on group 1 only");
}
group1 = parse_group(conf, "group1"); group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2"); group2 = parse_group(conf, "group2");
group3 = parse_group(conf, "group3"); group3 = parse_group(conf, "group3");
group4 = parse_group(conf, "group4"); group4 = parse_group(conf, "group4");
init_total_force_params(conf);
x.type(colvarvalue::type_scalar); x.type(colvarvalue::type_scalar);
} }
@ -422,7 +418,7 @@ void colvar::dihedral::calc_force_invgrads()
cvm::real const fact4 = d34 * std::sqrt(1.0 - dot4 * dot4); cvm::real const fact4 = d34 * std::sqrt(1.0 - dot4 * dot4);
group1->read_total_forces(); group1->read_total_forces();
if ( b_1site_force ) { if (is_enabled(f_cvc_one_site_total_force)) {
// This is only measuring the force on group 1 // This is only measuring the force on group 1
ft.real_value = PI/180.0 * fact1 * (cross1 * group1->total_force()); ft.real_value = PI/180.0 * fact1 * (cross1 * group1->total_force());
} else { } else {

148
lib/colvars/colvarcomp_coordnums.cpp
View File

@ -338,3 +338,151 @@ void colvar::selfcoordnum::apply_force(colvarvalue const &force)
} }
} }
// groupcoordnum member functions
colvar::groupcoordnum::groupcoordnum(std::string const &conf)
: distance(conf), b_anisotropic(false)
{
function_type = "groupcoordnum";
x.type(colvarvalue::type_scalar);
// group1 and group2 are already initialized by distance()
if (group1->b_dummy || group2->b_dummy)
cvm::fatal_error("Error: neither group can be a dummy atom\n");
bool const b_scale = get_keyval(conf, "cutoff", r0,
cvm::real(4.0 * cvm::unit_angstrom()));
if (get_keyval(conf, "cutoff3", r0_vec,
cvm::rvector(4.0, 4.0, 4.0), parse_silent)) {
if (b_scale)
cvm::fatal_error("Error: cannot specify \"scale\" and "
"\"scale3\" at the same time.\n");
b_anisotropic = true;
// remove meaningless negative signs
if (r0_vec.x < 0.0) r0_vec.x *= -1.0;
if (r0_vec.y < 0.0) r0_vec.y *= -1.0;
if (r0_vec.z < 0.0) r0_vec.z *= -1.0;
}
get_keyval(conf, "expNumer", en, int(6) );
get_keyval(conf, "expDenom", ed, int(12));
if ( (en%2) || (ed%2) ) {
cvm::fatal_error("Error: odd exponents provided, can only use even ones.\n");
}
}
colvar::groupcoordnum::groupcoordnum()
: b_anisotropic(false)
{
function_type = "groupcoordnum";
x.type(colvarvalue::type_scalar);
}
template<bool calculate_gradients>
cvm::real colvar::groupcoordnum::switching_function(cvm::real const &r0,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::real const l2 = diff.norm2()/(r0*r0);
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx = (2.0/(r0*r0))*diff;
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
#if 0 // AMG: I don't think there's any reason to support anisotropic,
// and I don't have those flags below in calc_value, but
// if I need them, I'll also need to uncomment this method
template<bool calculate_gradients>
cvm::real colvar::groupcoordnum::switching_function(cvm::rvector const &r0_vec,
int const &en,
int const &ed,
cvm::atom &A1,
cvm::atom &A2)
{
cvm::rvector const diff = cvm::position_distance(A1.pos, A2.pos);
cvm::rvector const scal_diff(diff.x/r0_vec.x, diff.y/r0_vec.y, diff.z/r0_vec.z);
cvm::real const l2 = scal_diff.norm2();
// Assume en and ed are even integers, and avoid sqrt in the following
int const en2 = en/2;
int const ed2 = ed/2;
cvm::real const xn = std::pow(l2, en2);
cvm::real const xd = std::pow(l2, ed2);
cvm::real const func = (1.0-xn)/(1.0-xd);
if (calculate_gradients) {
cvm::real const dFdl2 = (1.0/(1.0-xd))*(en2*(xn/l2) - func*ed2*(xd/l2))*(-1.0);
cvm::rvector const dl2dx((2.0/(r0_vec.x*r0_vec.x))*diff.x,
(2.0/(r0_vec.y*r0_vec.y))*diff.y,
(2.0/(r0_vec.z*r0_vec.z))*diff.z);
A1.grad += (-1.0)*dFdl2*dl2dx;
A2.grad += dFdl2*dl2dx;
}
return func;
}
#endif
void colvar::groupcoordnum::calc_value()
{
// create fake atoms to hold the com coordinates
cvm::atom group1_com_atom;
cvm::atom group2_com_atom;
group1_com_atom.pos = group1->center_of_mass();
group2_com_atom.pos = group2->center_of_mass();
x.real_value = coordnum::switching_function<false>(r0, en, ed,
group1_com_atom, group2_com_atom);
}
void colvar::groupcoordnum::calc_gradients()
{
cvm::atom group1_com_atom;
cvm::atom group2_com_atom;
group1_com_atom.pos = group1->center_of_mass();
group2_com_atom.pos = group2->center_of_mass();
coordnum::switching_function<true>(r0, en, ed, group1_com_atom, group2_com_atom);
group1->set_weighted_gradient(group1_com_atom.grad);
group2->set_weighted_gradient(group2_com_atom.grad);
}
void colvar::groupcoordnum::apply_force(colvarvalue const &force)
{
if (!group1->noforce)
group1->apply_colvar_force(force.real_value);
if (!group2->noforce)
group2->apply_colvar_force(force.real_value);
}

28
lib/colvars/colvarcomp_distances.cpp
View File

@ -18,14 +18,14 @@ colvar::distance::distance(std::string const &conf)
provide(f_cvc_Jacobian); provide(f_cvc_Jacobian);
provide(f_cvc_com_based); provide(f_cvc_com_based);
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) { if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log("Computing distance using absolute positions (not minimal-image)"); cvm::log("Computing distance using absolute positions (not minimal-image)");
} }
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing total force on group 1 only"); init_total_force_params(conf);
}
group1 = parse_group(conf, "group1");
group2 = parse_group(conf, "group2");
x.type(colvarvalue::type_scalar); x.type(colvarvalue::type_scalar);
} }
@ -38,7 +38,6 @@ colvar::distance::distance()
provide(f_cvc_inv_gradient); provide(f_cvc_inv_gradient);
provide(f_cvc_Jacobian); provide(f_cvc_Jacobian);
provide(f_cvc_com_based); provide(f_cvc_com_based);
b_1site_force = false;
b_no_PBC = false; b_no_PBC = false;
x.type(colvarvalue::type_scalar); x.type(colvarvalue::type_scalar);
} }
@ -67,7 +66,7 @@ void colvar::distance::calc_gradients()
void colvar::distance::calc_force_invgrads() void colvar::distance::calc_force_invgrads()
{ {
group1->read_total_forces(); group1->read_total_forces();
if ( b_1site_force ) { if (is_enabled(f_cvc_one_site_total_force)) {
ft.real_value = -1.0 * (group1->total_force() * dist_v.unit()); ft.real_value = -1.0 * (group1->total_force() * dist_v.unit());
} else { } else {
group2->read_total_forces(); group2->read_total_forces();
@ -97,6 +96,7 @@ colvar::distance_vec::distance_vec(std::string const &conf)
: distance(conf) : distance(conf)
{ {
function_type = "distance_vec"; function_type = "distance_vec";
provide(f_cvc_com_based);
x.type(colvarvalue::type_3vector); x.type(colvarvalue::type_3vector);
} }
@ -105,6 +105,7 @@ colvar::distance_vec::distance_vec()
: distance() : distance()
{ {
function_type = "distance_vec"; function_type = "distance_vec";
provide(f_cvc_com_based);
x.type(colvarvalue::type_3vector); x.type(colvarvalue::type_3vector);
} }
@ -185,9 +186,9 @@ colvar::distance_z::distance_z(std::string const &conf)
if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) { if (get_keyval(conf, "forceNoPBC", b_no_PBC, false)) {
cvm::log("Computing distance using absolute positions (not minimal-image)"); cvm::log("Computing distance using absolute positions (not minimal-image)");
} }
if (get_keyval(conf, "oneSiteSystemForce", b_1site_force, false)) {
cvm::log("Computing total force on group \"main\" only"); init_total_force_params(conf);
}
} }
colvar::distance_z::distance_z() colvar::distance_z::distance_z()
@ -251,7 +252,7 @@ void colvar::distance_z::calc_force_invgrads()
{ {
main->read_total_forces(); main->read_total_forces();
if (fixed_axis && !b_1site_force) { if (fixed_axis && !is_enabled(f_cvc_one_site_total_force)) {
ref1->read_total_forces(); ref1->read_total_forces();
ft.real_value = 0.5 * ((main->total_force() - ref1->total_force()) * axis); ft.real_value = 0.5 * ((main->total_force() - ref1->total_force()) * axis);
} else { } else {
@ -351,7 +352,7 @@ void colvar::distance_xy::calc_force_invgrads()
{ {
main->read_total_forces(); main->read_total_forces();
if (fixed_axis && !b_1site_force) { if (fixed_axis && !is_enabled(f_cvc_one_site_total_force)) {
ref1->read_total_forces(); ref1->read_total_forces();
ft.real_value = 0.5 / x.real_value * ((main->total_force() - ref1->total_force()) * dist_v_ortho); ft.real_value = 0.5 / x.real_value * ((main->total_force() - ref1->total_force()) * dist_v_ortho);
} else { } else {
@ -382,6 +383,7 @@ colvar::distance_dir::distance_dir(std::string const &conf)
: distance(conf) : distance(conf)
{ {
function_type = "distance_dir"; function_type = "distance_dir";
provide(f_cvc_com_based);
x.type(colvarvalue::type_unit3vector); x.type(colvarvalue::type_unit3vector);
} }
@ -390,6 +392,7 @@ colvar::distance_dir::distance_dir()
: distance() : distance()
{ {
function_type = "distance_dir"; function_type = "distance_dir";
provide(f_cvc_com_based);
x.type(colvarvalue::type_unit3vector); x.type(colvarvalue::type_unit3vector);
} }
@ -461,7 +464,6 @@ colvar::distance_inv::distance_inv()
{ {
function_type = "distance_inv"; function_type = "distance_inv";
exponent = 6; exponent = 6;
b_1site_force = false;
x.type(colvarvalue::type_scalar); x.type(colvarvalue::type_scalar);
} }

8
lib/colvars/colvardeps.cpp
View File

@ -293,6 +293,9 @@ void colvardeps::init_cv_requires() {
f_description(f_cv_output_total_force, "output total force"); f_description(f_cv_output_total_force, "output total force");
f_req_self(f_cv_output_total_force, f_cv_total_force); f_req_self(f_cv_output_total_force, f_cv_total_force);
f_description(f_cv_subtract_applied_force, "subtract applied force from total force");
f_req_self(f_cv_subtract_applied_force, f_cv_total_force);
f_description(f_cv_lower_boundary, "lower boundary"); f_description(f_cv_lower_boundary, "lower boundary");
f_req_self(f_cv_lower_boundary, f_cv_scalar); f_req_self(f_cv_lower_boundary, f_cv_scalar);
@ -376,6 +379,11 @@ void colvardeps::init_cvc_requires() {
f_description(f_cvc_com_based, "depends on group centers of mass"); f_description(f_cvc_com_based, "depends on group centers of mass");
// Compute total force on first site only to avoid unwanted
// coupling to other colvars (see e.g. Ciccotti et al., 2005)
f_description(f_cvc_one_site_total_force, "compute total collective force only from one group center");
f_req_self(f_cvc_one_site_total_force, f_cvc_com_based);
f_description(f_cvc_scalable, "scalable calculation"); f_description(f_cvc_scalable, "scalable calculation");
f_req_self(f_cvc_scalable, f_cvc_scalable_com); f_req_self(f_cvc_scalable, f_cvc_scalable_com);

3
lib/colvars/colvardeps.h
View File

@ -176,6 +176,8 @@ public:
f_cv_total_force, f_cv_total_force,
/// \brief Calculate total force from atomic forces /// \brief Calculate total force from atomic forces
f_cv_total_force_calc, f_cv_total_force_calc,
/// \brief Subtract the applied force from the total force
f_cv_subtract_applied_force,
/// \brief Estimate Jacobian derivative /// \brief Estimate Jacobian derivative
f_cv_Jacobian, f_cv_Jacobian,
/// \brief Do not report the Jacobian force as part of the total force /// \brief Do not report the Jacobian force as part of the total force
@ -236,6 +238,7 @@ public:
/// \brief If enabled, calc_gradients() will call debug_gradients() for every group needed /// \brief If enabled, calc_gradients() will call debug_gradients() for every group needed
f_cvc_debug_gradient, f_cvc_debug_gradient,
f_cvc_Jacobian, f_cvc_Jacobian,
f_cvc_one_site_total_force,
f_cvc_com_based, f_cvc_com_based,
f_cvc_scalable, f_cvc_scalable,
f_cvc_scalable_com, f_cvc_scalable_com,

157
lib/colvars/colvargrid.h
View File

@ -382,8 +382,8 @@ public:
inline int current_bin_scalar(int const i, int const iv) const inline int current_bin_scalar(int const i, int const iv) const
{ {
return value_to_bin_scalar(actual_value[i] ? return value_to_bin_scalar(actual_value[i] ?
cv[i]->actual_value().vector1d_value[iv] : cv[i]->actual_value().vector1d_value[iv] :
cv[i]->value().vector1d_value[iv], i); cv[i]->value().vector1d_value[iv], i);
} }
/// \brief Use the lower boundary and the width to report which bin /// \brief Use the lower boundary and the width to report which bin
@ -395,8 +395,8 @@ public:
/// \brief Same as the standard version, but uses another grid definition /// \brief Same as the standard version, but uses another grid definition
inline int value_to_bin_scalar(colvarvalue const &value, inline int value_to_bin_scalar(colvarvalue const &value,
colvarvalue const &new_offset, colvarvalue const &new_offset,
cvm::real const &new_width) const cvm::real const &new_width) const
{ {
return (int) std::floor( (value.real_value - new_offset.real_value) / new_width ); return (int) std::floor( (value.real_value - new_offset.real_value) / new_width );
} }
@ -410,22 +410,22 @@ public:
/// \brief Same as the standard version, but uses different parameters /// \brief Same as the standard version, but uses different parameters
inline colvarvalue bin_to_value_scalar(int const &i_bin, inline colvarvalue bin_to_value_scalar(int const &i_bin,
colvarvalue const &new_offset, colvarvalue const &new_offset,
cvm::real const &new_width) const cvm::real const &new_width) const
{ {
return new_offset.real_value + new_width * (0.5 + i_bin); return new_offset.real_value + new_width * (0.5 + i_bin);
} }
/// Set the value at the point with index ix /// Set the value at the point with index ix
inline void set_value(std::vector<int> const &ix, inline void set_value(std::vector<int> const &ix,
T const &t, T const &t,
size_t const &imult = 0) size_t const &imult = 0)
{ {
data[this->address(ix)+imult] = t; data[this->address(ix)+imult] = t;
has_data = true; has_data = true;
} }
/// \brief Get the change from this to other_grid /// \brief Get the change from this to other_grid
/// and store the result in this. /// and store the result in this.
/// this_grid := other_grid - this_grid /// this_grid := other_grid - this_grid
/// Grids must have the same dimensions. /// Grids must have the same dimensions.
@ -434,13 +434,13 @@ public:
if (other_grid.multiplicity() != this->multiplicity()) { if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error("Error: trying to subtract two grids with " cvm::error("Error: trying to subtract two grids with "
"different multiplicity.\n"); "different multiplicity.\n");
return; return;
} }
if (other_grid.data.size() != this->data.size()) { if (other_grid.data.size() != this->data.size()) {
cvm::error("Error: trying to subtract two grids with " cvm::error("Error: trying to subtract two grids with "
"different size.\n"); "different size.\n");
return; return;
} }
@ -457,13 +457,13 @@ public:
{ {
if (other_grid.multiplicity() != this->multiplicity()) { if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error("Error: trying to copy two grids with " cvm::error("Error: trying to copy two grids with "
"different multiplicity.\n"); "different multiplicity.\n");
return; return;
} }
if (other_grid.data.size() != this->data.size()) { if (other_grid.data.size() != this->data.size()) {
cvm::error("Error: trying to copy two grids with " cvm::error("Error: trying to copy two grids with "
"different size.\n"); "different size.\n");
return; return;
} }
@ -493,7 +493,7 @@ public:
/// \brief Get the binned value indexed by ix, or the first of them /// \brief Get the binned value indexed by ix, or the first of them
/// if the multiplicity is larger than 1 /// if the multiplicity is larger than 1
inline T const & value(std::vector<int> const &ix, inline T const & value(std::vector<int> const &ix,
size_t const &imult = 0) const size_t const &imult = 0) const
{ {
return data[this->address(ix) + imult]; return data[this->address(ix) + imult];
} }
@ -541,7 +541,7 @@ public:
/// boundaries; a negative number is returned if the given point is /// boundaries; a negative number is returned if the given point is
/// off-grid /// off-grid
inline cvm::real bin_distance_from_boundaries(std::vector<colvarvalue> const &values, inline cvm::real bin_distance_from_boundaries(std::vector<colvarvalue> const &values,
bool skip_hard_boundaries = false) bool skip_hard_boundaries = false)
{ {
cvm::real minimum = 1.0E+16; cvm::real minimum = 1.0E+16;
for (size_t i = 0; i < nd; i++) { for (size_t i = 0; i < nd; i++) {
@ -574,7 +574,7 @@ public:
{ {
if (other_grid.multiplicity() != this->multiplicity()) { if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error("Error: trying to merge two grids with values of " cvm::error("Error: trying to merge two grids with values of "
"different multiplicity.\n"); "different multiplicity.\n");
return; return;
} }
@ -593,8 +593,8 @@ public:
for (size_t i = 0; i < nd; i++) { for (size_t i = 0; i < nd; i++) {
oix[i] = oix[i] =
value_to_bin_scalar(bin_to_value_scalar(ix[i], gb[i], gw[i]), value_to_bin_scalar(bin_to_value_scalar(ix[i], gb[i], gw[i]),
ogb[i], ogb[i],
ogw[i]); ogw[i]);
} }
if (! other_grid.index_ok(oix)) { if (! other_grid.index_ok(oix)) {
@ -614,11 +614,11 @@ public:
/// \brief Add data from another grid of the same type, AND /// \brief Add data from another grid of the same type, AND
/// identical definition (boundaries, widths) /// identical definition (boundaries, widths)
void add_grid(colvar_grid<T> const &other_grid, void add_grid(colvar_grid<T> const &other_grid,
cvm::real scale_factor = 1.0) cvm::real scale_factor = 1.0)
{ {
if (other_grid.multiplicity() != this->multiplicity()) { if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error("Error: trying to sum togetehr two grids with values of " cvm::error("Error: trying to sum togetehr two grids with values of "
"different multiplicity.\n"); "different multiplicity.\n");
return; return;
} }
if (scale_factor != 1.0) if (scale_factor != 1.0)
@ -636,7 +636,7 @@ public:
/// \brief Return the value suitable for output purposes (so that it /// \brief Return the value suitable for output purposes (so that it
/// may be rescaled or manipulated without changing it permanently) /// may be rescaled or manipulated without changing it permanently)
virtual inline T value_output(std::vector<int> const &ix, virtual inline T value_output(std::vector<int> const &ix,
size_t const &imult = 0) size_t const &imult = 0)
{ {
return value(ix, imult); return value(ix, imult);
} }
@ -645,9 +645,9 @@ public:
/// into the internal representation (the two may be different, /// into the internal representation (the two may be different,
/// e.g. when using colvar_grid_count) /// e.g. when using colvar_grid_count)
virtual inline void value_input(std::vector<int> const &ix, virtual inline void value_input(std::vector<int> const &ix,
T const &t, T const &t,
size_t const &imult = 0, size_t const &imult = 0,
bool add = false) bool add = false)
{ {
if ( add ) if ( add )
data[address(ix) + imult] += t; data[address(ix) + imult] += t;
@ -737,7 +737,8 @@ public:
} }
/// Read a grid definition from a config string /// Read a grid definition from a config string
int parse_params(std::string const &conf) int parse_params(std::string const &conf,
colvarparse::Parse_Mode const parse_mode = colvarparse::parse_normal)
{ {
if (cvm::debug()) cvm::log("Reading grid configuration from string.\n"); if (cvm::debug()) cvm::log("Reading grid configuration from string.\n");
@ -746,30 +747,33 @@ public:
{ {
size_t nd_in = 0; size_t nd_in = 0;
// this is only used in state files
colvarparse::get_keyval(conf, "n_colvars", nd_in, nd, colvarparse::parse_silent); colvarparse::get_keyval(conf, "n_colvars", nd_in, nd, colvarparse::parse_silent);
if (nd_in != nd) { if (nd_in != nd) {
cvm::error("Error: trying to read data for a grid " cvm::error("Error: trying to read data for a grid "
"that contains a different number of colvars ("+ "that contains a different number of colvars ("+
cvm::to_str(nd_in)+") than the grid defined " cvm::to_str(nd_in)+") than the grid defined "
"in the configuration file("+cvm::to_str(nd)+ "in the configuration file("+cvm::to_str(nd)+
").\n"); ").\n");
return COLVARS_ERROR; return COLVARS_ERROR;
} }
} }
// underscore keywords are used in state file
colvarparse::get_keyval(conf, "lower_boundaries", colvarparse::get_keyval(conf, "lower_boundaries",
lower_boundaries, lower_boundaries, colvarparse::parse_silent); lower_boundaries, lower_boundaries, colvarparse::parse_silent);
colvarparse::get_keyval(conf, "upper_boundaries", colvarparse::get_keyval(conf, "upper_boundaries",
upper_boundaries, upper_boundaries, colvarparse::parse_silent); upper_boundaries, upper_boundaries, colvarparse::parse_silent);
// support also camel case // camel case keywords are used in config file
colvarparse::get_keyval(conf, "lowerBoundaries", colvarparse::get_keyval(conf, "lowerBoundaries",
lower_boundaries, lower_boundaries, colvarparse::parse_silent); lower_boundaries, lower_boundaries, parse_mode);
colvarparse::get_keyval(conf, "upperBoundaries", colvarparse::get_keyval(conf, "upperBoundaries",
upper_boundaries, upper_boundaries, colvarparse::parse_silent); upper_boundaries, upper_boundaries, parse_mode);
colvarparse::get_keyval(conf, "widths", widths, widths, colvarparse::parse_silent); colvarparse::get_keyval(conf, "widths", widths, widths, parse_mode);
// only used in state file
colvarparse::get_keyval(conf, "sizes", nx, nx, colvarparse::parse_silent); colvarparse::get_keyval(conf, "sizes", nx, nx, colvarparse::parse_silent);
if (nd < lower_boundaries.size()) nd = lower_boundaries.size(); if (nd < lower_boundaries.size()) nd = lower_boundaries.size();
@ -808,13 +812,13 @@ public:
{ {
for (size_t i = 0; i < nd; i++) { for (size_t i = 0; i < nd; i++) {
if ( (std::sqrt(cv[i]->dist2(cv[i]->lower_boundary, if ( (std::sqrt(cv[i]->dist2(cv[i]->lower_boundary,
lower_boundaries[i])) > 1.0E-10) || lower_boundaries[i])) > 1.0E-10) ||
(std::sqrt(cv[i]->dist2(cv[i]->upper_boundary, (std::sqrt(cv[i]->dist2(cv[i]->upper_boundary,
upper_boundaries[i])) > 1.0E-10) || upper_boundaries[i])) > 1.0E-10) ||
(std::sqrt(cv[i]->dist2(cv[i]->width, (std::sqrt(cv[i]->dist2(cv[i]->width,
widths[i])) > 1.0E-10) ) { widths[i])) > 1.0E-10) ) {
cvm::error("Error: restart information for a grid is " cvm::error("Error: restart information for a grid is "
"inconsistent with that of its colvars.\n"); "inconsistent with that of its colvars.\n");
return; return;
} }
} }
@ -830,19 +834,19 @@ public:
// matter: boundaries should be EXACTLY the same (otherwise, // matter: boundaries should be EXACTLY the same (otherwise,
// map_grid() should be used) // map_grid() should be used)
if ( (std::fabs(other_grid.lower_boundaries[i] - if ( (std::fabs(other_grid.lower_boundaries[i] -
lower_boundaries[i]) > 1.0E-10) || lower_boundaries[i]) > 1.0E-10) ||
(std::fabs(other_grid.upper_boundaries[i] - (std::fabs(other_grid.upper_boundaries[i] -
upper_boundaries[i]) > 1.0E-10) || upper_boundaries[i]) > 1.0E-10) ||
(std::fabs(other_grid.widths[i] - (std::fabs(other_grid.widths[i] -
widths[i]) > 1.0E-10) || widths[i]) > 1.0E-10) ||
(data.size() != other_grid.data.size()) ) { (data.size() != other_grid.data.size()) ) {
cvm::error("Error: inconsistency between " cvm::error("Error: inconsistency between "
"two grids that are supposed to be equal, " "two grids that are supposed to be equal, "
"aside from the data stored.\n"); "aside from the data stored.\n");
return; return;
}
} }
} }
}
/// \brief Read grid entry in restart file /// \brief Read grid entry in restart file
@ -853,7 +857,7 @@ public:
if ((is >> key) && (key == std::string("grid_parameters"))) { if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg); is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf); is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf); parse_params(conf, colvarparse::parse_silent);
} else { } else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n"); cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg); is.seekg(start_pos, std::ios::beg);
@ -871,11 +875,11 @@ public:
} }
/// \brief Write the grid data without labels, as they are /// \brief Write the grid data without labels, as they are
/// represented in memory /// represented in memory
/// \param buf_size Number of values per line /// \param buf_size Number of values per line
std::ostream & write_raw(std::ostream &os, std::ostream & write_raw(std::ostream &os,
size_t const buf_size = 3) size_t const buf_size = 3)
{ {
std::streamsize const w = os.width(); std::streamsize const w = os.width();
std::streamsize const p = os.precision(); std::streamsize const p = os.precision();
@ -935,10 +939,10 @@ public:
os << std::setw(2) << "# " << nd << "\n"; os << std::setw(2) << "# " << nd << "\n";
for (size_t i = 0; i < nd; i++) { for (size_t i = 0; i < nd; i++) {
os << "# " os << "# "
<< std::setw(10) << lower_boundaries[i] << std::setw(10) << lower_boundaries[i]
<< std::setw(10) << widths[i] << std::setw(10) << widths[i]
<< std::setw(10) << nx[i] << " " << std::setw(10) << nx[i] << " "
<< periodic[i] << "\n"; << periodic[i] << "\n";
} }
@ -951,14 +955,14 @@ public:
for (size_t i = 0; i < nd; i++) { for (size_t i = 0; i < nd; i++) {
os << " " os << " "
<< std::setw(w) << std::setprecision(p) << std::setw(w) << std::setprecision(p)
<< bin_to_value_scalar(ix[i], i); << bin_to_value_scalar(ix[i], i);
} }
os << " "; os << " ";
for (size_t imult = 0; imult < mult; imult++) { for (size_t imult = 0; imult < mult; imult++) {
os << " " os << " "
<< std::setw(w) << std::setprecision(p) << std::setw(w) << std::setprecision(p)
<< value_output(ix, imult); << value_output(ix, imult);
} }
os << "\n"; os << "\n";
} }
@ -986,7 +990,7 @@ public:
if ( !(is >> hash) || (hash != "#") ) { if ( !(is >> hash) || (hash != "#") ) {
cvm::error("Error reading grid at position "+ cvm::error("Error reading grid at position "+
cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n"); cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n");
return is; return is;
} }
@ -1008,7 +1012,7 @@ public:
for (size_t i = 0; i < nd; i++ ) { for (size_t i = 0; i < nd; i++ ) {
if ( !(is >> hash) || (hash != "#") ) { if ( !(is >> hash) || (hash != "#") ) {
cvm::error("Error reading grid at position "+ cvm::error("Error reading grid at position "+
cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n"); cvm::to_str(is.tellg())+" in stream(read \"" + hash + "\")\n");
return is; return is;
} }
@ -1016,10 +1020,10 @@ public:
if ( (std::fabs(lower - lower_boundaries[i].real_value) > 1.0e-10) || if ( (std::fabs(lower - lower_boundaries[i].real_value) > 1.0e-10) ||
(std::fabs(width - widths[i] ) > 1.0e-10) || (std::fabs(width - widths[i] ) > 1.0e-10) ||
(nx_read[i] != nx[i]) ) { (nx_read[i] != nx[i]) ) {
cvm::log("Warning: reading from different grid definition (colvar " cvm::log("Warning: reading from different grid definition (colvar "
+ cvm::to_str(i+1) + "); remapping data on new grid.\n"); + cvm::to_str(i+1) + "); remapping data on new grid.\n");
remap = true; remap = true;
} }
} }
@ -1063,7 +1067,6 @@ public:
/// \brief Write the grid data without labels, as they are /// \brief Write the grid data without labels, as they are
/// represented in memory /// represented in memory
/// \param buf_size Number of values per line
std::ostream & write_opendx(std::ostream &os) std::ostream & write_opendx(std::ostream &os)
{ {
// write the header // write the header
@ -1122,11 +1125,11 @@ public:
/// Constructor /// Constructor
colvar_grid_count(std::vector<int> const &nx_i, colvar_grid_count(std::vector<int> const &nx_i,
size_t const &def_count = 0); size_t const &def_count = 0);
/// Constructor from a vector of colvars /// Constructor from a vector of colvars
colvar_grid_count(std::vector<colvar *> &colvars, colvar_grid_count(std::vector<colvar *> &colvars,
size_t const &def_count = 0); size_t const &def_count = 0);
/// Increment the counter at given position /// Increment the counter at given position
inline void incr_count(std::vector<int> const &ix) inline void incr_count(std::vector<int> const &ix)
@ -1136,7 +1139,7 @@ public:
/// \brief Get the binned count indexed by ix from the newly read data /// \brief Get the binned count indexed by ix from the newly read data
inline size_t const & new_count(std::vector<int> const &ix, inline size_t const & new_count(std::vector<int> const &ix,
size_t const &imult = 0) size_t const &imult = 0)
{ {
return new_data[address(ix) + imult]; return new_data[address(ix) + imult];
} }
@ -1145,9 +1148,9 @@ public:
/// into the internal representation (it may have been rescaled or /// into the internal representation (it may have been rescaled or
/// manipulated) /// manipulated)
virtual inline void value_input(std::vector<int> const &ix, virtual inline void value_input(std::vector<int> const &ix,
size_t const &t, size_t const &t,
size_t const &imult = 0, size_t const &imult = 0,
bool add = false) bool add = false)
{ {
if (add) { if (add) {
data[address(ix)] += t; data[address(ix)] += t;
@ -1164,7 +1167,7 @@ public:
/// \brief Return the log-gradient from finite differences /// \brief Return the log-gradient from finite differences
/// on the *same* grid for dimension n /// on the *same* grid for dimension n
inline const cvm::real log_gradient_finite_diff( const std::vector<int> &ix0, inline const cvm::real log_gradient_finite_diff( const std::vector<int> &ix0,
int n = 0) int n = 0)
{ {
cvm::real A0, A1; cvm::real A0, A1;
std::vector<int> ix; std::vector<int> ix;
@ -1377,7 +1380,7 @@ public:
/// \brief Return the value of the function at ix divided by its /// \brief Return the value of the function at ix divided by its
/// number of samples (if the count grid is defined) /// number of samples (if the count grid is defined)
virtual inline cvm::real value_output(std::vector<int> const &ix, virtual inline cvm::real value_output(std::vector<int> const &ix,
size_t const &imult = 0) size_t const &imult = 0)
{ {
if (samples) if (samples)
return (samples->value(ix) > 0) ? return (samples->value(ix) > 0) ?
@ -1391,9 +1394,9 @@ public:
/// into the internal representation (it may have been rescaled or /// into the internal representation (it may have been rescaled or
/// manipulated) /// manipulated)
virtual inline void value_input(std::vector<int> const &ix, virtual inline void value_input(std::vector<int> const &ix,
cvm::real const &new_value, cvm::real const &new_value,
size_t const &imult = 0, size_t const &imult = 0,
bool add = false) bool add = false)
{ {
if (add) { if (add) {
if (samples) if (samples)

3
lib/colvars/colvarmodule.cpp
View File

@ -293,6 +293,9 @@ int colvarmodule::parse_biases(std::string const &conf)
/// initialize histograms /// initialize histograms
parse_biases_type<colvarbias_histogram>(conf, "histogram", n_histo_biases); parse_biases_type<colvarbias_histogram>(conf, "histogram", n_histo_biases);
/// initialize histogram restraints
parse_biases_type<colvarbias_restraint_histogram>(conf, "histogramRestraint", n_rest_biases);
/// initialize linear restraints /// initialize linear restraints
parse_biases_type<colvarbias_restraint_linear>(conf, "linear", n_rest_biases); parse_biases_type<colvarbias_restraint_linear>(conf, "linear", n_rest_biases);

2
lib/colvars/colvarmodule.h
View File

@ -4,7 +4,7 @@
#define COLVARMODULE_H #define COLVARMODULE_H
#ifndef COLVARS_VERSION #ifndef COLVARS_VERSION
#define COLVARS_VERSION "2016-09-14" #define COLVARS_VERSION "2016-09-30"
#endif #endif
#ifndef COLVARS_DEBUG #ifndef COLVARS_DEBUG

8
lib/colvars/colvarscript.cpp
View File

@ -243,11 +243,17 @@ int colvarscript::proc_colvar(int argc, char const *argv[]) {
} }
if (subcmd == "getappliedforce") { if (subcmd == "getappliedforce") {
result = (cv->bias_force()).to_simple_string(); result = (cv->applied_force()).to_simple_string();
return COLVARS_OK; return COLVARS_OK;
} }
if (subcmd == "getsystemforce") { if (subcmd == "getsystemforce") {
// TODO warning here
result = (cv->total_force()).to_simple_string();
return COLVARS_OK;
}
if (subcmd == "gettotalforce") {
result = (cv->total_force()).to_simple_string(); result = (cv->total_force()).to_simple_string();
return COLVARS_OK; return COLVARS_OK;
} }

44
lib/colvars/colvartypes.h
View File

@ -57,6 +57,12 @@ public:
} }
} }
/// Return a reference to the data
inline std::vector<T> &data_array()
{
return data;
}
inline ~vector1d() inline ~vector1d()
{ {
data.clear(); data.clear();
@ -203,6 +209,16 @@ public:
return std::sqrt(this->norm2()); return std::sqrt(this->norm2());
} }
inline cvm::real sum() const
{
cvm::real result = 0.0;
size_t i;
for (i = 0; i < this->size(); i++) {
result += (*this)[i];
}
return result;
}
/// Slicing /// Slicing
inline vector1d<T> const slice(size_t const i1, size_t const i2) const inline vector1d<T> const slice(size_t const i1, size_t const i2) const
{ {
@ -295,11 +311,23 @@ public:
{ {
std::stringstream stream(s); std::stringstream stream(s);
size_t i = 0; size_t i = 0;
while ((stream >> (*this)[i]) && (i < this->size())) { if (this->size()) {
i++; while ((stream >> (*this)[i]) && (i < this->size())) {
} i++;
if (i < this->size()) { }
return COLVARS_ERROR; if (i < this->size()) {
return COLVARS_ERROR;
}
} else {
T input;
while (stream >> input) {
if ((i % 100) == 0) {
data.reserve(data.size()+100);
}
data.resize(data.size()+1);
data[i] = input;
i++;
}
} }
return COLVARS_OK; return COLVARS_OK;
} }
@ -434,6 +462,12 @@ public:
this->clear(); this->clear();
} }
/// Return a reference to the data
inline std::vector<T> &data_array()
{
return data;
}
inline row & operator [] (size_t const i) inline row & operator [] (size_t const i)
{ {
return rows[i]; return rows[i];