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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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157
lib/colvars/colvargrid.h
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@ -382,8 +382,8 @@ public:
inline int current_bin_scalar(int const i, int const iv) const
{
return value_to_bin_scalar(actual_value[i] ?
cv[i]->actual_value().vector1d_value[iv] :
cv[i]->value().vector1d_value[iv], i);
cv[i]->actual_value().vector1d_value[iv] :
cv[i]->value().vector1d_value[iv], i);
}
/// \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
inline int value_to_bin_scalar(colvarvalue const &value,
colvarvalue const &new_offset,
cvm::real const &new_width) const
colvarvalue const &new_offset,
cvm::real const &new_width) const
{
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
inline colvarvalue bin_to_value_scalar(int const &i_bin,
colvarvalue const &new_offset,
cvm::real const &new_width) const
colvarvalue const &new_offset,
cvm::real const &new_width) const
{
return new_offset.real_value + new_width * (0.5 + i_bin);
}
/// Set the value at the point with index ix
inline void set_value(std::vector<int> const &ix,
T const &t,
size_t const &imult = 0)
T const &t,
size_t const &imult = 0)
{
data[this->address(ix)+imult] = t;
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.
/// this_grid := other_grid - this_grid
/// Grids must have the same dimensions.
@ -434,13 +434,13 @@ public:
if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error("Error: trying to subtract two grids with "
"different multiplicity.\n");
"different multiplicity.\n");
return;
}
if (other_grid.data.size() != this->data.size()) {
cvm::error("Error: trying to subtract two grids with "
"different size.\n");
"different size.\n");
return;
}
@ -457,13 +457,13 @@ public:
{
if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error("Error: trying to copy two grids with "
"different multiplicity.\n");
"different multiplicity.\n");
return;
}
if (other_grid.data.size() != this->data.size()) {
cvm::error("Error: trying to copy two grids with "
"different size.\n");
"different size.\n");
return;
}
@ -493,7 +493,7 @@ public:
/// \brief Get the binned value indexed by ix, or the first of them
/// if the multiplicity is larger than 1
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];
}
@ -541,7 +541,7 @@ public:
/// boundaries; a negative number is returned if the given point is
/// off-grid
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;
for (size_t i = 0; i < nd; i++) {
@ -574,7 +574,7 @@ public:
{
if (other_grid.multiplicity() != this->multiplicity()) {
cvm::error("Error: trying to merge two grids with values of "
"different multiplicity.\n");
"different multiplicity.\n");
return;
}
@ -593,8 +593,8 @@ public:
for (size_t i = 0; i < nd; i++) {
oix[i] =
value_to_bin_scalar(bin_to_value_scalar(ix[i], gb[i], gw[i]),
ogb[i],
ogw[i]);
ogb[i],
ogw[i]);
}
if (! other_grid.index_ok(oix)) {
@ -614,11 +614,11 @@ public:
/// \brief Add data from another grid of the same type, AND
/// identical definition (boundaries, widths)
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()) {
cvm::error("Error: trying to sum togetehr two grids with values of "
"different multiplicity.\n");
"different multiplicity.\n");
return;
}
if (scale_factor != 1.0)
@ -636,7 +636,7 @@ public:
/// \brief Return the value suitable for output purposes (so that it
/// may be rescaled or manipulated without changing it permanently)
virtual inline T value_output(std::vector<int> const &ix,
size_t const &imult = 0)
size_t const &imult = 0)
{
return value(ix, imult);
}
@ -645,9 +645,9 @@ public:
/// into the internal representation (the two may be different,
/// e.g. when using colvar_grid_count)
virtual inline void value_input(std::vector<int> const &ix,
T const &t,
size_t const &imult = 0,
bool add = false)
T const &t,
size_t const &imult = 0,
bool add = false)
{
if ( add )
data[address(ix) + imult] += t;
@ -737,7 +737,8 @@ public:
}
/// 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");
@ -746,30 +747,33 @@ public:
{
size_t nd_in = 0;
// this is only used in state files
colvarparse::get_keyval(conf, "n_colvars", nd_in, nd, colvarparse::parse_silent);
if (nd_in != nd) {
cvm::error("Error: trying to read data for a grid "
"that contains a different number of colvars ("+
cvm::to_str(nd_in)+") than the grid defined "
"in the configuration file("+cvm::to_str(nd)+
").\n");
"that contains a different number of colvars ("+
cvm::to_str(nd_in)+") than the grid defined "
"in the configuration file("+cvm::to_str(nd)+
").\n");
return COLVARS_ERROR;
}
}
// underscore keywords are used in state file
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",
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",
lower_boundaries, lower_boundaries, colvarparse::parse_silent);
lower_boundaries, lower_boundaries, parse_mode);
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);
if (nd < lower_boundaries.size()) nd = lower_boundaries.size();
@ -808,13 +812,13 @@ public:
{
for (size_t i = 0; i < nd; i++) {
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,
upper_boundaries[i])) > 1.0E-10) ||
upper_boundaries[i])) > 1.0E-10) ||
(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 "
"inconsistent with that of its colvars.\n");
"inconsistent with that of its colvars.\n");
return;
}
}
@ -830,19 +834,19 @@ public:
// matter: boundaries should be EXACTLY the same (otherwise,
// map_grid() should be used)
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] -
upper_boundaries[i]) > 1.0E-10) ||
upper_boundaries[i]) > 1.0E-10) ||
(std::fabs(other_grid.widths[i] -
widths[i]) > 1.0E-10) ||
widths[i]) > 1.0E-10) ||
(data.size() != other_grid.data.size()) ) {
cvm::error("Error: inconsistency between "
"two grids that are supposed to be equal, "
"aside from the data stored.\n");
return;
cvm::error("Error: inconsistency between "
"two grids that are supposed to be equal, "
"aside from the data stored.\n");
return;
}
}
}
}
/// \brief Read grid entry in restart file
@ -853,7 +857,7 @@ public:
if ((is >> key) && (key == std::string("grid_parameters"))) {
is.seekg(start_pos, std::ios::beg);
is >> colvarparse::read_block("grid_parameters", conf);
parse_params(conf);
parse_params(conf, colvarparse::parse_silent);
} else {
cvm::log("Grid parameters are missing in the restart file, using those from the configuration.\n");
is.seekg(start_pos, std::ios::beg);
@ -871,11 +875,11 @@ public:
}
/// \brief Write the grid data without labels, as they are
/// represented in memory
/// \param buf_size Number of values per line
/// \brief Write the grid data without labels, as they are
/// represented in memory
/// \param buf_size Number of values per line
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 p = os.precision();
@ -935,10 +939,10 @@ public:
os << std::setw(2) << "# " << nd << "\n";
for (size_t i = 0; i < nd; i++) {
os << "# "
<< std::setw(10) << lower_boundaries[i]
<< std::setw(10) << widths[i]
<< std::setw(10) << nx[i] << " "
<< periodic[i] << "\n";
<< std::setw(10) << lower_boundaries[i]
<< std::setw(10) << widths[i]
<< std::setw(10) << nx[i] << " "
<< periodic[i] << "\n";
}
@ -951,14 +955,14 @@ public:
for (size_t i = 0; i < nd; i++) {
os << " "
<< std::setw(w) << std::setprecision(p)
<< bin_to_value_scalar(ix[i], i);
<< std::setw(w) << std::setprecision(p)
<< bin_to_value_scalar(ix[i], i);
}
os << " ";
for (size_t imult = 0; imult < mult; imult++) {
os << " "
<< std::setw(w) << std::setprecision(p)
<< value_output(ix, imult);
<< std::setw(w) << std::setprecision(p)
<< value_output(ix, imult);
}
os << "\n";
}
@ -986,7 +990,7 @@ public:
if ( !(is >> hash) || (hash != "#") ) {
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;
}
@ -1008,7 +1012,7 @@ public:
for (size_t i = 0; i < nd; i++ ) {
if ( !(is >> hash) || (hash != "#") ) {
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;
}
@ -1016,10 +1020,10 @@ public:
if ( (std::fabs(lower - lower_boundaries[i].real_value) > 1.0e-10) ||
(std::fabs(width - widths[i] ) > 1.0e-10) ||
(nx_read[i] != nx[i]) ) {
(std::fabs(width - widths[i] ) > 1.0e-10) ||
(nx_read[i] != nx[i]) ) {
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;
}
}
@ -1063,7 +1067,6 @@ public:
/// \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
@ -1122,11 +1125,11 @@ public:
/// Constructor
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
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
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
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];
}
@ -1145,9 +1148,9 @@ public:
/// into the internal representation (it may have been rescaled or
/// manipulated)
virtual inline void value_input(std::vector<int> const &ix,
size_t const &t,
size_t const &imult = 0,
bool add = false)
size_t const &t,
size_t const &imult = 0,
bool add = false)
{
if (add) {
data[address(ix)] += t;
@ -1164,7 +1167,7 @@ public:
/// \brief Return the log-gradient from finite differences
/// on the *same* grid for dimension n
inline const cvm::real log_gradient_finite_diff( const std::vector<int> &ix0,
int n = 0)
int n = 0)
{
cvm::real A0, A1;
std::vector<int> ix;
@ -1377,7 +1380,7 @@ public:
/// \brief Return the value of the function at ix divided by its
/// number of samples (if the count grid is defined)
virtual inline cvm::real value_output(std::vector<int> const &ix,
size_t const &imult = 0)
size_t const &imult = 0)
{
if (samples)
return (samples->value(ix) > 0) ?
@ -1391,9 +1394,9 @@ public:
/// into the internal representation (it may have been rescaled or
/// manipulated)
virtual inline void value_input(std::vector<int> const &ix,
cvm::real const &new_value,
size_t const &imult = 0,
bool add = false)
cvm::real const &new_value,
size_t const &imult = 0,
bool add = false)
{
if (add) {
if (samples)