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Update Colvars to version 2020-02-27

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This update contains several small new features or usability improvements.
    Descriptions and authorship information can be accessed from the pull
    requests listed below.

    Allow setting sigma parameter directly for metadynamics
    https://github.com/Colvars/colvars/pull/325

    Remove default values for lowerWall and upperWall legacy keywords
    https://github.com/Colvars/colvars/pull/324

    biasActualColvar option to bypass extended-Lagragian for a bias
    https://github.com/Colvars/colvars/pull/321

    Flexible restart-reading
    https://github.com/Colvars/colvars/pull/320
This commit is contained in:
Giacomo Fiorin
2020-02-27 19:44:33 -05:00
parent 6e7e365981
commit 7be004512f
24 changed files with 508 additions and 365 deletions
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17
lib/colvars/colvarbias.h
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@ -23,9 +23,12 @@ public:
/// Name of this bias
std::string name;
/// Type of this bias
/// Keyword indicating the type of this bias
std::string bias_type;
/// Keyword used in state files (== bias_type most of the time)
std::string state_keyword;
/// If there is more than one bias of this type, record its rank
int rank;
@ -65,7 +68,7 @@ public:
virtual int calc_forces(std::vector<colvarvalue> const *values);
/// Send forces to the collective variables
virtual void communicate_forces();
void communicate_forces();
/// Carry out operations needed before next step is run
virtual int end_of_step();
@ -144,10 +147,10 @@ public:
std::istream & read_state_data_key(std::istream &is, char const *key);
/// Write the bias configuration to a restart file or other stream
virtual std::ostream & write_state(std::ostream &os);
std::ostream & write_state(std::ostream &os);
/// Read the bias configuration from a restart file or other stream
virtual std::istream & read_state(std::istream &is);
std::istream & read_state(std::istream &is);
/// Write a label to the trajectory file (comment line)
virtual std::ostream & write_traj_label(std::ostream &os);
@ -207,6 +210,9 @@ protected:
/// through each colvar object
std::vector<colvar *> colvars;
/// \brief Up to date value of each colvar
std::vector<colvarvalue> colvar_values;
/// \brief Current forces from this bias to the variables
std::vector<colvarvalue> colvar_forces;
@ -226,6 +232,9 @@ protected:
/// \brief Step number read from the last state file
cvm::step_number state_file_step;
/// Flag used to tell if the state string being read is for this bias
bool matching_state;
};