Commit 3e89b270 authored by Giacomo Fiorin's avatar Giacomo Fiorin
Browse files

Update Colvars to version 2017-10-11 

Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
parent a973c65d

doc/src/PDF/colvars-refman-lammps.pdf

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lib/colvars/Makefile.common

+1 −2
Original line number Diff line number Diff line
@@ -59,8 +59,7 @@ LEPTON_OBJS = \ 
COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o) $(LEPTON_OBJS)



%.o: %.cpp

	$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) \

	-Ilepton/include -DLEPTON -c -o $@ $<

	$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) -Ilepton/include -DLEPTON -c -o $@ $<



$(COLVARS_LIB):	Makefile.deps $(COLVARS_OBJS)

	$(AR) $(ARFLAGS) $(COLVARS_LIB) $(COLVARS_OBJS) $(LEPTON_OBJS)

lib/colvars/Makefile.deps

+6 −5
Original line number Diff line number Diff line
@@ -14,7 +14,7 @@ $(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarbias_abf.h colvarbias.h colvargrid.h

 colvarbias_abf.h colvarbias.h colvargrid.h colvar_UIestimator.h

$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarbias_alb.h colvar.h colvarparse.h colvardeps.h \
@@ -39,7 +39,8 @@ $(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \ 
 lepton/include/lepton/ExpressionTreeNode.h \

 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvargrid.h

$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvar.h colvarparse.h colvardeps.h \
@@ -198,9 +199,9 @@ $(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \ 
 lepton/include/lepton/Operation.h lepton/include/lepton/CustomFunction.h \

 lepton/include/lepton/Exception.h \

 lepton/include/lepton/ParsedExpression.h lepton/include/lepton/Parser.h \

 colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \

 colvarbias_histogram.h colvarbias_meta.h colvarbias_restraint.h \

 colvarscript.h colvaratoms.h

 colvarbias.h colvarbias_abf.h colvargrid.h colvar_UIestimator.h \

 colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \

 colvarbias_restraint.h colvarscript.h colvaratoms.h colvarcomp.h

$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h

lib/colvars/colvar.cpp

+18 −5
Original line number Diff line number Diff line
@@ -1008,6 +1008,8 @@ int colvar::calc() 


int colvar::calc_cvcs(int first_cvc, size_t num_cvcs)

{

  colvarproxy *proxy = cvm::main()->proxy;



  int error_code = COLVARS_OK;

  if (cvm::debug())

    cvm::log("Calculating colvar \""+this->name+"\", components "+
@@ -1018,14 +1020,18 @@ int colvar::calc_cvcs(int first_cvc, size_t num_cvcs) 
    return error_code;

  }



  if (cvm::step_relative() > 0) {

    // Total force depends on Jacobian derivative from previous timestep

  if ((cvm::step_relative() > 0) && (!proxy->total_forces_same_step())){

    // Use Jacobian derivative from previous timestep

    error_code |= calc_cvc_total_force(first_cvc, num_cvcs);

  }

  // atom coordinates are updated by the next line

  error_code |= calc_cvc_values(first_cvc, num_cvcs);

  error_code |= calc_cvc_gradients(first_cvc, num_cvcs);

  error_code |= calc_cvc_Jacobians(first_cvc, num_cvcs);

  if (proxy->total_forces_same_step()){

    // Use Jacobian derivative from this timestep

    error_code |= calc_cvc_total_force(first_cvc, num_cvcs);

  }



  if (cvm::debug())

    cvm::log("Done calculating colvar \""+this->name+"\".\n");
@@ -1043,6 +1049,7 @@ int colvar::collect_cvc_data() 


  if (cvm::step_relative() > 0) {

    // Total force depends on Jacobian derivative from previous timestep

    // collect_cvc_total_forces() uses the previous value of jd

    error_code |= collect_cvc_total_forces();

  }

  error_code |= collect_cvc_values();
@@ -1471,9 +1478,15 @@ cvm::real colvar::update_forces_energy() 
    // Coupling force is a slow force, to be applied to atomic coords impulse-style

    f *= cvm::real(time_step_factor);



    if (is_enabled(f_cv_subtract_applied_force)) {

      // Report a "system" force without the biases on this colvar

      // that is, just the spring force

      ft_reported = (-0.5 * ext_force_k) * this->dist2_lgrad(xr, x);

    } else {

      // 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;

lib/colvars/colvar.h

+14 −1
Original line number Diff line number Diff line
@@ -61,6 +61,9 @@ public: 
  /// \brief Current actual value (not extended DOF)

  colvarvalue const & actual_value() const;

  

  /// \brief Force constant of the spring

  cvm::real const & force_constant() const;

   

  /// \brief Current velocity (previously set by calc() or by read_traj())

  colvarvalue const & velocity() const;
@@ -96,6 +99,12 @@ public: 
  {

    return cv_features;

  }

  static void delete_features() {

    for (size_t i=0; i < cv_features.size(); i++) {

      delete cv_features[i];

    }

    cv_features.clear();

  }



  /// Implements possible actions to be carried out

  /// when a given feature is enabled
@@ -592,6 +601,10 @@ public: 
  }

};



inline cvm::real const & colvar::force_constant() const

{

  return ext_force_k;

}



inline colvarvalue const & colvar::value() const

{

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