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Update Colvars to version 2017-10-11

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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]
This commit is contained in:
Giacomo Fiorin
2017-10-13 13:25:02 -04:00
parent a973c65d67
commit 3e89b270fd
34 changed files with 1795 additions and 275 deletions
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23
lib/colvars/colvar.cpp
View File

@ -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);
// The total force acting on the extended variable is f_ext
// This will be used in the next timestep
ft_reported = f_ext;
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;