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Update Colvars to version 2017-07-15 and support automated builds for it

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This commit is contained in:
Giacomo Fiorin
2017-07-19 14:10:43 -04:00
parent cc9b3864bf
commit ee6cac826e
52 changed files with 3473 additions and 2413 deletions
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24
lib/colvars/colvarbias.cpp
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@ -23,9 +23,7 @@ colvarbias::colvarbias(char const *key)
b_output_energy = false;
reset();
state_file_step = 0;
// Start in active state by default
enable(f_cvb_active);
description = "uninitialized " + cvm::to_str(key) + " bias";
}
@ -74,7 +72,6 @@ int colvarbias::init(std::string const &conf)
cvm::error("Error: no collective variables specified.\n", INPUT_ERROR);
return INPUT_ERROR;
}
} else {
cvm::log("Reinitializing bias \""+name+"\".\n");
}
@ -83,6 +80,16 @@ int colvarbias::init(std::string const &conf)
get_keyval(conf, "outputEnergy", b_output_energy, b_output_energy);
get_keyval(conf, "timeStepFactor", time_step_factor, 1);
if (time_step_factor < 1) {
cvm::error("Error: timeStepFactor must be 1 or greater.\n");
return COLVARS_ERROR;
}
// Now that children are defined, we can solve dependencies
enable(f_cvb_active);
if (cvm::debug()) print_state();
return COLVARS_OK;
}
@ -110,6 +117,8 @@ colvarbias::~colvarbias()
int colvarbias::clear()
{
free_children_deps();
// Remove references to this bias from colvars
for (std::vector<colvar *>::iterator cvi = colvars.begin();
cvi != colvars.end();
@ -200,7 +209,12 @@ void colvarbias::communicate_forces()
cvm::log("Communicating a force to colvar \""+
variables(i)->name+"\".\n");
}
variables(i)->add_bias_force(colvar_forces[i]);
// Impulse-style multiple timestep
// Note that biases with different values of time_step_factor
// may send forces to the same colvar
// which is why rescaling has to happen now: the colvar is not
// aware of this bias' time_step_factor
variables(i)->add_bias_force(cvm::real(time_step_factor) * colvar_forces[i]);
}
}