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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8701 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2012-08-23 13:09:47 +00:00
parent 7ebff3faf6
commit 81ec0e96e1
12 changed files with 86 additions and 163 deletions
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12
lib/colvars/colvar.cpp
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@ -98,8 +98,8 @@ colvar::colvar (std::string const &conf)
"on an axis", "distanceZ", distance_z);
initialize_components ("distance projection "
"on a plane", "distanceXY", distance_xy);
initialize_components ("average distance weighted by inverse sixth power",
"distance6", distance6);
initialize_components ("average distance weighted by inverse power",
"distanceInv", distance_inv);
initialize_components ("coordination "
"number", "coordNum", coordnum);
@ -132,7 +132,7 @@ colvar::colvar (std::string const &conf)
initialize_components ("moment of "
"inertia", "inertia", inertia);
initialize_components ("moment of inertia around an axis",
"inertia_z", inertia_z);
"inertiaZ", inertia_z);
initialize_components ("eigenvector", "eigenvector", eigenvector);
if (!cvcs.size())
@ -318,13 +318,13 @@ colvar::colvar (std::string const &conf)
"by enabling a thermostat, or through \"extendedTemp\".\n");
}
get_keyval (conf, "extendedFluctuation", tolerance, 0.2*width);
get_keyval (conf, "extendedFluctuation", tolerance, width);
if (tolerance <= 0.0)
cvm::fatal_error ("Error: \"extendedFluctuation\" must be positive.\n");
ext_force_k = cvm::boltzmann() * temp / (tolerance * tolerance);
cvm::log ("Computed extended system force constant: " + cvm::to_str(ext_force_k) + " kcal/mol/U^2");
get_keyval (conf, "extendedTimeConstant", period, 40.0 * cvm::dt());
get_keyval (conf, "extendedTimeConstant", period, 200.0);
if (period <= 0.0)
cvm::fatal_error ("Error: \"extendedTimeConstant\" must be positive.\n");
ext_mass = (cvm::boltzmann() * temp * period * period)
@ -339,7 +339,7 @@ colvar::colvar (std::string const &conf)
}
}
get_keyval (conf, "extendedLangevinDamping", ext_gamma, 0.0);
get_keyval (conf, "extendedLangevinDamping", ext_gamma, 1.0);
if (ext_gamma < 0.0)
cvm::fatal_error ("Error: \"extendedLangevinDamping\" may not be negative.\n");
if (ext_gamma != 0.0) {