someone may need it in the future) to make things easier and less complicated.
Cleaning plenty of regtests in the FIST regtest directory.
svn-origin-rev: 7413
energy/forces and virial.. Major rewriting of the routine and heavy cleaning.. Bug
fix in stress tensor for shell models (was missing the contribution from shell_i//core_i)..
Added two more regtests to check that PBC will be preserved since now on..
Resetted several regtests due to numerics (and to the bug fix for the shell model)
svn-origin-rev: 6124
possible define a single molecule with PSFs of fragments and explicitly declaring
the further terms.. This required a reorganization both of the input sections (sorry about that guys!!)
but also in the code handling the reading and post_process of PSF info.
Few regtests added and changed the syntax of MOL_SET in MC regtests.
Added also a preliminary section of the new free energy method(not working yet).
svn-origin-rev: 5958
Possibility to dump lagrange multipliers (X Chris) activating the proper print_key.
Cleaning debug comments left in the code.. and moving psf, xyz, and pdb out of the regtest directory
of fist.
svn-origin-rev: 5879
One more regtest. Reorganization of themetadynamic section. now all free
energy method are contained in a main folder called free_energy.
Cleaning the regtest directory of fist, moving the xyz, pot and psf files
in correspondingly appropriate directories. few more work on free energy
calculations later on..
svn-origin-rev: 5732
Now we can handle scrambled (but really scrambled PDB)
reorder them, match similar kind of molecules (on the basis of the connectivity only
, built starting from coordinates) and pack everything in a very efficient way.
The matching could fail only for very high symmetric molecular system.. in that case
two different molecules will be created instead of one.. added few more regtests..
Last: bug fix in the dipole of FIST.
svn-origin-rev: 5447
Introduced the possibility to modify by input the generated connectivity.
Bug fix in the neighbour_lists of fist for non-periodic case.
cleaned the particle_types routine.
created a new section in the subsys section called GENERATE that contains all
possible parameters influencing the generation of the connectivity.
Added few more regtests for the new connectivity generator.
svn-origin-rev: 5403
defined like contraints (see new regtests based on restraints). Added several regtests
testing the different kind of restraints.
New definition for torsional angle that avoids the singularity at pi or -pi.
Due to this new defition 2 regtests resetted.
Also the 2 regtests using restraints have been resetted due to the different implementation.
svn-origin-rev: 5307
other tests to check that amber and fist will be compatible in the future..
Introduced a keyword to avoid the scaling of the cutoff energy.. In this way amber and fist
give exactly the same results.A bug fix also in the topology_converter.. cosmetics around..
reset 2 regtests.
svn-origin-rev: 5204
Bug fix for double counting of 1-4 interactions..
Bug fix for spline_bond_env (1-4) generations..
Introduced a test used to compare the single energy contributions with AMBER.
The energies agree 10^-6-10^-7 if the e_cutoff_coul and e_cutoff_vdw is not
taken into account..
Infact AMBER defines the electrostatic and VDW potential with a step at the
r_cutoff.. (the potential does NOT go to zero at the cutoff distance)
Since we want a potential that is zero at the r_cutoff
our values will be still in agreement with the ones of AMBER though not
numerically similar (just shifted of a fixed amount)
FIST and AMBER synchronized..
svn-origin-rev: 5195
