topology file. These routines are linear scaling, MUCH faster than leap2fist.
Once the forcefield part will be parsed the leap2fist will be totally obsolete.
Added 1 regtest using the connectivity of AMBER topology file.
svn-origin-rev: 7868
added a new choice for the selected vector (INVOLVED_ATOMS) which allows to look for the
mode most localized on the selected atoms, removed preconditioner (it's useless)
svn-origin-rev: 7078
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
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
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
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
Include a bigger qm/mm example with link atom to check in the future possible
changes to the topology building/reorganization/ blah blah blah ;-)
svn-origin-rev: 3416
