Commit Graph

61 Commits

Author SHA1 Message Date
sbraccia 5116aacd55 Clean-up of routines used for meta-dynamics and for the calculation of
free-energy barriers. C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3382 c92efa57-630b-4861-b058-cf58834340f0
2006-09-12 18:28:57 +00:00
sbraccia 9a057786ad Cleanup of unused variables. C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3193 c92efa57-630b-4861-b058-cf58834340f0
2006-06-22 13:21:17 +00:00
giannozz c7f3d7ed2b Some cleanup of unit conversion variables (more to come):
scmass => amu_au , au => autoev


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3183 c92efa57-630b-4861-b058-cf58834340f0
2006-06-16 10:10:53 +00:00
sbraccia ca607fd936 Fixed a bug in the code for the calculation of free-energy barriers. C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3179 c92efa57-630b-4861-b058-cf58834340f0
2006-06-15 13:56:16 +00:00
sbraccia 59fbce102c Minor modifications of the output format. C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3078 c92efa57-630b-4861-b058-cf58834340f0
2006-05-04 14:37:45 +00:00
sbraccia 0b843c9e55 neb&string: fixed a bug in the broyden algorithm (only for string).
Modification of the parallel implementation: only masternode moves the path
and then broadcasts the result to the others. C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3038 c92efa57-630b-4861-b058-cf58834340f0
2006-04-24 13:01:38 +00:00
sbraccia 463d1d0f03 Cleanup of NEB code. Climbing image implemented also for the string method.
Mariginal improvement of the broyden optimisation algorithm. The reference
output of example17 not yet regenerated.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@3033 c92efa57-630b-4861-b058-cf58834340f0
2006-04-21 03:44:20 +00:00
sbraccia b7bd2b52ad Fixed bugs in the allocation of neb/string input arrays. Cleanup of unused
parameters. C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2990 c92efa57-630b-4861-b058-cf58834340f0
2006-04-02 00:28:20 +00:00
sbraccia 798f511ab2 Fixed an error in the initialization of neb variables introduced recently. C.S
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2968 c92efa57-630b-4861-b058-cf58834340f0
2006-03-27 22:34:53 +00:00
giannozz c09d36277b Minor fixes
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2935 c92efa57-630b-4861-b058-cf58834340f0
2006-03-22 16:36:24 +00:00
sbraccia 1e86d9fef7 Cleanup of unused variables. C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2881 c92efa57-630b-4861-b058-cf58834340f0
2006-03-08 04:00:02 +00:00
sbraccia f51e3403c1 oops ... C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2860 c92efa57-630b-4861-b058-cf58834340f0
2006-03-01 20:10:59 +00:00
sbraccia da14a044fe Cleanup of NEB related stuff: unused variables and algorithms have been
removed. C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2858 c92efa57-630b-4861-b058-cf58834340f0
2006-03-01 19:57:03 +00:00
sbraccia 5eee750bb7 Fixed several bugs in the code used to compute free-energy barriers (for both
CP and PW). C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2855 c92efa57-630b-4861-b058-cf58834340f0
2006-02-27 20:06:23 +00:00
sbraccia 06776e5fb9 Fixed some bugs affecting meta-dynamics.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2759 c92efa57-630b-4861-b058-cf58834340f0
2006-02-03 04:12:18 +00:00
giannozz 8eda231bbb - Variable cell: use Cesar Da Silva's version of the damping algorithm
(he claims it is more tested); documentation updated (sort of)
- routines find_free_unit, delete_if_present, moved from 'parser'
  to 'io_files' (it is a more natural place)
- routines int_to_char moved from 'parser' to flib/ (it is quite
  unrelated with the rest of the module)
- routine trimcheck moved from flib/ to 'io_files' (more natural place)


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2753 c92efa57-630b-4861-b058-cf58834340f0
2006-02-01 17:56:16 +00:00
sbraccia a5eeeee8c5 All functions used to generate random number collected in a single module. Added two routines
random numbers from a normal distribution.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2725 c92efa57-630b-4861-b058-cf58834340f0
2006-01-25 04:24:49 +00:00
degironc 5df233178a my old ifc 7.0 does not like unbalanced assignement statement like
pos_(:,1) = pos(1:dim,1)
and crashes with Address error

pos_(1:dim,1) = pos(1:dim,1)
is reuired

stefano


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2394 c92efa57-630b-4861-b058-cf58834340f0
2005-10-31 15:18:25 +00:00
sbraccia ba4d2bef4b Several bug-fix and clean-up.
NEB: removed unused variables; removed allocatable input arrays from input_parameters (to be
consistent with the rest of the input stuff) and replaced by static arrays.
XML: unit 99 used to read/write wfc's replaced by a call to iotk_free_unit.
constraints: the static array "fion" is passed as an array-section to constraint subroutines.
metadyn: fe_step must be defined as an array of "time-steps" (one for each deg-of-freedom).
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2322 c92efa57-630b-4861-b058-cf58834340f0
2005-10-20 15:22:12 +00:00
sbraccia c81ff3deba Cleanup. C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2212 c92efa57-630b-4861-b058-cf58834340f0
2005-09-24 02:42:07 +00:00
giannozz f533b052d5 dbl => DP (defined as previously dbl was)
syntax for declarations: real(DP), without "kind="


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2135 c92efa57-630b-4861-b058-cf58834340f0
2005-08-28 14:09:42 +00:00
sbraccia c36cdb3385 NEB cleanup. Fixed a bug in the identification of frozen images
(relevant only for use_freezing=.TRUE.). C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2109 c92efa57-630b-4861-b058-cf58834340f0
2005-08-22 13:50:03 +00:00
sbraccia 0230fb8de4 Fixed a severe bug in the NEB restart procedure. The broyden optimiser has been made
simpler (the previous version did't work well). C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2031 c92efa57-630b-4861-b058-cf58834340f0
2005-07-16 15:15:33 +00:00
sbraccia 65c98fa35b Fixed a bug in NEB that appeared after removing PBCs.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2022 c92efa57-630b-4861-b058-cf58834340f0
2005-07-14 18:12:22 +00:00
sbraccia 40304e2015 stop_pw renamed stop_run to be consistent with the similar rutine for cp.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@2012 c92efa57-630b-4861-b058-cf58834340f0
2005-07-10 23:48:37 +00:00
sbraccia 249168882f Fixed some bugs in the code for the computation of free energy barriers.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1958 c92efa57-630b-4861-b058-cf58834340f0
2005-06-13 16:36:29 +00:00
sbraccia cb6c7438d1 Added new methods and variables for the calculation of potential-energy and free-energy barriers
using neb or smd in a coarse-grained space (as in metadynamics). Still under development.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1933 c92efa57-630b-4861-b058-cf58834340f0
2005-06-06 17:53:32 +00:00
sbraccia 9ee776b63e Fixed a bug in the use of mass-weighted coordinates.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1888 c92efa57-630b-4861-b058-cf58834340f0
2005-05-20 14:23:49 +00:00
sbraccia 17ab30a094 Added the possibility of using mass weighted coordinates. Other minor fixes.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1834 c92efa57-630b-4861-b058-cf58834340f0
2005-04-27 21:48:39 +00:00
sbraccia 5ce7ef07c0 NEB and STRING dynamics reorganised. Added a new module containing the routines used for the reparametrisations.
Added the possibility of doing the string dynamics in real space (the original recipe).
The Fourier representation of the path is switched on by setting the logical input variable "use_fourier".
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1810 c92efa57-630b-4861-b058-cf58834340f0
2005-04-16 17:07:39 +00:00
sbraccia 86cde8cc19 Path optimisation: the actual number of images was not written in the "broyden" file.
This caused a crash in the case of string dynamics. C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1781 c92efa57-630b-4861-b058-cf58834340f0
2005-04-08 15:18:11 +00:00
sbraccia 79f461531a Improved version of the Broyden algorithm for path optimisation: some variables useful to understand
possible failures of the algorithm have been added in the output. C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1771 c92efa57-630b-4861-b058-cf58834340f0
2005-03-30 14:46:16 +00:00
sbraccia edf9539c5e Fixed a bug in the freezing procedure (spotted by G.Fratesi). C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1699 c92efa57-630b-4861-b058-cf58834340f0
2005-03-10 14:22:37 +00:00
sbraccia 54174553e0 Fixed a variable not declared spotted by S.Fabris.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1693 c92efa57-630b-4861-b058-cf58834340f0
2005-03-09 09:45:41 +00:00
sbraccia d51d9cadb4 The file containig broyden's history moved in the scratch dir. The file is
automatically removed when the run is started from scratch. C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1674 c92efa57-630b-4861-b058-cf58834340f0
2005-03-02 12:46:52 +00:00
sbraccia e3510cf3dc NEB and Fourier String dynamics: the quasi-Newton Broyden's second method has
been fully implemented: it is ~2 times faster than the quick-min optimisation scheme.
It does not make use of the input step ds (the step is automatically upgraded as in the
BFGS method). Still to be tested on difficoult cases (I ask some help from those
who have encountered convergence problems with the previous versions of NEB). C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1668 c92efa57-630b-4861-b058-cf58834340f0
2005-02-25 14:51:41 +00:00
sbraccia 198649869c Fixed other problems related to the image-parallelisation of NEB and SMD.
Documentation updated.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1616 c92efa57-630b-4861-b058-cf58834340f0
2005-02-06 11:04:03 +00:00
sbraccia 5f87767056 Fixed some bugs in path_base. image-parallelisation of NEB and SMD modified in order
to be compatible with global filesystems exported via NFS (needed by N.Marzari's group).
NEB and SMD still require a global filesystem.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1611 c92efa57-630b-4861-b058-cf58834340f0
2005-02-01 16:59:22 +00:00
ballabio 838d98085b another g95 fix [Gerardo]
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1606 c92efa57-630b-4861-b058-cf58834340f0
2005-02-01 12:19:25 +00:00
sbraccia c9f34109db The code which implements the zero temperature string dynamics in pwscf has been rewritten.
Added The Broyden acceleration scheme for path optimisations (not yet tested).
Finite temperature string dynamics (langevin dynamics) fully implemented (for the moment only in pwscf).
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1603 c92efa57-630b-4861-b058-cf58834340f0
2005-02-01 10:36:23 +00:00
degironc 3c3dc8f611 a FORALL statement replaced with a do/enddo.
code was craching with ifc 7.0
 stefano


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1602 c92efa57-630b-4861-b058-cf58834340f0
2005-02-01 09:21:09 +00:00
sbraccia 96a62192a0 Implemented a new and cleaner way of rescaling the elastic constants. Some bugs
affecting the I/O of the restart file fixed. Added a check on the existence of
such file. Path interpolator facility updated (now it should work with all the
versions of restart files). C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1521 c92efa57-630b-4861-b058-cf58834340f0
2004-12-21 15:29:09 +00:00
sbraccia 01023df017 path optimization:
1) cleanup of the output format (more informative)
   2) some cleanup of internal routines
   3) added a couple of input variables and changed the default value
      of ds from 1.5 to 1.0.
BFGS optimization:
   1) implemented a mixed BFGS + Murtag-Sargent update of the inverse
      hessian which is generally faster than the pure BFGS
   2) trust_radius_max increased to 0.8 bohr
   3) some cleanup of internal routines
(C.S.)


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1414 c92efa57-630b-4861-b058-cf58834340f0
2004-11-03 09:53:12 +00:00
sbraccia 3fd1e87edd Several improvements of the string dynamics.
Added a use_multistep input variable that allows fourier modes to be gradually included.
Added a langevin opt_scheme in which the string performs a langevin dynamics in the path space.
In the langevin scheme a canonical sampling of the initial and final configurations can also be done "on the fly" setting first_last_opt=.TRUE..
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1373 c92efa57-630b-4861-b058-cf58834340f0
2004-10-13 08:18:15 +00:00
sbraccia f0f7f8ab91 Workaround for PGI compiler. C.S.
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1364 c92efa57-630b-4861-b058-cf58834340f0
2004-10-01 15:39:58 +00:00
sbraccia 6631211a33 REAL replaced by DBLE to avoid any problem with the pgi compiler.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1358 c92efa57-630b-4861-b058-cf58834340f0
2004-09-28 10:46:18 +00:00
sbraccia 2d0f907723 Fourier String Method Dynamics improved: the number of fourier modes used to represent the path are gradually included (starting from one up to num_of_images-2), so that the overall number of scf loops needed to reach convergence is considerably reduced (of a factor of 2-3).
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1339 c92efa57-630b-4861-b058-cf58834340f0
2004-09-27 09:17:48 +00:00
sbraccia 750cb74acb Fixed a bug in path optimizations: the case nstep = 0 was ignored.
C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1328 c92efa57-630b-4861-b058-cf58834340f0
2004-09-21 13:42:51 +00:00
giannozz 5d30d073d6 format X => 1X
git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1296 c92efa57-630b-4861-b058-cf58834340f0
2004-09-15 15:38:29 +00:00
sbraccia f50f901233 path optimizations: added the possibility to write the prefix.save file (logical varible write_save) relative to each
image (needed for post-processing). C.S.


git-svn-id: http://qeforge.qe-forge.org/svn/q-e/trunk/espresso@1290 c92efa57-630b-4861-b058-cf58834340f0
2004-09-15 12:35:54 +00:00