scnc
/
qmcpack
mirror of https://github.com/QMCPACK/qmcpack.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
6,497 Commits 5 Branches 23 Tags 570 MiB
Commit Graph

161 Commits

Author SHA1 Message Date
Jaron Krogel c4ab3a2f4f test commit 2, remove a space from nexus.py 2017-01-18 17:06:37 -05:00
Jaron Krogel 10183b59fa test commit, add a space to nexus readme 2017-01-18 15:43:23 -05:00
Jaron Krogel a84adc6e3f nexus: fix for structure dependency resolution 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7384 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-28 21:58:18 +00:00
Jaron Krogel 165ebe2c18 nexus: enable bypass of orbital dependency via user defined orbital file 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7382 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-27 21:10:01 +00:00
Raymond Clay db62146644 add return_system() to VASP input file class 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7366 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-20 23:04:02 +00:00
Yubo “Paul” 848bc4cdb5 nexus: addionion flag to force estimator 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7365 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-20 22:51:19 +00:00
Jaron Krogel b7e9bf54e4 nexus: small changes to jastrow opt workflow 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7347 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-15 15:03:57 +00:00
Yubo “Paul” cf2c8fdcbe nexus: allow manual nbnd input 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7345 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-13 16:58:54 +00:00
Jaron Krogel f2a97e44f0 nexus: small fixes 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7338 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-09 17:34:55 +00:00
Jaron Krogel 8006dc5b4d nexus: improve jastrow input handling 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7330 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-08 21:33:38 +00:00
Mark Dewing 17221f3c91 Improve nexus runtime monitoring output. 
Print the actual elapsed time rather than the poll iteration number.
If the progress_tty setting is True and the log output is to a terminal,
update the progress output by overwriting the line.


git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7329 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-08 18:47:21 +00:00
Jaron Krogel b0a49c532a nexus: enable job bundling in scanned qmcpack workflows 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7312 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-05 22:31:28 +00:00
Jaron Krogel 80b64ef00d nexus: fixed for mixed use of scf and nscf in qmcpack_workflows 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7305 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-12-01 21:22:15 +00:00
Jaron Krogel e5c1826014 nexus: enable custom directory naming for scanned variables in qmcpack workflows 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7293 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-29 20:19:25 +00:00
Jaron Krogel 3dc2646099 nexus: support for generating partitioned sposet input 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7288 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-28 21:14:22 +00:00
Jaron Krogel bba3a5f524 nexus: groundwork for symmetrized k-point dependency 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7286 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-28 18:33:04 +00:00
Yubo “Paul” bcda61b128 nexus: make sure integers are integers after tiling 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7285 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-28 17:43:39 +00:00
Jaron Krogel 858274eca0 nexus: fix for rare tiling case where an integer tiling vector cannot be found 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7260 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-22 17:58:45 +00:00
Jaron Krogel a8326395c8 nexus: fix multilevel scans in qmcpack workflows involving physical system inputs 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7254 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-21 21:58:36 +00:00
Jaron Krogel c67b90fd4d nexus: bug fix for interdependent workflows 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7252 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-21 19:23:42 +00:00
Yubo “Paul” ce3a312582 nexus: allow QIxml initialized from dictionary 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7251 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-21 16:19:44 +00:00
Jaron Krogel 19b9948e90 nexus: enable permissive I/O for qmcpack input 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7250 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-21 15:21:36 +00:00
Yubo “Paul” 923b332185 nexus: error out if optimal tilematrix not found 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7248 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-20 17:52:18 +00:00
Yubo “Paul” 9cd40452bd nexus: added support for skall estimator 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7247 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-19 19:50:44 +00:00
Jaron Krogel 4cf1e2d2cf nexus: enable multiple independent nscf via rsync of scf output 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7241 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-18 19:49:08 +00:00
Jaron Krogel 57e9f4d350 nexus: preliminary equation of state fitting capabilities 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7236 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-17 17:32:09 +00:00
Jaron Krogel 2772668409 nexus: allow omp thread oversubscription by providing processes per node 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7222 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-11 21:21:52 +00:00
Jaron Krogel b460478317 small fixes 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7220 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-10 17:06:18 +00:00
Jaron Krogel 1492bb4a8d nexus: add Cooley to machines.py 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7216 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-09 21:23:42 +00:00
Jaron Krogel 72dc06ded9 nexus: small fixes for qmcpack workflows and input generation 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7215 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-09 20:29:30 +00:00
Jaron Krogel f0ebc469e5 allow for fake jobs as well as fake sims 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7214 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-08 22:19:28 +00:00
Jaron Krogel 689de3b95b Greatly expand qmcpack workflows. Major commit, see main text of message. 
qmcpack workflows (this is the main part of the commit)
  comprehensive generation of qmcpack workflows
  attempts to allow user to create flexible workflows w/o resorting to Python logic
  enabled adaptive workflow generation via qmcpack_chain function
  enabled (multiple) scans over input paramters via qmcpack_workflows function
  possible to fix e.g. jastrow factor optimization to a single scan value (e.g. ecutwfc)
  ability to plot generated workflow graphs supported via pydot
  example use cases will be written (soon) into Nexus and QMCPACK user manuals


user ability to group pseudopotentials into sets
  user interface: ppset from pseudopotential.py
  user provides list of pseudopotential files and a label
  user can provide label to "generate_*" functions via "pseudos" parameter instead of PP file names

  
support for PWscf 5.4 input keywords
  also added support for "ATOMIC_FORCES" card
  added "bandfac" parameter, sets bands as band_fac*max(nup,ndown)
  full support for array-type inputs still pending

  
better recognition for pseudopotential file naming schemes
  PP files must start with element symbol (case insensitive) followed by ".", "_", or "-"


updates to atomic structure interface
  better detection/handling of periodic boundary conditions
  ability to read/write geometry.in files for FHI-AIMS


ability to mark simulations as "fake" 
  simulations marked in this way will not be executed  
  used so far to understand workflow structure prior to scans in qmcpack_workflows.py


new methods by class/file 
  obj               : tree, get_path, path_exists
  Particles         : electron_counts
  ProjectManager    : screen_fake_sims
  pseudopotential.py: pp_elem_label
  Structure         : corners, miller_direction, miller_normal, project_plane, 
                      rwigner_cube, rinscribe_cube, read_fhi_aims



git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7213 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-08 19:40:15 +00:00
Yubo “Paul” cc5fa23aef nexus: enable the use of vdW-DF functional 
pass 'vdw_table' variable in settings to point to the van der Waals table generated by generate_vdW_kernel_table.x

pwscf simulations using the vdW-DF functional will copy the given vdw_table to run directory



git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7199 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-11-01 21:49:24 +00:00
Jaron Krogel f981b71cb6 nexus: fix for bundling twist averaged qmcpack runs 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7185 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-10-19 17:26:15 +00:00
Jaron Krogel 26ee7c8fc1 nexus: allow user to demand the jastrow from the last optimization series be used 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7163 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-10-06 20:57:27 +00:00
Jaron Krogel aa9617d2aa nexus: update nersc machines to slurm 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7160 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-10-06 17:56:26 +00:00
Yubo “Paul” 59a218b963 nexus: remove obselete cell parameter read loop 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7153 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-29 17:16:37 +00:00
Yubo “Paul” 63c3e72c24 nexus: more user control over input_type='relax' 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7152 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-29 17:15:07 +00:00
Yubo “Paul” c7c8f511c1 nexus: add basic support for input_type='vc-relax' 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7151 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-29 15:31:28 +00:00
Luke Shulenburger 92f490fe1c add several machines to nexus definitions 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7137 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-27 20:26:39 +00:00
Jaron Krogel f5b66e5858 nexus: do not rescale positions, handled already by alat specifier 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7132 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-26 17:30:19 +00:00
Jaron Krogel 54293ec622 nexus: add support for vc-relax 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7131 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-26 17:22:56 +00:00
Jaron Krogel e243fff328 qmca: fix for twist averaging with user provided weights 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7130 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-26 13:58:43 +00:00
Jaron Krogel 5ff859317b nexus: more on PP label fix 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7129 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-26 13:06:35 +00:00
Jaron Krogel d57a46e6fd nexus: fix in hamiltonian input for repeated elements with different labels 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7128 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-09-26 13:01:10 +00:00
Jaron Krogel 0ef3950060 nexus: fix tiling corner case, also add function to find tiling nearest to cubic 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7090 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-08-29 21:09:48 +00:00
Jaron Krogel 355c6afa31 nexus: attempt to fix job bundling by imposing strict synchronization 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7087 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-08-25 21:08:00 +00:00
Jaron Krogel 27dd51868e nexus: more detailed status reporting 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7085 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-08-25 18:52:30 +00:00
Jaron Krogel fc3ca5efc7 nexus: ensure opt.xml exists prior to resolving jastrow dependency 
git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7074 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-08-17 19:38:32 +00:00
Mark Dewing 71a4fdb4a2 Workaround for issue with Numpy 1.10 and greater. 
The problem appears with a default install of Ubuntu 16.04.

Error message:
  File "/home/user/qmcpack/assembla/trunk/nexus/library/machines.py", line 1075, in submit_jobs
    if job.cores>self.cores and not nexus_core.generate_only:                
AttributeError: 'numpy.ndarray' object has no attribute 'cores'

I have not been able to create a simple reproducer that demonstrates the
problem.  It must be something with one the methods on the Job object 
(or its super classes) that causes numpy to convert that object to an array
of type bool.


git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@7072 e5b18d87-469d-4833-9cc0-8cdfa06e9491
 2016-08-15 18:06:35 +00:00