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542 Commits

Author SHA1 Message Date
Steve Plimpton c46d5ff422 Merge pull request #612 from giacomofiorin/colvars-update-2017-08-10 
Minor fixes to Colvars module
 2017-08-17 11:32:38 -06:00
Steve Plimpton dd67989c76 Merge pull request #601 from stanmoore1/kokkos_update 
Update Kokkos library to v2.03.13
 2017-08-17 11:32:18 -06:00
Steve Plimpton 00aafef1a8 Merge pull request #597 from ndtrung81/three-body-short-nlist 
Implementing short neighbor lists for three-body gpu styles
 2017-08-17 11:31:59 -06:00
Axel Kohlmeyer c6d923b6c8 make download function more resilient by also catching failed execution 2017-08-10 21:15:35 -04:00
Axel Kohlmeyer 6d24be8bb7 whitespace cleanup 2017-08-10 21:14:40 -04:00
Giacomo Fiorin da01be7c18 More robust change from initial to target restraint centers in Colvars 2017-08-10 09:22:53 -04:00
Axel Kohlmeyer 146aa4cdbd fall back to wget when curl is not available 2017-08-10 09:05:23 -04:00
Axel Kohlmeyer 2f3747eb6e we need to override compiler flags in lib/voronoi/Install.py 
The default compiler flags in voro++'s config.mk file do not include
-fPIC, which makes it incompatible with building the shared object for
the python wrapper.
 2017-08-10 08:34:46 -04:00
Axel Kohlmeyer 2bc6ad80d4 avoid writable string and deprecated implicit conversion warning 2017-08-10 07:45:21 -04:00
Axel Kohlmeyer 6780c73907 restore mpic++ makefile to resolve regression test failure 2017-08-09 07:10:08 -04:00
Axel Kohlmeyer b7b1257b01 remove attempts to use urllib and use curl for all downloading. restore printing help with no flags. 2017-08-08 17:00:09 -04:00
Axel Kohlmeyer 30431d4edb rework Install.py for gpu library. make it consistent with other lib folders and support python3 2017-08-08 16:57:27 -04:00
Stan Moore 8a7a831bd6 Remove redundant check in Makefile.kokkos 2017-08-08 12:57:22 -06:00
Axel Kohlmeyer c53a84a967 update README file for lib/mscg 2017-08-08 13:55:12 -04:00
Axel Kohlmeyer d2b0c287d2 add local makefile overrides to be compatible with standard suffixes 2017-08-08 13:19:44 -04:00
Axel Kohlmeyer b3244f9c98 more lib compilation updates 2017-08-08 07:20:33 -04:00
Axel Kohlmeyer 8bba29d91e more lib installation cleanup 2017-08-07 17:21:45 -04:00
Axel Kohlmeyer 135b1650f1 revamp of library builds 
- remove cross compiler stuff
- make use of Install.py consistent
- provide options for Makefile.serial and Makefile.mpi that match those in src
 2017-08-07 17:13:01 -04:00
Axel Kohlmeyer 163ed27618 update .gitignore 2017-08-04 16:10:59 -04:00
Axel Kohlmeyer 23ca0099f7 more updates to kim/Install.py to restore missing functionality and align with other scripts 
- build into local directory to replace existing installation is now default
- add wrapper function that calls curl in case python package has not ssl support
- have to specify -n flag to avoid wiping out the existing installation
- can specify -p to point to an existing kim-api installation (implies -n)
 2017-08-04 14:47:32 -04:00
Stan Moore 8431ca5fec Remove tpls directory 2017-07-31 10:54:07 -06:00
Stan Moore 13f2d39f55 Update Kokkos library to v2.03.13 2017-07-31 10:34:21 -06:00
Axel Kohlmeyer 9bfd9267fa update and automate the QUIP configuration so that no environment variables are needed 2017-07-28 16:11:13 -04:00
Axel Kohlmeyer 3ebf561e0d remove tarball after unpacking 2017-07-28 14:25:47 -04:00
Axel Kohlmeyer ffb778cf9b make Install.py for lib/smd and lib/voronoi consistent 2017-07-28 14:03:29 -04:00
Axel Kohlmeyer f3850da9fe clean up makefiles provide "serial" and "mpi" targets for atc and awpmd 2017-07-28 13:36:06 -04:00
Axel Kohlmeyer e7d9aabca6 Merge branch 'kim-install' into install-and-docs-reviewed 2017-07-28 11:25:08 -04:00
Axel Kohlmeyer c494ec35e2 correct symbolic links to shared Install.py file 2017-07-27 12:48:32 -04:00
Axel Kohlmeyer acf6d54ec1 python3 port, yet untested 2017-07-27 09:25:39 -04:00
Axel Kohlmeyer 0427f6205e fix typo 2017-07-27 09:25:02 -04:00
Axel Kohlmeyer da7a5f55d3 Merge branch 'kim-install' into install-and-docs-reviewed 2017-07-26 19:32:55 -04:00
Axel Kohlmeyer 715c797df0 simplify Install.py for voronoi 2017-07-26 15:14:12 -04:00
Axel Kohlmeyer fd6e11f821 convert copies of Install.py files to symlinks 2017-07-26 14:29:52 -04:00
Axel Kohlmeyer f7a243a4d9 convert explicit copies back into symbolic links 2017-07-26 14:20:03 -04:00
Axel Kohlmeyer f0d286358e must not include system headers within 'extern "C"' blocks. breaks with MPICH 2017-07-26 14:02:02 -04:00
Trung Nguyen aa60ef6ed8 Cleaned up 3-body kernels, reverted some mistaken changes to vashishta 2017-07-23 00:08:55 -05:00
Trung Nguyen a71f5a0c20 Enabled again neigh no with tpa > 1 for 3-body gpu styles for backward compatibility, could be slower than neigh no tpa 1 in many cases 2017-07-22 22:57:37 -05:00
Trung Nguyen 3d1d0c58c7 Cleaned up 3-body gpu styles, and fixed a bug for tersoff/zbl/gpu. 
There is a unresolved bug for neigh no with tpa > 1 with BaseThree, enforce tpa = 1 for neigh no in BaseThree for now.
 2017-07-21 12:08:04 -05:00
Axel Kohlmeyer 1b704bab18 Merge branch 'colvars-safer-makefiles' of https://github.com/giacomofiorin/lammps into colvars-quickfix 2017-07-20 15:59:23 -04:00
Giacomo Fiorin c98f6140e7 Change order of targets in Makefiles for Colvars 2017-07-20 15:49:31 -04:00
Giacomo Fiorin 5031f5b807 Comment out use by Colvars of Makefile.lammps from other packages 2017-07-20 15:48:10 -04:00
Axel Kohlmeyer 9d0d90c038 README clarification from giacomo 2017-07-20 15:25:27 -04:00
Axel Kohlmeyer 66154e8a8b avoid makefile failure, if LAMMPS has not been configured yet 2017-07-20 15:05:58 -04:00
Ryan S. Elliott 84065dde21 Refactor lib/kim/Install.py; works with phtyon 3 2.7 2017-07-20 12:02:50 -05:00
Giacomo Fiorin ef9fb944c7 Detect number of processors for make 2017-07-20 10:53:08 -04:00
Giacomo Fiorin 187a80be77 Add forgotten decode() in Install.py 2017-07-19 22:21:49 -04:00
Axel Kohlmeyer 355aad9691 restore python3 support. this now can run with python 2.7.13 and 3.5.3. 2017-07-19 17:19:44 -04:00
Giacomo Fiorin ee6cac826e Update Colvars to version 2017-07-15 and support automated builds for it 2017-07-19 14:24:07 -04:00
Ryan S. Elliott f181a0bfab Update lib/kim/Install.py for phthon 2.7 conversion 2017-07-19 12:54:33 -05:00
Axel Kohlmeyer 81f342aafa fix variable name bug and synchronize with other ported Install.py files 2017-07-18 18:06:18 -04:00