Commit Graph

605 Commits

Author SHA1 Message Date
a2756db66b Update to Kokkos library v2.5.00 2017-12-15 16:42:06 -07:00
da83feb8ca Merge branch 'master' into kk_update 2017-12-15 16:36:21 -07:00
319508bd29 fix scoping ambiguity issue that confuses nvcc 2017-11-30 10:56:58 -05:00
7d07f062b6 Remove const from variable 2017-11-20 10:21:19 -07:00
f3ed148828 Fix for big endian machines 2017-11-20 10:18:53 -07:00
c4c59b909e Merge pull request #716 from akohlmey/collected-small-changes
Collected small changes and bugfixes for next patch
2017-11-13 09:00:26 -07:00
88474fc5c2 Remove Kokkos tpls directory 2017-11-06 13:48:26 -07:00
16b5315845 Update Kokkos to v2.04.11 2017-11-06 13:47:33 -07:00
b34000a5e1 make *_gpu_reinit() functions consistent in returning void. correct prototypes in src/GPU, too.
this supersedes and closes #719
2017-11-04 02:49:22 -04:00
2dbb44f2c6 provide Makefile.lammps template for use with bundled linalg lib 2017-10-24 13:38:04 -04:00
d1630bbe34 add missing BLAS/LAPACK functions used by LATTE to linalg lib 2017-10-24 13:22:20 -04:00
f479f02589 Fix a Colvars error that was hidden by the previous segfault 2017-10-20 13:41:31 -04:00
6e7504f153 Import segfault fix in Colvars module 2017-10-19 08:09:44 -04:00
3e89b270fd Update Colvars to version 2017-10-11
Notable features are the umbrella-integration based free energy estimator for
eABF, and the traditional thermodynamic integration estimator now available
for umbrella sampling, SMD, metadynamics.  Also included are several small fixes.

Below is a list of relevant commits in the Colvars repository since the last update.

321d06a 2017-10-10 Add macros to manage colvarscript commands [Giacomo Fiorin]
26c3bec 2017-10-09 Document coming availability of Lepton in LAMMPS [Giacomo Fiorin]
cc8f249 2017-10-04 Clarify that SMP depends on code build [Giacomo Fiorin]
0b2ffac 2017-10-04 Summarize colvar definition options, clarify some details [Giacomo Fiorin]
28002e0 2017-10-01 Separate writing of restart file from other output (e.g. PMFs) [Giacomo Fiorin]
92f7c1d 2017-10-01 Deprecate colvarsTrajAppend [Giacomo Fiorin]
12a707f 2017-09-26 Accurate Jacobian calculation for RMSD variants [Jérôme Hénin]
fe389c9 2017-09-21 Allow subtractAppliedForce with extended-L again [Jérôme Hénin]
c050ce0 2017-09-18 Silence compiler warnings, remove Tabs [Giacomo Fiorin]
cb41905 2017-01-11 Add base class for TI estimator in other biases than ABF [Giacomo Fiorin]
a1bc676 2017-09-14 Avoid writing to unopened traj file [Jérôme Hénin]
b58d8cd 2017-09-08 Function to check for overlapping groups [Jérôme Hénin]
1e5efec 2017-09-07 Check for overlapping groups in coordNum [Jérôme Hénin]
03a61a4 2017-04-06 Add UI-based estimator [fhh2626]
ae43754 2017-08-17 Fix outputCenters parsing [Josh Vermaas]
1619e0e 2017-08-14 Delete static feature arrays in cvm destructor [Jérôme Hénin]
2017-10-13 13:45:10 -04:00
18ca2292c2 Merge pull request #686 from giacomofiorin/lepton-library
Add Lepton library within lib/colvars
2017-10-13 09:48:42 -06:00
d90aad887e Add Lepton library within lib/colvars 2017-10-09 15:25:43 -04:00
775a15b9da Update lib/kim for kim-api-v1.9.2 2017-10-09 14:06:30 -05:00
439c2fd980 Merge pull request #677 from stanmoore1/kk_update
Update to Kokkos r2.04.04 and add workaround for performance regression
2017-10-05 17:10:00 -06:00
a55adf4a68 Update to Kokkos r2.04.04 and add workaround for performance regression 2017-10-03 11:30:00 -06:00
e6969002ce having plain filelink instead of filelink.o confuses KOKKOS linking with nvcc 2017-09-25 19:37:37 -04:00
ee487ef4aa Merge pull request #652 from junghans/latte
Add LATTE fix
2017-09-22 10:32:19 -06:00
a8ae886667 update fix latte examples and virial 2017-09-21 10:40:54 -06:00
dd49d54889 new SNAP potentials and examples 2017-09-20 08:54:30 -06:00
59d2e13d48 add .gitignore and add Makefile.lammps.* symlinks to stay consistent with other libraries 2017-09-19 19:06:02 -04:00
ac897ea645 LATTE package doc update and some small code changes 2017-09-19 16:27:25 -06:00
be96486d66 compile all objects in the GPU library with -fPIC for building shared object 2017-09-19 11:24:48 -04:00
48dd824b26 ignore generated header files with OpenCL kernels 2017-09-19 11:24:38 -04:00
02665e45a4 fix doc in lib/latte/Makefile.lammps.* 2017-09-15 17:52:14 -06:00
17aeccf19f Merge remote-tracking branch 'origin/master' into latte 2017-09-15 16:18:13 -06:00
f1fce64ff9 Fix small typo to calculation of accumulated work in Colvars 2017-09-14 12:58:00 -04:00
f971cd6e45 Merge pull request #647 from rbberger/gpu_opencl_2
Use OpenCL 2.x API in GPU package when supported
2017-09-12 10:56:13 -06:00
e927794696 Merge pull request #643 from andeplane/gpu_opencl_compile_fix
Fixed OpenCL compilation issues with __global keywords
2017-09-12 10:31:22 -06:00
84b84c10db Use OpenCL 2.x API in GPU package when supported 2017-09-09 19:53:56 -04:00
2f6be88c4a Merge remote-tracking branch 'origin/master' into exaalt 2017-09-08 07:04:12 -06:00
7b1542a0ba merging stable and exaalt branches into exaaltstable 2017-09-07 16:31:50 -06:00
dbc60d949f Fixed OpenCL compilation issues with __global keywords 2017-09-06 15:08:02 +02:00
cbf3646806 Merge branch 'master' into USER-DPD_kokkos 2017-08-23 15:20:56 -06:00
b6c93f96cf Merge pull request #629 from stanmoore1/kokkos_update
Update Kokkos library to v2.04.00
2017-08-23 14:39:42 -06:00
e88ff8d6f9 correct embedded help for GPU lib Install.py 2017-08-23 15:20:30 -04:00
5c985946d5 Merge branch 'master' into USER-DPD_kokkos 2017-08-22 13:50:19 -06:00
090c792d90 Update Kokkos library to v2.04.00 2017-08-22 13:42:02 -06:00
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
dd67989c76 Merge pull request #601 from stanmoore1/kokkos_update
Update Kokkos library to v2.03.13
2017-08-17 11:32:18 -06:00
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
4041db8d1a Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17 2017-08-11 13:25:28 -04:00
c6d923b6c8 make download function more resilient by also catching failed execution 2017-08-10 21:15:35 -04:00
6d24be8bb7 whitespace cleanup 2017-08-10 21:14:40 -04:00
da01be7c18 More robust change from initial to target restraint centers in Colvars 2017-08-10 09:22:53 -04:00
146aa4cdbd fall back to wget when curl is not available 2017-08-10 09:05:23 -04:00
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