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744 Commits

Author SHA1 Message Date
Giacomo Fiorin f479f02589 Fix a Colvars error that was hidden by the previous segfault 2017-10-20 13:41:31 -04:00
Giacomo Fiorin 6e7504f153 Import segfault fix in Colvars module 2017-10-19 08:09:44 -04:00
Giacomo Fiorin 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
Steve Plimpton 18ca2292c2 Merge pull request #686 from giacomofiorin/lepton-library 
Add Lepton library within lib/colvars
 2017-10-13 09:48:42 -06:00
Giacomo Fiorin d90aad887e Add Lepton library within lib/colvars 2017-10-09 15:25:43 -04:00
Ryan S. Elliott 775a15b9da Update lib/kim for kim-api-v1.9.2 2017-10-09 14:06:30 -05:00
Steve Plimpton 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
Stan Moore a55adf4a68 Update to Kokkos r2.04.04 and add workaround for performance regression 2017-10-03 11:30:00 -06:00
Axel Kohlmeyer e6969002ce having plain filelink instead of filelink.o confuses KOKKOS linking with nvcc 2017-09-25 19:37:37 -04:00
Steve Plimpton ee487ef4aa Merge pull request #652 from junghans/latte 
Add LATTE fix
 2017-09-22 10:32:19 -06:00
Steve Plimpton a8ae886667 update fix latte examples and virial 2017-09-21 10:40:54 -06:00
Steve Plimpton dd49d54889 new SNAP potentials and examples 2017-09-20 08:54:30 -06:00
Axel Kohlmeyer 59d2e13d48 add .gitignore and add Makefile.lammps.* symlinks to stay consistent with other libraries 2017-09-19 19:06:02 -04:00
Steve Plimpton ac897ea645 LATTE package doc update and some small code changes 2017-09-19 16:27:25 -06:00
Axel Kohlmeyer be96486d66 compile all objects in the GPU library with -fPIC for building shared object 2017-09-19 11:24:48 -04:00
Axel Kohlmeyer 48dd824b26 ignore generated header files with OpenCL kernels 2017-09-19 11:24:38 -04:00
Christoph Junghans 02665e45a4 fix doc in lib/latte/Makefile.lammps.* 2017-09-15 17:52:14 -06:00
Christoph Junghans 17aeccf19f Merge remote-tracking branch 'origin/master' into latte 2017-09-15 16:18:13 -06:00
Giacomo Fiorin f1fce64ff9 Fix small typo to calculation of accumulated work in Colvars 2017-09-14 12:58:00 -04:00
Steve Plimpton 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
Steve Plimpton 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
Richard Berger 84b84c10db Use OpenCL 2.x API in GPU package when supported 2017-09-09 19:53:56 -04:00
Christoph Junghans 2f6be88c4a Merge remote-tracking branch 'origin/master' into exaalt 2017-09-08 07:04:12 -06:00
Richard Zamora 7b1542a0ba merging stable and exaalt branches into exaaltstable 2017-09-07 16:31:50 -06:00
Anders Hafreager dbc60d949f Fixed OpenCL compilation issues with __global keywords 2017-09-06 15:08:02 +02:00
Stan Moore cbf3646806 Merge branch 'master' into USER-DPD_kokkos 2017-08-23 15:20:56 -06:00
Steve Plimpton b6c93f96cf Merge pull request #629 from stanmoore1/kokkos_update 
Update Kokkos library to v2.04.00
 2017-08-23 14:39:42 -06:00
Axel Kohlmeyer e88ff8d6f9 correct embedded help for GPU lib Install.py 2017-08-23 15:20:30 -04:00
Stan Moore 5c985946d5 Merge branch 'master' into USER-DPD_kokkos 2017-08-22 13:50:19 -06:00
Stan Moore 090c792d90 Update Kokkos library to v2.04.00 2017-08-22 13:42:02 -06:00
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
Tim Mattox 4041db8d1a Merge branch 'master' into USER-DPD_kokkos as of patch 10Aug17 2017-08-11 13:25:28 -04:00
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
Stan Moore 9695aa6092 Merge branch 'master' into USER-DPD_kokkos_testing 2017-07-27 15:51:56 -06:00
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
Stan Moore bc446bb8b0 Merge branch 'master' into USER-DPD_kokkos_testing 2017-07-25 12:12:30 -06:00
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
Axel Kohlmeyer 7ccb0d37cd port USER-SMD folder. make voronoi consistent with it 2017-07-18 17:37:48 -04:00
Axel Kohlmeyer 03cd4c5255 ported lib/voronoi/Install.py to python 3.x and tested with 2.7 2017-07-18 17:16:10 -04:00
Richard Berger d7355801df Make KIM Install.py Python 3 compatible 2017-07-15 12:03:04 -05:00
Steve Plimpton 296e572e69 better Install.py script for KIM from Ryan Elliott 2017-07-14 16:25:16 -06:00
Trung Nguyen cdac5f496c Built 3-body short neighbor list for the 3-body kernels using per-pair cutoffs for vashishta gpu style 2017-07-11 00:13:56 -05:00
Trung Nguyen 8c9db3ea00 Built 2-body short neighbor list and used for 2-body kernels in tersoff gpu styles 2017-07-10 23:50:21 -05:00
Ryan S. Elliott e30c5fc956 Fixed shebang and renamed to lib/kim/Install.py 2017-07-10 21:05:29 -05:00
Ryan S. Elliott c29e8fba9b Updated lib/kim/README file to go along with new install.py 2017-07-10 17:00:30 -05:00
Ryan S. Elliott 8d592f4b9e Finalized code for lib/kim/install.py 2017-07-10 16:43:23 -05:00
Trung Nguyen ea2b01e83b Refactored 3-body gpu styles to remove code duplication 2017-07-08 20:17:31 -05:00
Trung Nguyen 34fe2273f6 Added short neighbor list implementation for tersoff/zbl/gpu and tersoff/mod/gpu 2017-07-08 14:59:48 -05:00
Trung Nguyen 77c60189b8 Minor cleanups for tersoff/gpu 2017-07-08 14:43:53 -05:00
Trung Nguyen 1c6533e53d Working on short neighbor list for tersoff/gpu 2017-07-08 14:15:26 -05:00
Trung Nguyen 68206079da Supported short neighbor lists for 3-body kernels in sw/gpu and vashishta/gpu 2017-07-07 16:47:24 -05:00
Ryan S. Elliott b0be8b24ea Further work on lib/kim/install.py 2017-07-06 15:50:03 -05:00
Ryan S. Elliott 16fc2d6fe1 Add install.py and update config for kim lib 2017-07-06 15:49:58 -05:00
Stan Moore da0dcbe0bb Updating to master 2017-06-19 10:56:24 -06:00
sjplimp d3c90f3c14 Merge pull request #510 from akohlmey/collected-small-changes 
Collected small changes
 2017-06-15 11:12:14 -06:00
sjplimp 7227bc415d Merge pull request #526 from andeplane/vashishta_gpu 
Implemented pair style vashishta in GPU package
 2017-06-15 08:52:13 -06:00
Anders Hafreager d7646aeeed Fixed opencl error 2017-06-14 12:03:47 +02:00
Anders Hafreager 5f9341813d Removed debug output 2017-06-14 10:57:54 +02:00
Anders Hafreager 8441307185 Removed non-general CUDA-dir in makefile 2017-06-14 10:28:46 +02:00
Anders Hafreager 720af5c360 Added vashishta to OpenCL makefile 2017-06-14 10:27:52 +02:00
Anders Hafreager eeff0b8633 Added vashishta GPU package for NVidia 2017-06-14 10:24:16 +02:00
Axel Kohlmeyer 0ecdb99885 fix uninitialized data access as reported by @martok in #174 2017-06-08 13:50:17 -04:00
Stan Moore 00ce15d043 Remove tpls dir 2017-06-08 10:43:19 -06:00
Stan Moore 5c1d17d1c0 Updating Kokkos lib to v2.03.05 2017-06-08 10:42:08 -06:00
Stan Moore 2cf83d9fca Updating from master to 19May17 2017-05-25 11:21:10 -06:00
Christian Negre 98713680ec added alternative linking line for intel mkl 2017-05-17 11:36:31 -06:00
Richard Berger f8af7edf92 Merge remote-tracking branch 'upstream/master' into python_refactoring 2017-05-06 16:00:22 -04:00
sjplimp fbddfe2729 Merge pull request #455 from stanmoore1/kokkos_update 
Updating Kokkos library to version 2.03.00
 2017-05-04 11:23:39 -06:00
sjplimp dcc5472cba Merge pull request #452 from akohlmey/small-fixes-and-updates 
Small fixes and updates
 2017-05-04 11:23:23 -06:00
Steve Plimpton addd87c0f7 new Section package and start doc pages and build scripts 2017-05-04 11:22:20 -06:00
Axel Kohlmeyer b8cb80b219 rename files in GPU library from cg_cmm to lj_sdk 2017-04-26 19:46:10 -04:00
Axel Kohlmeyer cd435c0c58 change references from cg_cmm to lj_sdk and from cmm to sdk 2017-04-26 19:44:25 -04:00
Stan Moore cc6104aeaf Merge branch 'master' into kokkos_update 2017-04-25 14:11:36 -06:00
Stan Moore 8910ec6e59 Updating Kokkos lib to 2.03.00 2017-04-25 13:48:51 -06:00
Axel Kohlmeyer 25e8ed63a2 whitespace cleanup in VMD plugin headers 2017-04-18 11:46:19 -04:00
Axel Kohlmeyer dee3536144 update VMD molfile plugin headers and move them to lib/molfile (where they belong) 2017-04-18 11:42:31 -04:00
Axel Kohlmeyer 3cbf4f3b58 correct logic bug in else branch of the conditional 2017-04-14 11:57:53 -04:00
Axel Kohlmeyer 6c2dd7ebb1 pass the name of the python interpreter compatible with the python package to 'make install-python' 2017-04-14 11:44:36 -04:00
Richard Berger 9a027a01da Add Python 3 compatibility to PYTHON package 2017-04-11 20:24:42 -04:00
Steve Plimpton 49dd9449b8 fix gcmc updates from Aidan, trimming of output for replica commands 2017-04-11 08:35:09 -06:00
Tim Mattox 17c8e695a4 Merge branch 'master' into USER-DPD_kokkos as of patch 10 Mar 2017 2017-03-10 21:37:52 -05:00
Giacomo Fiorin 5fe6206638 Update Colvars module to version 2017-03-10 2017-03-10 09:16:58 -05:00
Christian Negre 3298c37982 Makefile.lammps.gfortran for latte 2017-03-09 14:30:21 -07:00
Stan Moore de27305227 Merge branch 'master' of https://github.com/lammps/lammps into USER-DPD_kokkos 2017-03-07 11:47:18 -07:00
Richard Berger e261bef7bb Spelling fixes in source files 2017-03-05 18:30:39 -05:00
Tim Mattox 641bf72f20 lib kokkos: Enable deterministic use of Random_XorShift*_Pool. 
Add support for lock-free and deterministic use of Random_XorShift*_Pool
by giving state_idx selection and lock responsibility up to the
application.  Done by an overload of get_state() to take sate_idx as
an argument that the appplication guarantees is concurrently unique
and within the range of num_states that the application passed to init().
In other words, this allows the RNG state to be associated with some
application specific index, rather than a runtime arbitrary thread ID,
and thus the application can control which work is performed using
which RNG in a deterministic manner, regardless of which thread
performs the work.
 2017-03-01 11:52:33 -05:00
Tim Mattox 6e26358ec3 lib kokkos bugfix: on a CUDA host, the random state wasn't preserved. 
Random_XorShift*_Pool<Kokkos::Cuda>::free_state() has two purposes:
1) update the state value kept in the pool
2) unlock the state
For a CUDA host thread, ONLY skip step 2, not both.
 2017-03-01 11:46:26 -05:00
Christian Negre 2dcbc805ba min latte partially fixed 2017-02-23 18:20:02 -07:00
Stan Moore 90e5ae965d Add missing flags to Kokkos Makefile 2017-02-13 11:19:46 -07:00
Stan Moore 33af7ab248 Remove merge line 2017-02-13 10:59:22 -07:00
Stan Moore 8f9b2aca06 Removing unused files in Kokkos lib 2017-02-13 10:53:51 -07:00
Stan Moore 383da816c2 Updating Kokkos lib 2017-02-13 10:50:34 -07:00
Christian Negre 6d47cf350c Makefile for latte_dev 2017-01-19 15:42:09 -07:00
sjplimp d8bc590aaf Merge pull request #327 from stanmoore1/kokkos_lib_update 
Updating Kokkos lib
 2017-01-17 09:04:12 -07:00
Christian Negre aaa7dca21b Makefile.lammps.gfortran 2017-01-12 17:13:02 -07:00
Christian Negre 6bd17be454 Makefile.lammps.gfortran 2017-01-12 16:58:27 -07:00
Christian Negre f51ddf8450 Makefile.lammps.gfortran 2017-01-12 13:50:02 -07:00
Stan Moore 7162cafdf5 Squelching output from Makefile 2017-01-10 14:46:30 -07:00
Stan Moore ee9e7cfbd5 Fixing Kokkos CUDA Makefile issue 2017-01-10 13:22:36 -07:00
Stan Moore 7839c335da Fixing compile error with Kokkos CUDA Makefiles 2017-01-10 13:05:00 -07:00
Christian Negre 1f6cfb1b31 Makefile.lammps.gfortran changed 2017-01-10 10:56:31 -07:00
Steve Plimpton c31f1e9f22 add fix mscg command, example, lib 2017-01-09 13:36:40 -07:00
Stan Moore 9250a55923 Adding enable_lambda to KOKKOS_CUDA_OPTIONS 2017-01-09 12:24:30 -07:00
Stan Moore a9f0b7d523 Updating Kokkos lib 2017-01-09 10:39:46 -07:00
Christian Negre 967cdd947e cleanup 2017-01-05 15:37:01 -07:00
Giacomo Fiorin b0263e87bb Fix missing force with extended-Lagrangian mass 2016-12-27 17:16:32 -05:00
Giacomo Fiorin f553e230db Update Colvars library to version 2016-12-22 
Significant code cleanup and several fixes (walls + extended Lagrangian)

New harmonicWalls bias to apply confining boundaries with time-dependent force
constant & integration
 2016-12-27 13:17:34 -05:00
Giacomo Fiorin 6ab716164b Fix seg fault for gyration collective variable 2016-12-27 13:17:02 -05:00
Giacomo Fiorin 7a45c72b97 Allow extended Lagrangian on non-scalar collective variables 2016-12-27 12:35:30 -05:00
Christian Negre fe99fc287d changes in fix_latte 2016-11-28 15:29:37 -07:00
Christian Negre f040f15218 changes in latte makefile for lattelib and README 2016-11-14 16:11:12 -07:00
Christian Negre f3d6ecf07b changes for lattelib 2016-11-14 07:58:47 -07:00
Steve Plimpton 6f23f6535c initial dummy version of fix_latte.cpp 2016-11-09 13:48:11 -07:00
Giacomo Fiorin 182141b850 Make SMP parallelism for Colvars optional 2016-10-24 17:13:34 -04:00
Giacomo Fiorin e02505c8cc Add ensemble-biased metadynamics (Fabrizio Marinelli, NIH) 2016-10-24 17:11:09 -04:00
Giacomo Fiorin be2d155cef Minor changes and fixes not relevant to LAMMPS 2016-10-24 17:10:52 -04:00
Giacomo Fiorin c243093980 Fix wall forces and subtractAppliedForce for extended-Lagrangian ABF 2016-10-24 17:05:47 -04:00
Giacomo Fiorin ad57a17f48 Add C-linkage wrapper for colvarscript (useful with ctypes) 2016-10-24 16:48:20 -04:00
Axel Kohlmeyer 019bc0ba0b fix typos in Makefile.lammps for NetCDF support 2016-10-19 07:39:03 -04:00
Axel Kohlmeyer 27796b431e avoid distracting error output 2016-10-18 15:32:20 -04:00
Axel Kohlmeyer 2b47fa6653 update Makefile.lammps and add README according to suggestions by lars pastewka 2016-10-18 15:05:30 -04:00
Axel Kohlmeyer 4502d3276b updated Makefile.lammps for NetCDF support based on suggestions from lars pastewka 2016-10-18 14:45:06 -04:00
Axel Kohlmeyer ecb03dd2df import lammps-netcdf code as USER-NC-DUMP package 2016-10-11 23:03:18 -04:00
Axel Kohlmeyer 683689c808 revert to previous style conventions for size_t constants 2016-10-08 11:00:23 -04:00
Axel Kohlmeyer e01e90eb96 workaround for double free issue when using USER-COLVARS with lammps code loaded as shared library into a standalone executable 2016-10-08 10:45:22 -04:00
sjplimp 54fc194e5b Merge pull request #199 from akohlmey/small-changes 
Collected small changes and bugfixes
 2016-10-06 15:49:24 -06:00
A Bartok-Partay 8ea063378e add NETCDF libs (as defined in QUIP) to the linking line if QUIP was built with NETCDF support 2016-10-06 12:16:25 +01:00
Giacomo Fiorin 8809a603fb Colvars update: issue a warning that cannot be ignored regarding total forces 2016-10-05 18:26:21 -04:00
Giacomo Fiorin 969d3cf4b0 Colvars update: make ABF check that the colvar isn't using already subtractAppliedForce 2016-10-05 18:25:40 -04:00
Axel Kohlmeyer 03766dbda7 apply bugfix for MEAM provided by Wolfgang Verestek on lammps-users 
this closes lammps/#188
 2016-10-03 16:28:59 -04:00
Axel Kohlmeyer a3e05a2bac permission cleanup 2016-10-01 06:34:45 -04:00
Axel Kohlmeyer 6d200061ca update colvars library to version 2016-09-30 2016-09-30 08:15:44 -04:00
Axel Kohlmeyer 5b2becd09b Merge branch 'integration' into new-master 2016-09-29 10:37:09 -04:00
sjplimp 484122b8b6 sync with GH 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15592 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-16 19:21:34 +00:00
Axel Kohlmeyer 9637a5b530 colvars bugfix. updates colvars library to version 2016-09-14 2016-09-15 19:44:26 -04:00
Axel Kohlmeyer 14bed44743 ignore Makefile.lammps in lib tree 2016-09-13 09:36:48 -04:00
Axel Kohlmeyer 18cacb8e1d ignore *.mod generated by fortran compilers 2016-09-13 09:36:19 -04:00
sjplimp b190abea39 sync with GH 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15561 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-08 20:20:32 +00:00
sjplimp 07e55ef61e Merge pull request #22 from akohlmey/colvars-update 
accumulated colvars library update and lib "make clean" improvement
 2016-09-08 14:14:49 -06:00
Steve Plimpton 236ebf7fab Kokkos lib update 2016-09-08 13:56:18 -06:00
Axel Kohlmeyer 3a74ccffa2 update colvars library to version 2016-09-03 
(cherry picked from commit 4181f5ac9d)
 2016-09-06 21:28:59 -04:00
Axel Kohlmeyer c8cfd53c1b adjust makefiles in lib tree, so they don't return an error exit code on "make clean" targets. 
(cherry picked from commit 4117218ca3)
 2016-09-06 21:28:55 -04:00
Axel Kohlmeyer 16607a0132 update colvars library to version 2016-08-19 
(cherry picked from commit c67326be6d)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 3b476d914f update colvars to version 2016-08-10 
(cherry picked from commit eba3ad9abb)
 2016-09-06 21:27:46 -04:00
Axel Kohlmeyer 977b9e542f update colvars to another set of changes from the upstream repo 
(cherry picked from commit cb816f8cba)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer 1b33d00785 update colvars makefile dependencies 
(cherry picked from commit df99a85930)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer 3d2e5d0a50 suppress compiler warning 
(cherry picked from commit 6f227e194e)
 2016-09-06 21:27:45 -04:00
Axel Kohlmeyer ec2a6b9f0d update colvars to version 2016-08-10 
(cherry picked from commit f2ddf828e4)
 2016-09-06 21:27:41 -04:00
Axel Kohlmeyer 77620106a4 update colvars library to version 2016-08-05 
(cherry picked from commit 459db2eb6b)

# Conflicts:
#	doc/src/PDF/colvars-refman-lammps.pdf
 2016-09-06 21:26:50 -04:00
stamoor 39be4185c4 Updating Kokkos lib 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15556 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-06 23:06:32 +00:00
stamoor 1ad033ec0c Updating Kokkos lib 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15555 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-09-06 23:02:50 +00:00
sjplimp 083ff54c0c small bug fixes 
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15527 f3b2605a-c512-4ea7-a41b-209d697bcdaa
 2016-08-31 20:26:15 +00:00
Steve Plimpton 4051aedf2c Merge branch 'small' into integration 
Conflicts:
	src/compute_omega_chunk.cpp
 2016-08-31 13:58:12 -06:00
Steve Plimpton ec8b9e21db sync with SVN 2016-08-31 13:28:26 -06:00