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12556 Commits

Author SHA1 Message Date
dstelter92 3214d639aa removed unneeded .gitignore 2017-06-14 12:26:52 -04:00
dstelter92 0ad66ecb89 Added compute_scalar to fix_grem for easier output managment, updated example to show use 2017-06-14 12:18:22 -04:00
Anders Hafreager e139a7fd45 Updated docs for vashishta/gpu 2017-06-14 13:52:03 +02:00
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 32b967ed9c add rigid body overlap warnings to change_box and delete_atoms 2017-06-13 16:26:49 -04:00
Axel Kohlmeyer 11751521e7 remove dead code 2017-06-12 22:49:31 -04:00
Axel Kohlmeyer 7a05d87f7c update USER-TALLY examples 2017-06-12 22:20:36 -04:00
Axel Kohlmeyer b01143102d refactoring of USER-TALLY computes to handle sparse and hybrid systems 
with sparse and hybrid systems, Pair::ev_tally() may not be called on
every processor and thus the computes in USER-TALLY may hang during
reverse communication because of the error->all() call after checking
whether callback from Pair::ev_tally() has been called at least once.
To address this cleanly, a second callback function needs to be added,
which is run during Pair::ev_setup() and will now handle all memory
re-allocation and clearing of accumulators, just like it is done for
regular tallied data.
 2017-06-12 22:12:12 -04:00
Axel Kohlmeyer e530ba46f4 cleanup and bugfix for compute heat/flux/tally 
- make heatj a pointer instead of a static array
- fix memory leaks for eatom, stress
- simplify and streamline computation
 2017-06-12 21:46:00 -04:00
Axel Kohlmeyer 420db44596 print incompatible pair style warnings in USER-TALLY only on MPI rank 0 2017-06-12 20:05:15 -04:00
Axel Kohlmeyer cfeb9b5ba5 Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes 2017-06-12 14:20:50 -04:00
Axel Kohlmeyer 0c805d0b70 correctly skip over point particles and point dipoles when counting extendend particles in fix rigid/small 2017-06-12 14:20:38 -04:00
Axel Kohlmeyer 6b289b0794 change incorrect EINERTIA constant in rigid body integrators from 4.0 to 2.0 (same as in other integrators) 2017-06-12 14:07:40 -04:00
Axel Kohlmeyer daa77176ad add restart support to fix deform. only "initial" data is restored and some consistency check performed 2017-06-10 17:28:17 -04:00
Axel Kohlmeyer 8f18c284d3 add crude check to print warning when using compute cnp/atom on multi-type system 2017-06-10 17:08:07 -04:00
Axel Kohlmeyer 06915162b0 whitespace cleanup 2017-06-10 16:56:54 -04:00
Axel Kohlmeyer a849f35dcd adjust compute cnp/atom to match the documentation. need to skip atoms not in compute group. 2017-06-10 16:55:42 -04:00
Axel Kohlmeyer 4c69bbcf5c apply rigid body check to displace_atoms command 2017-06-10 11:37:54 -04:00
Axel Kohlmeyer dd44189d1f fix bug in compute orientorder/atom argument parsing 2017-06-10 04:35:11 -04:00
Axel Kohlmeyer 2f6bbcfbbc output detailed multi-thread performance data only with "timer full" 2017-06-09 15:11:40 -04:00
Axel Kohlmeyer 2686b7f830 simplify compatibility check for fix reax/c/bonds with pair styles 2017-06-09 14:39:52 -04:00
Axel Kohlmeyer d3a863e7af when identifying molecules/clusters fall back to unfiltered coordinates for ghost atoms 2017-06-09 14:35:12 -04:00
Axel Kohlmeyer 64e8000720 expand error message requiring a reax/c derived pair style 2017-06-09 11:42:35 -04:00
Axel Kohlmeyer c160d0cd5e fix reax/c/species/omp doesn't is not needed anymore 2017-06-09 11:04:11 -04:00
Axel Kohlmeyer 9222278fb5 match reax/c pair style variants against prefix and not full name 2017-06-09 11:00:16 -04:00
Lars Pastewka bdf03757e6 MAINT: Simplified GPL headers. 2017-06-08 23:20:21 +02:00
Lars Pastewka c81bc108f9 DOC: Updated dump_modify and dump netcdf documentation. 2017-06-08 23:19:38 +02:00
Lars Pastewka 10d2e7c380 MAINT: DumpNetCDF and DumpNetCDFMPIIO need access to thermo output. 2017-06-08 23:18:54 +02:00
Lars Pastewka bd83c7c7f9 MAINT: Updated contact data and fixed typos. 2017-06-08 23:02:22 +02:00
Lars Pastewka d51cee1b82 MAINT: Turned 'global' options into a 'thermo yes'/'thermo no' option that enables dumping of thermo data to the netcdf file (for parallel NetCDF/MPIIO variant). 2017-06-08 22:58:27 +02:00
Lars Pastewka be476c9e1d MAINT: Turned 'global' options into a 'thermo yes'/'thermo no' option that enables dumping of thermo data to the netcdf file. 2017-06-08 22:43:10 +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
Axel Kohlmeyer afd4f5b0a6 Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes 2017-06-07 17:37:13 -04:00
Axel Kohlmeyer 31a734b03d sbmask function should be flagged as const indicating no side effects 2017-06-07 17:10:33 -04:00
Axel Kohlmeyer 2e728972e2 make pair styles lj/cut/tip4p/long/omp, lj/long/tip4p/long and lj/long/tip4p/long/omp consistent with the reset of tip4p styles 2017-06-07 17:09:45 -04:00
Lars Pastewka 36c8b26fef BUG: DumpNCMPIIO is now called DumpNetCDFMPIIO 2017-06-07 14:01:36 +02:00
Lars Pastewka 99ef36f440 MAINT: Switched NetCDF from 64BIT_OFFSET to 64BIT_DATA which can handle frames (of unlimited dimension) > 2 GB. This becomes important for system sizes 100 Mio atoms and upwards. 2017-06-07 13:52:33 +02:00
Axel Kohlmeyer a2edef7c9c local variable fp in pair style eam/cd was shadowing class member. renamed local variable to fptr 2017-06-07 00:23:53 -04:00
Axel Kohlmeyer 1f9504c546 some more bookkeeping updates triggered by the lj/sf style removal 2017-06-06 17:31:45 -04:00
Axel Kohlmeyer 04ebd81ac5 minor whitespace cleanup 2017-06-06 17:26:18 -04:00
Axel Kohlmeyer 5cb56796a2 alias pair style lj/sf to lj/smooth/linear and remove/update related files 2017-06-06 17:26:06 -04:00
Axel Kohlmeyer 0c1b87c8cf Merge branch 'collected-small-changes' of github.com:akohlmey/lammps into collected-small-changes 2017-06-06 16:27:07 -04:00
Axel Kohlmeyer cd67eaa5f4 update e-mail and affiliation for stefan paquay in USER-MANIFOLD related files 2017-06-06 16:26:57 -04:00
Stefan Paquay 18dee3f78e Added Gaussian bump. Updated e-mail address. 2017-06-06 16:03:09 -04:00