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12752 Commits

Author SHA1 Message Date
Axel Kohlmeyer afed8bb978 make changes to pass compilation test 
- move MEAM class into LAMMPS_NS namespace
- move inclusion of meam.h header to pair_meamc.cpp to reduce namespace pollution
- use forward declaration for MEAM class reference
- make that class reference a pointer and add a destructor
- replace MAX/MIN macros with versions compatible with older compilers
 2017-06-11 07:18:13 -04:00
Sebastian Hütter 03c93b31d6 Convert to C++, allow multiple instances 2017-06-11 11:29:24 +02:00
Sebastian Hütter d3f31547f9 Reformat code with clang-format (Mozilla style guide) 2017-06-11 11:29:24 +02:00
Sebastian Hütter 7c7468ffc2 Change c->cpp for better integration with makefile 2017-06-11 11:29:23 +02:00
Sebastian Hütter bab292b551 Create package USER-MEAMC 
Step 1: very literal translation of lib/meam
 2017-06-11 11:29:23 +02:00
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
Stefan Paquay 13643e185c Merge branch 'USER-MANIFOLD-gaussian-bump' 2017-06-06 15:47:41 -04:00
Emile Maras 06c8e95774 corrected the fix_neb documentation 2017-06-06 14:20:54 +02:00
Axel Kohlmeyer d437650c77 make certain Domain::box_change is initialized before use 2017-06-06 08:08:10 -04:00
Axel Kohlmeyer 46c5cbae8f update rigid fix documentation for added `reinit` keyword 2017-06-05 18:04:09 -04:00
Axel Kohlmeyer deff6c666e add flag "reinit" with args "yes" / "no" to fixes rigid & rigid/small 2017-06-05 17:31:43 -04:00
Axel Kohlmeyer 3a01836325 simplify code for rigid body overlap checks 2017-06-05 16:39:17 -04:00
Axel Kohlmeyer 0034d2db35 apply the rigid body checks to some more example codes 2017-06-05 16:30:30 -04:00
Stan Moore ed50bd2254 Removing unnecessary fences 2017-06-05 13:54:13 -06:00
Axel Kohlmeyer 90ca0852c7 use "body" list via Fix::extract() to correctly identify atoms in bodies 2017-06-05 15:48:23 -04:00
Axel Kohlmeyer 968de8548c apply test for overlap with rigid bodies to set and velocity command 2017-06-05 13:06:53 -04:00
Axel Kohlmeyer 95d6f05a76 add 3 APIs to Modify for checking if atoms overlap with any rigid fixes 2017-06-05 12:41:37 -04:00
Axel Kohlmeyer ff58ccac28 add clarification to impact of special bonds to manybody potentials 2017-06-04 21:21:32 -04:00