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12684 Commits

Author SHA1 Message Date
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
Emile Maras e03cc99467 made the command options more lammps standard style 2017-06-02 23:42:16 +02:00
Axel Kohlmeyer f59ee5bd62 enable support for dynamic groups in fix planeforce and fix lineforce 2017-06-02 08:45:15 -04:00
Axel Kohlmeyer af5f19604c remove no longer correct sentence from set command docs 2017-05-31 23:36:39 -04:00
Axel Kohlmeyer 3025996407 Merge branch 'master' into add-user-reaxc-omp 
This updates the code base with several required updates from master
 2017-05-31 12:53:38 -04:00
Stan Moore d2b6559039 Fixing issue in fix_qeq_reax 2017-05-31 10:52:03 -06:00
Axel Kohlmeyer 3c0cef9927 Merge branch 'fix_domain_pointer' of https://github.com/andeplane/lammps into collected-small-changes 2017-05-31 07:10:16 -04:00
Markus Hoehnerbach 937cf0b996 Bugfix: Kronecker term ignored in spline forces. 
The code ignored the kronecker(ktype, 0) or kronecker(ltype, 0)
terms in the contributing terms to NconjtmpI and NconjtmpJ.
The issue was present both in ::bondorder and ::bondorderLJ and
led to energy conservation issues.
It has been fixed by checking for the atom type before entering
the offending calculations and adding clarifying comments.
 2017-05-31 12:20:12 +02:00
Anders Hafreager f57f1efdff Setting lattice to NULL before creating 2017-05-31 00:34:26 -07:00
Axel Kohlmeyer 2b3c124e61 add example input for compute cnp/atom 2017-05-31 00:43:53 -04:00
Axel Kohlmeyer 85e917ae52 integrate compute cnp/atom contributed by Paulo Branicio (USC) 2017-05-31 00:38:44 -04:00
Axel Kohlmeyer 0be2cd3d43 fix bug reported on lammps-users, when not using the first molecule template 2017-05-30 23:58:56 -04:00