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12724 Commits

Author SHA1 Message Date
Axel Kohlmeyer 06fe703eed add missing mergesort header 2017-06-14 23:22:49 -04:00
Axel Kohlmeyer 8500a197ae whitespace cleanup 2017-06-14 23:13:10 -04:00
Axel Kohlmeyer 1f17e8ebbb remove need for static class member variables in Dump and Irregular 
The dump and irregular classes were using qsort() from the C-library
for sorting lists through custom comparison functions, which required
access to additional data, which was passed via static class variables,
i.e. globals. This collides with having multiple LAMMPS instances in
the same address space.

the calls to qsort() are replaced with a custom merge sort, which passes
a void pointer to the comparison functions, which can contain any kind
of desired information, e.g. a class handle or a list
 2017-06-14 23:10:53 -04:00
Axel Kohlmeyer fcc387f232 change ring communication API to no longer require a static variable pointing to 'this' of the caller 2017-06-14 17:01:06 -04:00
dstelter92 e7634a44f4 updated thermo_modify in example 2017-06-14 13:11:54 -04:00
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
Sebastian Hütter 3d066283b6 fix compilation, move meam_cleanup to destructor 2017-06-13 19:41:29 +02:00
Sebastian Hütter 29e60fa53a Move rho/gamma arrays to fields of MEAM, remove arguments and arrdim macros 2017-06-13 18:39:40 +02:00
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
Sebastian Hütter 078f2a0a47 Convert/Reindex phir* arrays 2017-06-12 17:41:09 +02:00
Axel Kohlmeyer bdd908c303 update documentation for USER-MEAMC package and pair style meam/c 2017-06-11 21:54:18 -04:00
Axel Kohlmeyer b45a95107d remove ambiguous access conflict to fm_exp() in pair style agni/omp after moving fm_exp() to math_special.h 2017-06-11 18:45:40 -04:00
Sebastian Hütter 9f852f5f58 Improve C++-ness, eliminate some macros 
- fm_exp moved to math_special (exp2 was already there)
- use std::min/max template instead of macros
- use memory->create for dynamic arrays (still 1-indexed with macro)
- remove _ from function names, adjust method visibility
 2017-06-11 16:55:41 +02:00
Axel Kohlmeyer fea28d8028 ensure that allocatable_double_2d types are initialized 2017-06-11 07:29:44 -04:00
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