moebiusband/MD-Bench
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42 Commits

Author SHA1 Message Date
Rafael Ravedutti 493915fe95 Fix code for AVX and remove warnings 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-08 15:30:37 +01:00
Rafael Ravedutti 437b380229 Adjust NVCC flags 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-11-07 20:37:01 +01:00
Jan Eitzinger 3d0f4b97ee Switch copyright header in source files. 2022-09-05 10:39:42 +02:00
Rafael Ravedutti 28d3946072 Move common modules to common directory 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-17 17:56:31 +02:00
Rafael Ravedutti 47db9e86b0 Introduce common directory 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-17 17:20:57 +02:00
Rafael Ravedutti 911ba63336 Adjust ISA options and improve output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-16 18:36:47 +02:00
Rafael Ravedutti 0caeea0494 Rename cuda.c to device.c 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 18:17:07 +02:00
Rafael Ravedutti 90609a2b5f Adjust file structure for CUDA 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 18:12:29 +02:00
Rafael Ravedutti 939197a785 Create separate structs DeviceAtom and DeviceNeighbor with device pointers 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 17:28:06 +02:00
Rafael Ravedutti 065b596074 Initial refactoring of CUDA code 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 04:19:38 +02:00
Rafael Ravedutti 959ff65126 Fix macro condition 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-12 01:29:40 +02:00
Rafael Ravedutti 87d006d418 Fix GPU version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-11 16:42:41 +02:00
Rafael Ravedutti 3d95ec4b0a Small fixes 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-09 19:19:48 +02:00
Rafael Ravedutti c18124b066 Integrate LAMMPS CUDA versions into master branch 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-08-09 18:53:53 +02:00
Rafael Ravedutti eb77e1a3bd Fix DEM setup 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-19 04:13:06 +02:00
Rafael Ravedutti 2e77f6207b Avoid errors when compiling for AVX2 due to SIMD LJ implementation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-19 02:30:26 +02:00
Rafael Ravedutti 577955dfb7 Apply first changes to DEM kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-13 02:34:33 +02:00
Rafael Ravedutti 99237241fb Include domain box on DEM input file 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-08 23:15:30 +02:00
Rafael Ravedutti 814f561993 Allow PBC in just some directions 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-08 02:30:03 +02:00
Rafael Ravedutti 32836eebcb Setup first DEM example with input file from lecture 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-07 02:11:50 +02:00
Rafael Ravedutti 9ffc09f497 Add DEM kernel to parameter options 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-07 00:47:38 +02:00
Rafael Ravedutti 79483a446e Adjust code with DEM to be compilable 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-06 01:07:39 +02:00
Rafael Ravedutti bb599c9ea8 Add first version of DEM kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-07-05 15:33:31 +02:00
Rafael Ravedutti e4d7faf91b Adjust cutforce and atom positions in stubbed version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-05-14 01:02:08 +02:00
Rafael Ravedutti bbdcaf2983 New stubbed version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-05-14 00:55:33 +02:00
Rafael Ravedutti 14838389ff Fix stubbed variant for LAMMPS algorithm 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-30 04:08:18 +02:00
Rafael Ravedutti ab2eb1ff50 Write LAMMPS kernel with SIMD intrinsics and implement AVX512 with double-precision functions 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-05 02:57:23 +02:00
Jan Eitzinger 5585ebcf42 Add ONEAPI config. Remove omp simd for full neigh. 2022-04-01 15:57:54 +02:00
Rafael Ravedutti 2a555a7deb Add simd reduction pragma to vectorize innermost loop on half-neighbor variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-21 17:02:09 +01:00
Rafael Ravedutti 719330807b Change data layout for force arrays according to position 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-18 01:40:51 +01:00
Rafael Ravedutti e7737e9151 Refactor half neighbor lists code 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-18 01:28:11 +01:00
Rafael Ravedutti 5df544637f Fix force calculation time in LAMMPS variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-17 02:53:58 +01:00
Rafael Ravedutti 887f41871c Add parameter reading for LAMMPS variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-17 02:44:34 +01:00
rafaelravedutti 459853dc25 Merge pull request #4 from RRZE-HPC/gromacs_sp 
Gromacs sp
 2022-03-15 20:31:42 +01:00
Rafael Ravedutti d61576699d Add first compilable version of Gromacs with SP 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-15 02:40:56 +01:00
Jan Eitzinger c2fcd50773 Initial version of lammps halfneighbor list 2022-03-10 17:06:45 +01:00
Jan Eitzinger ba3a0524f6 Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2022-03-10 16:30:40 +01:00
Jan Eitzinger 6203cb12b6 Start to introduce halfneigh version 2022-03-10 16:30:37 +01:00
Rafael Ravedutti 022aa75c75 Add cutoff radius and skin as parameters of simulation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-28 22:34:42 +01:00
Rafael Ravedutti ed2929c813 Add percentage of atoms within cutoff radius when using LAMMPS reference version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-25 14:40:33 +01:00
Rafael Ravedutti 1a708f2d3b Add PDB reading functions to lammps variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-24 15:17:51 +01:00
Rafael Ravedutti aa0f4048d0 Rename default directory to lammps and reorganize gromacs variant steps 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-25 21:00:11 +01:00