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Author SHA1 Message Date
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
Rafael Ravedutti
af1756bfe4 Fix skin for Argon simulation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-04 22:22:35 +02:00
Rafael Ravedutti
4d11c5a3c2 Merge branch 'master' of github.com:RRZE-HPC/MD-Bench 2022-04-04 21:52:47 +02:00
Rafael Ravedutti
e48b3fb653 Add option to check if cj is local before applying reaction force 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-04-04 21:52:40 +02:00
Jan Eitzinger
7a0d6479a1 Merge branch 'master' of https://github.com/RRZE-HPC/MD-Bench 2022-04-01 15:58:05 +02:00
Jan Eitzinger
5585ebcf42 Add ONEAPI config. Remove omp simd for full neigh. 2022-04-01 15:57:54 +02:00
Rafael Ravedutti
fdbeed4368 Fix AVX2 versions with half neighbor lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-27 16:39:39 +02:00
Rafael Ravedutti
0e742766b7 Add working version of Simd4xn kernel with half neighbor lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-23 15:54:18 +01:00
Rafael Ravedutti
e72323ab6a Fix Simd2xnn Kernel with half neighbor lists and add AVX512 intrinsics with double 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-23 15:21:07 +01:00
Rafael Ravedutti
94521f03b3 Fix reference version with half neighbor lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-23 14:31:47 +01:00
Rafael Ravedutti
8709bc2a06 Add first version for half neighbor lists in GROMACS variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-22 23:47:05 +01:00
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
Rafael Ravedutti
d4b34e1fa4 Fix intrinsics for AVX2 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-17 00:35:21 +01:00
Rafael Ravedutti
4090f43095 Optimize partial forces reduction for compute_4xn kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-16 17:54:52 +01:00
Rafael Ravedutti
f3263a2d48 Separate simd file into multiple files 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-16 14:52:55 +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
d47173d7a2 Fix Simd2xNN kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-15 19:59:10 +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
Rafael Ravedutti
8669f2f6d7 Fix LJ Simd4xN kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-11 01:12:59 +01:00
Rafael Ravedutti
d79c3c2a1d Add first working version with 4x8 config (ref kernel) 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-10 22:33:41 +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
22d0f0b958 Commit version that works for M=N 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-10 01:31:50 +01:00
Rafael Ravedutti
2b441e691e Make code compilable 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-09 17:23:49 +01:00
Rafael Ravedutti
c7360305c8 Add first draft version of GROMACS method separating i-clusters and j-clusters 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-09 02:25:39 +01:00
Rafael Ravedutti
cecb31d6a9 Update params for argon_1000 test case 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-07 14:49:38 +01:00
Rafael Ravedutti
ba6785a865 Allow parameter reading from files and update data 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-05 03:21:52 +01:00
Rafael Ravedutti
aae29a5b5a Add code to read GRO files 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-03 20:03:33 +01:00
Rafael Ravedutti
af92800c64 Add SIMD version with AVX (no AVX2) and XTC output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-03-02 23:12:04 +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
1389f89fb7 Add prunning kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-28 17:20:39 +01:00
Rafael Ravedutti
c62e4ea4ad Add clusters efficiency on stats 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-28 16:10:09 +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
e637a26844 Add percentage of atoms within cutoff radius when using GROMACS reference version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-25 14:19:48 +01:00
Rafael Ravedutti
fdd18df816 Fix argon simulation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-24 16:42:58 +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
d0ec9520f2 Write function to read PDB files and include data for Argon simulation 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-24 02:36:17 +01:00
Rafael Ravedutti
ca7775a62a Add average atoms per cluster on stats 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-09 17:50:54 +01:00
Rafael Ravedutti
769bab0faa Separate local and ghost cluster edges on VTK output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-08 16:12:22 +01:00