moebiusband/MD-Bench
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26 Commits

Author SHA1 Message Date
Rafael Ravedutti
43259eb3cf Adjust neighbor lists layout to keep neighbor ids contiguous in memory 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-30 01:57:26 +02:00
Rafael Ravedutti
04ade6bcec Pre-compute masks for 2xnn kernel with full neighbor-lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 19:33:26 +02:00
Rafael Ravedutti
85f1484449 Specialize force kernel when there are no masks to be checked 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-28 18:04:18 +02:00
Rafael Ravedutti
296a4c4e01 Set interaction masks as gromacs does 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2023-03-23 00:58:25 +01:00
Jan Eitzinger
3d0f4b97ee Switch copyright header in source files. 2022-09-05 10:39:42 +02:00
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
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
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
1389f89fb7 Add prunning kernel 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-28 17:20:39 +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
cd15911a97 When building neighbor lists, skip first iterations until z is in range 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-07 18:28:53 +01:00
Rafael Ravedutti
0eacb2453e Inline getBoundingBoxDistanceSq and avoid redundant loads from bbminz and bbmaxz 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-07 18:00:21 +01:00
Rafael Ravedutti
6ad1e58a3e Add first kernel using SIMD instrinsics for 4xn cases 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-02 18:00:44 +01:00
Rafael Ravedutti
85e7954932 Check all clusters in cell when building neighbor lists because ghost clusters may not be sorted 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-01 20:16:04 +01:00
Rafael Ravedutti
4a5216a177 Remove bb z-check on while loop when building neighbor lists 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-01 00:46:12 +01:00
Rafael Ravedutti
e64c3345bc Fix a few more bugs on gromacs variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-31 23:46:20 +01:00
Rafael Ravedutti
e0e6b6a68c Perform a few fixes for gromacs variant 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-31 17:49:22 +01:00
Rafael Ravedutti
6691803910 Add first version of force calculation with cluster scheme 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-28 18:07:41 +01:00
Rafael Ravedutti
eedcc97e4a Remove segfaults 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-28 15:18:54 +01:00
Rafael Ravedutti
a119fcdfdd Fix some segfaults and add function to update single atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-27 03:07:31 +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
Rafael Ravedutti
cbe42b8149 Fix errors to make gromacs approach compilable so far 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-25 12:19:28 +01:00
Rafael Ravedutti
6291709ae7 Add first draft code with GROMACS approach 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-25 00:43:10 +01:00
Rafael Ravedutti
df09c2861e Add first version with more than one optimization scheme 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-01-17 14:15:02 +01:00