moebiusband/MD-Bench
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35 Commits

Author SHA1 Message Date
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
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
Rafael Ravedutti
6a35a7a482 Update stats for cluster version 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-08 00:55:27 +01:00
Rafael Ravedutti
8deee3d954 Add cluster edges in VTK output 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-08 00:11:10 +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
cdb1d5b9f1 Add version with AVX2 intrinsics for gromacs scheme 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-04 17:52:48 +01:00
Rafael Ravedutti
34ce407f18 Update stats for gromacs scheme 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-04 14:47:37 +01:00
Rafael Ravedutti
6e6a3f6502 Use aligned loads when gathering j atoms 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-04 14:29:32 +01:00
Rafael Ravedutti
7b90800a2b Setting forces to zero before calculation is not required 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-04 14:05:04 +01:00
Rafael Ravedutti
9daf9e5f4d Fix exclusion masks and add SIMD debug tools 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-02 21:54:18 +01:00
Rafael Ravedutti
4c5f013bf4 Assign masked adds results to forces 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-02 18:07:56 +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
5fd2d422ee Adjust kernels to work with MxN loops 
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
 2022-02-02 00:49:55 +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