Commit Graph

25 Commits

Author SHA1 Message Date
Rafael Ravedutti
151f0c0e6f Add extendend param option
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2023-05-29 02:27:32 +02:00
Rafael Ravedutti
6eedf1776e Small fixes into GROMACS GPU code
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-11-14 18:21:14 +01:00
Rafael Ravedutti
c70ebce4c1 Integrate GROMACS GPU implementation into master branch
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-11-08 18:33:23 +01:00
Jan Eitzinger
3d0f4b97ee Switch copyright header in source files. 2022-09-05 10:39:42 +02:00
Rafael Ravedutti
29fa08fa7f Enhance output for gromacs variant
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
2022-08-16 19:32:49 +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
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
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
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
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
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
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
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