Rafael Ravedutti
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ba6785a865
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Allow parameter reading from files and update data
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-03-05 03:21:52 +01:00 |
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Rafael Ravedutti
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aae29a5b5a
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Add code to read GRO files
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-03-03 20:03:33 +01:00 |
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Rafael Ravedutti
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af92800c64
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Add SIMD version with AVX (no AVX2) and XTC output
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-03-02 23:12:04 +01:00 |
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Rafael Ravedutti
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022aa75c75
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Add cutoff radius and skin as parameters of simulation
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-28 22:34:42 +01:00 |
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Rafael Ravedutti
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1389f89fb7
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Add prunning kernel
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-28 17:20:39 +01:00 |
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Rafael Ravedutti
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c62e4ea4ad
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Add clusters efficiency on stats
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-28 16:10:09 +01:00 |
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Rafael Ravedutti
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e637a26844
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Add percentage of atoms within cutoff radius when using GROMACS reference version
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-25 14:19:48 +01:00 |
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Rafael Ravedutti
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d0ec9520f2
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Write function to read PDB files and include data for Argon simulation
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-24 02:36:17 +01:00 |
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Rafael Ravedutti
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769bab0faa
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Separate local and ghost cluster edges on VTK output
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-08 16:12:22 +01:00 |
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Rafael Ravedutti
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6a35a7a482
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Update stats for cluster version
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-08 00:55:27 +01:00 |
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Rafael Ravedutti
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8deee3d954
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Add cluster edges in VTK output
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-08 00:11:10 +01:00 |
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Rafael Ravedutti
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cdb1d5b9f1
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Add version with AVX2 intrinsics for gromacs scheme
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-04 17:52:48 +01:00 |
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Rafael Ravedutti
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6e6a3f6502
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Use aligned loads when gathering j atoms
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-04 14:29:32 +01:00 |
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Rafael Ravedutti
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9daf9e5f4d
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Fix exclusion masks and add SIMD debug tools
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-02 21:54:18 +01:00 |
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Rafael Ravedutti
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6ad1e58a3e
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Add first kernel using SIMD instrinsics for 4xn cases
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-02 18:00:44 +01:00 |
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Rafael Ravedutti
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85e7954932
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Check all clusters in cell when building neighbor lists because ghost clusters may not be sorted
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-02-01 20:16:04 +01:00 |
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Rafael Ravedutti
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e64c3345bc
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Fix a few more bugs on gromacs variant
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-31 23:46:20 +01:00 |
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Rafael Ravedutti
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e0e6b6a68c
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Perform a few fixes for gromacs variant
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-31 17:49:22 +01:00 |
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Rafael Ravedutti
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6691803910
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Add first version of force calculation with cluster scheme
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-28 18:07:41 +01:00 |
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Rafael Ravedutti
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eedcc97e4a
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Remove segfaults
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-28 15:18:54 +01:00 |
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Rafael Ravedutti
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a119fcdfdd
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Fix some segfaults and add function to update single atoms
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-27 03:07:31 +01:00 |
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Rafael Ravedutti
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aa0f4048d0
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Rename default directory to lammps and reorganize gromacs variant steps
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-25 21:00:11 +01:00 |
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Rafael Ravedutti
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cbe42b8149
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Fix errors to make gromacs approach compilable so far
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-25 12:19:28 +01:00 |
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Rafael Ravedutti
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6291709ae7
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Add first draft code with GROMACS approach
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-25 00:43:10 +01:00 |
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Rafael Ravedutti
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df09c2861e
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Add first version with more than one optimization scheme
Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>
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2022-01-17 14:15:02 +01:00 |
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