ad8164dfc0
Fixed bugs in the dispersion real-space term for hippo. NOTE: CPU version filter out neighbors with zero special_disp
2021-09-24 00:21:25 -05:00
2428f1f4d5
Updated hippo kernels
2021-09-22 11:44:41 -05:00
bebef18495
Cleaned up and minor changes
2021-09-21 23:46:21 -05:00
d77d5b7f0a
Added classes for hippo/gpu, refactored BaseAmoeba and made room for the dispersion real-space term in hippo
2021-09-21 15:40:06 -05:00
a2fd784034
Added the dispersion real space term, which is for HIPPO.
2021-09-21 10:55:38 -05:00
42034bd1c9
Fixed bugs for undefined tagint and ucl_powr ambiguity in kernels for OpenCL builds
2021-09-20 12:48:29 -05:00
4e88cd158e
Fixed bugs with _tep and _fieldp to allow mixed-precision builds, being defensive with acctyp for these variables
2021-09-20 11:38:50 -05:00
0228867d8e
Added the dispersion real space kernel and transfer special coeffs to the device
2021-09-19 23:40:43 -05:00
1166845fcf
Prepared data structure for the dispersion real-space term
2021-09-18 10:22:22 -05:00
5d801e985f
More cleanup
2021-09-17 23:24:23 -05:00
78045d8f76
Cleaned up debugging stuffs and unused variables
2021-09-17 23:13:51 -05:00
f5713a52b3
Added another kernel to accumulate forces, energies and virial on the device (similar to the tersoff kernels) as multiple kernels all added to those quantities; also only copy answers back to the host in the last kernel in a time step; cleaned up debugging messages
2021-09-17 16:39:57 -05:00
2e6df83b9b
Fixed bugs in the multipole real-space part on the GPU; separately multipole real and polar real work correctly (along with udirect2b and umutual2b), but
...
together they are conflicting due to the use of ans to copy forces back from device to host. The other 2 kernels (induce part) do not touch forces and energies.
2021-09-17 15:24:36 -05:00
d926705950
Short neighbor list for multipole real-space should be built with off2_mpole
2021-09-17 01:32:00 -05:00
003bebd31e
Working on the multipole real-space term, not ready yet
2021-09-17 01:19:33 -05:00
c0b967054e
Fixed bugs with zero local atoms (similar to what has been done to PPPM interp)
2021-09-16 17:27:44 -05:00
98c1a0178c
Refactored the API so that different off2 values are used for different kernels
2021-09-16 17:14:36 -05:00
a21095fded
More cleaning up
2021-09-13 13:47:15 -05:00
bc665999d5
Fixed bugs with the umutual2b kernel, now the field and fieldp seems correct
2021-09-13 01:11:03 -05:00
edd76733a1
Working on umutual2b, tdipdip are correct, but incorrect results for field and fieldp
2021-09-12 00:51:48 -05:00
94d6f7219c
Attempted to reduce the memory footprint of the per-atom arrays
2021-09-11 11:22:17 -05:00
c765861851
Cleaned up and re-arranged the functions to reflect the order of calling in a time step
2021-09-11 01:00:58 -05:00
7f5a82dc54
Switched to the short neighbor list implementation in the pre-10Feb21 version (the recent version enforces tpa = 1 for short nbor)
2021-09-11 00:34:43 -05:00
4ebe5833d3
Working on short nbor list for the amoeba kernels (based on what has been done with tersoff and ellipsod, nbor dev_packed needs to be allocated properly)
2021-09-10 16:51:16 -05:00
a22923aee2
Added the API for the umutual kernel, needs work for storing the tdiptdip array
2021-09-09 17:22:09 -05:00
b654f293ee
Working on the umutual2b kernel, the tdipdip values are computed on the fly for now, maybe a seprate neigh list as in the CPU version will be more efficient
2021-09-09 16:52:27 -05:00
efe0bf593f
Adding the umutual2b kernel, need to create another array for tdipdip on the GPU
2021-09-09 15:19:43 -05:00
6f6fd0999c
Both udirect2b and polar_real are working correctly on the GPU
2021-09-09 00:57:21 -05:00
8c5a116d30
Made dfield0c work to compute uind and uinp correctly; need to make sure they are correct for polar_real()
2021-09-08 16:43:33 -05:00
1c5d235f12
Working on the field and fieldp values from GPU back to the host for dfield0c
2021-09-07 16:15:08 -05:00
4e346c2de6
Refactored neighbor list builds and per-atom reallocation parts
2021-09-07 13:05:57 -05:00
7d69a870a4
Reverted the binsize function call from the GPU package in Atom, instead added atom_modify sort with a binsize to ensure matching virial values, enabled the udirect2b kernel, need more work to override dfield0c, and induce() to bypass reverse_comm() for field and fieldp (line amoeba_induce.cpp:111-112)
2021-09-03 13:43:22 -05:00
785a794d39
Added and renamed API to make room for additional kernels (udirect2b only computes the field and fieldp, not accumulating forces, energies, nor virials)
2021-09-01 14:37:11 -05:00
07b60827c4
Working on the udirect2b kernel for the induce real space term, need to add the API for the GPU library
2021-09-01 12:30:41 -05:00
91317b2879
Added changes to Atom and Device classes for allocation of extra fields and SBBITS15 and NEIGHMASK15
2021-08-26 09:33:20 -05:00
3825fee8e9
Added work on amoeba/gpu, some minor changes to PairAmoeba to allow function overriding in PairAmoebaGPU, added the package AMOEBA to cmake/CMakeLists.txt
2021-08-25 22:57:37 -05:00
92b5b159e5
replace tabs and remove trailing whitespace in lib folder with updated script
2021-08-22 20:45:24 -04:00
0123f9290f
update Eigen3 to support the latest stable release 3.3.9
2021-08-06 18:59:56 -04:00
eb52f7c290
Update Colvars to version 2021-08-06 (silence Coverity Scan warnings)
...
Also include PDF copy of the manual forgotten in previous PR.
2021-08-06 10:32:37 -04:00
2a9be42758
Update Colvars to version 2021-08-03
2021-08-03 18:03:18 -04:00
f39c5178d8
update plumed to version 2.7.2 and drop workaround for 2.7.1
2021-07-27 09:56:52 -04:00
88c8d1a3c6
rename "minimal" preset to "basic"
2021-06-30 20:39:17 -04:00
878795e64a
bulk rename of remaining USER- packages
2021-06-29 20:12:59 -04:00
c085e55695
rename USER-SMD package to MACHDYN
2021-06-29 17:19:39 -04:00
c582d5b5ce
update path to examples in README files
2021-06-29 15:58:08 -04:00
d52cd88492
rename USER-QUIP to ML-QUIP
2021-06-29 15:55:41 -04:00
fd24820603
rename USER-PACE to ML-PACE
2021-06-29 15:45:50 -04:00
031e537d3f
rename USER-HDNNP to ML-HDNNP
2021-06-29 15:38:45 -04:00
8ea9179a00
Correct device pointer datatype in HIP UCL_Const
2021-06-02 15:46:57 -04:00
62423b0c75
Disable new GPU neighbor for HIP
2021-06-02 15:45:06 -04:00
