From e195f1759f3286b043e1fce52e083310fbac727d Mon Sep 17 00:00:00 2001 From: exapde Date: Mon, 24 Jun 2024 22:32:35 -0400 Subject: [PATCH] Remove unused parameters, change command name, and update documentation and examples.. --- doc/src/Commands_compute.rst | 4 +- doc/src/compute.rst | 4 +- doc/src/compute_pod_atom.rst | 28 +- doc/src/fitpod_command.rst | 4 +- doc/src/pair_pod.rst | 4 +- examples/PACKAGES/pod/Ta/Ta_coefficients.pod | 12 +- .../PACKAGES/pod/Ta/Ta_training_analysis.pod | 726 +++++++++--------- examples/PACKAGES/pod/Ta/in.pod.compute | 4 +- .../PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 | 119 +++ .../pod/Ta/log.24June24.pod.compute.g++.1 | 293 +++++++ src/KOKKOS/pair_pod_kokkos.cpp | 12 +- src/KOKKOS/pair_pod_kokkos.h | 6 +- src/ML-POD/compute_pod_atom.cpp | 2 +- src/ML-POD/compute_pod_global.cpp | 2 +- src/ML-POD/compute_pod_global.h | 2 +- src/ML-POD/compute_pod_local.cpp | 2 +- src/ML-POD/compute_pod_local.h | 2 +- src/ML-POD/compute_podd_atom.cpp | 2 +- src/ML-POD/eapod.cpp | 16 +- src/ML-POD/eapod.h | 4 +- src/ML-POD/fitpod_command.cpp | 10 +- src/ML-POD/fitpod_command.h | 2 +- src/ML-POD/pair_pod.cpp | 32 +- src/ML-POD/pair_pod.h | 12 +- 24 files changed, 858 insertions(+), 446 deletions(-) create mode 100644 examples/PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 create mode 100644 examples/PACKAGES/pod/Ta/log.24June24.pod.compute.g++.1 diff --git a/doc/src/Commands_compute.rst b/doc/src/Commands_compute.rst index a291bea9cc..2e8f291c77 100644 --- a/doc/src/Commands_compute.rst +++ b/doc/src/Commands_compute.rst @@ -110,8 +110,8 @@ KOKKOS, o = OPENMP, t = OPT. * :doc:`plasticity/atom ` * :doc:`pod/atom ` * :doc:`podd/atom ` - * :doc:`pod/ldd ` - * :doc:`pod/gdd ` + * :doc:`pod/local ` + * :doc:`pod/global ` * :doc:`pressure ` * :doc:`pressure/alchemy ` * :doc:`pressure/uef ` diff --git a/doc/src/compute.rst b/doc/src/compute.rst index 95f5a500e2..05181b9e7e 100644 --- a/doc/src/compute.rst +++ b/doc/src/compute.rst @@ -274,8 +274,8 @@ The individual style names on the :doc:`Commands compute ` pag * :doc:`plasticity/atom ` - Peridynamic plasticity for each atom * :doc:`pod/atom ` - POD descriptors for each atom * :doc:`podd/atom ` - derivative of POD descriptors for each atom -* :doc:`pod/ldd ` - local POD descriptors and their derivatives -* :doc:`pod/gdd ` - global POD descriptors and their derivatives +* :doc:`pod/local ` - local POD descriptors and their derivatives +* :doc:`pod/global ` - global POD descriptors and their derivatives * :doc:`pressure ` - total pressure and pressure tensor * :doc:`pressure/alchemy ` - mixed system total pressure and pressure tensor for :doc:`fix alchemy ` runs * :doc:`pressure/uef ` - pressure tensor in the reference frame of an applied flow field diff --git a/doc/src/compute_pod_atom.rst b/doc/src/compute_pod_atom.rst index 659e4733f3..84cd750981 100644 --- a/doc/src/compute_pod_atom.rst +++ b/doc/src/compute_pod_atom.rst @@ -1,7 +1,7 @@ .. index:: compute pod/atom .. index:: compute podd/atom -.. index:: compute pod/ldd -.. index:: compute pod/gdd +.. index:: compute pod/local +.. index:: compute pod/global compute pod/atom command ======================== @@ -9,10 +9,10 @@ compute pod/atom command compute podd/atom command ========================= -compute pod/ldd command +compute pod/local command ======================= -compute pod/gdd command +compute pod/global command ======================= Syntax @@ -22,8 +22,8 @@ Syntax compute ID group-ID pod/atom param.pod coefficients.pod compute ID group-ID podd/atom param.pod coefficients.pod - compute ID group-ID pod/ldd param.pod coefficients.pod - compute ID group-ID pod/gdd param.pod coefficients.pod + compute ID group-ID pod/local param.pod coefficients.pod + compute ID group-ID pod/global param.pod coefficients.pod * ID, group-ID are documented in :doc:`compute ` command * pod/atom = style name of this compute command @@ -37,12 +37,12 @@ Examples compute d all pod/atom Ta_param.pod compute dd all podd/atom Ta_param.pod - compute ldd all pod/ldd Ta_param.pod - compute gdd all podd/gdd Ta_param.pod + compute ldd all pod/local Ta_param.pod + compute gdd all podd/global Ta_param.pod compute d all pod/atom Ta_param.pod Ta_coefficients.pod compute dd all podd/atom Ta_param.pod Ta_coefficients.pod - compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod - compute gdd all podd/gdd Ta_param.pod Ta_coefficients.pod + compute ldd all pod/local Ta_param.pod Ta_coefficients.pod + compute gdd all podd/global Ta_param.pod Ta_coefficients.pod Description """"""""""" @@ -61,9 +61,9 @@ Compute *pod/atom* calculates the per-atom POD descriptors. Compute *podd/atom* calculates derivatives of the per-atom POD descriptors with respect to atom positions. -Compute *pod/ldd* calculates the per-atom POD descriptors and their derivatives with respect to atom positions. +Compute *pod/local* calculates the per-atom POD descriptors and their derivatives with respect to atom positions. -Compute *pod/gdd* calculates the global POD descriptors and their derivatives with respect to atom positions. +Compute *pod/global* calculates the global POD descriptors and their derivatives with respect to atom positions. Examples how to use Compute POD commands are found in the directory lammps/examples/PACKAGES/pod. @@ -78,11 +78,11 @@ and :math:`M` is the number of descriptors. Each column corresponds to a particu Compute *podd/atom* produces an 2D array of size :math:`N \times (M * 3 N)`. Each column corresponds to a particular derivative of a POD descriptor. -Compute *pod/ldd* produces an 2D array of size :math:`(1 + 3N) \times (M * N)`. +Compute *pod/local* produces an 2D array of size :math:`(1 + 3N) \times (M * N)`. The first row contains the per-atom descriptors, and the last 3N rows contain the derivatives of the per-atom descriptors with respect to atom positions. -Compute *pod/gdd* produces an 2D array of size :math:`(1 + 3N) \times (M)`. +Compute *pod/global* produces an 2D array of size :math:`(1 + 3N) \times (M)`. The first row contains the global descriptors, and the last 3N rows contain the derivatives of the global descriptors with respect to atom positions. diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst index 8dd0db5c9e..f7c92837c0 100644 --- a/doc/src/fitpod_command.rst +++ b/doc/src/fitpod_command.rst @@ -343,8 +343,8 @@ Related commands :doc:`pair_style pod `, :doc:`compute pod/atom `, :doc:`compute podd/atom `, -:doc:`compute pod/ldd `, -:doc:`compute pod/gdd ` +:doc:`compute pod/local `, +:doc:`compute pod/global ` Default """"""" diff --git a/doc/src/pair_pod.rst b/doc/src/pair_pod.rst index 276faa73f6..5adf0410f9 100644 --- a/doc/src/pair_pod.rst +++ b/doc/src/pair_pod.rst @@ -114,8 +114,8 @@ Related commands :doc:`fitpod `, :doc:`compute pod/atom `, :doc:`compute podd/atom `, -:doc:`compute pod/ldd `, -:doc:`compute pod/gdd ` +:doc:`compute pod/local `, +:doc:`compute pod/global ` Default """"""" diff --git a/examples/PACKAGES/pod/Ta/Ta_coefficients.pod b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod index ee0681ef21..ab5e5fd43a 100644 --- a/examples/PACKAGES/pod/Ta/Ta_coefficients.pod +++ b/examples/PACKAGES/pod/Ta/Ta_coefficients.pod @@ -1,17 +1,17 @@ model_coefficients: 32 0 0 -4.45745 -29.40032 +29.40034 -13.69439 -0.32907 -0.14786 --1.35220 +-1.35221 -0.59315 --26.30410 --33.37232 -162.42475 +-26.30409 +-33.37233 +162.42473 144.67248 -149.50021 -1.78604 +1.78603 2.49026 -11.04768 -11.14333 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod index 2e7e64f95f..c1910e232d 100644 --- a/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod +++ b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod @@ -1,387 +1,387 @@ # Displaced_A15.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 1 64 1191.016129 -753.1698421 -754.220443 0.01641563886 7.402950217 8.398670477 0.1439759059 - 2 64 1191.016129 -752.7395784 -753.865255 0.0175886968 8.280515475 9.134430545 0.1607787445 - 3 64 1191.016129 -753.08785 -754.0221 0.01459765621 7.697535272 9.017261102 0.1420603193 - 4 64 1191.016129 -753.3517401 -754.279613 0.0144980134 7.132364745 8.381725092 0.1340575828 - 5 64 1191.016129 -752.7757043 -753.777209 0.01564851163 8.360253591 9.478314477 0.1513006244 - 6 64 1191.016129 -753.0381763 -754.048643 0.01578854277 7.591838765 8.465317938 0.1285134069 - 7 64 1191.016129 -753.3574797 -754.317603 0.01500192653 7.08201028 8.127690491 0.1223953178 - 8 64 1191.016129 -753.1004299 -753.969161 0.01357392286 7.903578164 9.425464952 0.1365521291 - 9 64 1191.016129 -753.1947122 -754.141988 0.01480118454 7.51662269 8.821346913 0.1457127117 + 1 64 1191.016129 -753.1698421 -754.220443 0.01641563835 7.40295037 8.398670477 0.1439758999 + 2 64 1191.016129 -752.7395784 -753.865255 0.01758869658 8.280515739 9.134430545 0.1607787343 + 3 64 1191.016129 -753.08785 -754.0221 0.01459765574 7.697535492 9.017261102 0.1420603113 + 4 64 1191.016129 -753.3517402 -754.279613 0.01449801277 7.132364917 8.381725092 0.1340575727 + 5 64 1191.016129 -752.7757043 -753.777209 0.01564851147 8.360253864 9.478314477 0.1513006151 + 6 64 1191.016129 -753.0381763 -754.048643 0.01578854208 7.591838888 8.465317938 0.1285134018 + 7 64 1191.016129 -753.3574797 -754.317603 0.01500192578 7.082010429 8.127690491 0.1223953112 + 8 64 1191.016129 -753.1004299 -753.969161 0.01357392266 7.903578432 9.425464952 0.1365521197 + 9 64 1191.016129 -753.1947122 -754.141988 0.01480118465 7.516622986 8.821346913 0.1457127007 # Displaced_BCC.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 10 54 988.0479474 -631.5404328 -631.019667 0.009643811173 15.64136863 16.625876 0.2725503795 - 11 54 988.0479474 -632.1993856 -631.719595 0.008885010996 14.51345044 15.58666626 0.2369927034 - 12 54 988.0479474 -631.7954038 -631.386255 0.007576830124 15.20757604 15.92378883 0.2310810815 - 13 54 988.0479474 -633.0131535 -632.575826 0.008098656542 13.46782396 14.55977162 0.2185066369 - 14 54 988.0479474 -630.6309513 -630.450212 0.003347023934 17.00218417 16.96340726 0.2580441716 - 15 54 988.0479474 -631.9637643 -631.669379 0.005451579603 15.32548018 16.05757315 0.2336752723 - 16 54 988.0479474 -632.6507521 -632.431277 0.004064354186 14.35795156 14.69810718 0.2158813047 - 17 54 988.0479474 -631.5521868 -630.960068 0.01096516281 14.75319252 15.99073148 0.2285673123 - 18 54 988.0479474 -624.854495 -623.378198 0.02733883315 23.58927715 24.67640432 0.3545479071 + 10 54 988.0479474 -631.5404329 -631.019667 0.009643812587 15.64136862 16.625876 0.2725503749 + 11 54 988.0479474 -632.1993857 -631.719595 0.008885012437 14.51345042 15.58666626 0.2369926956 + 12 54 988.0479474 -631.7954039 -631.386255 0.007576831115 15.20757603 15.92378883 0.2310810758 + 13 54 988.0479474 -633.0131535 -632.575826 0.00809865759 13.46782392 14.55977162 0.2185066317 + 14 54 988.0479474 -630.6309514 -630.450212 0.003347025529 17.00218411 16.96340726 0.2580441627 + 15 54 988.0479474 -631.9637644 -631.669379 0.00545158078 15.32548025 16.05757315 0.2336752679 + 16 54 988.0479474 -632.6507522 -632.431277 0.004064355464 14.35795151 14.69810718 0.2158812969 + 17 54 988.0479474 -631.5521869 -630.960068 0.0109651643 14.75319251 15.99073148 0.2285673047 + 18 54 988.0479474 -624.854495 -623.378198 0.02733883252 23.58927768 24.67640432 0.3545478911 # Displaced_FCC.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 19 48 889.0559462 -555.8989975 -555.899463 9.697613917e-06 6.387988926 6.084617063 0.0780590438 - 20 48 889.0559462 -555.8789297 -555.922478 0.000907256473 6.632232643 6.297071211 0.1040918577 - 21 48 889.0559462 -555.7628778 -555.800269 0.0007789837796 6.450578251 6.021098636 0.09471101722 - 22 48 889.0559462 -556.2253041 -556.196151 0.0006073562769 5.301350143 5.127955094 0.09123175475 - 23 48 889.0559462 -555.5406596 -555.488929 0.001077721139 7.195160678 7.050223459 0.08747135506 - 24 48 889.0559462 -556.0330633 -556.027926 0.0001070271085 6.00910365 5.611881174 0.08935441544 - 25 48 889.0559462 -555.9945281 -555.968399 0.0005443554061 6.212902154 5.979217189 0.08124426951 - 26 48 889.0559462 -555.9554151 -556.047132 0.001910769142 6.012019197 5.544452585 0.09545132441 - 27 48 889.0559462 -555.7366233 -555.747848 0.0002338484028 6.764939193 6.47892568 0.1011665161 + 19 48 889.0559462 -555.8989975 -555.899463 9.69792269e-06 6.387988875 6.084617063 0.07805905013 + 20 48 889.0559462 -555.8789297 -555.922478 0.000907256654 6.632232564 6.297071211 0.1040918647 + 21 48 889.0559462 -555.7628778 -555.800269 0.0007789836645 6.45057814 6.021098636 0.09471102034 + 22 48 889.0559462 -556.2253041 -556.196151 0.0006073561042 5.301350042 5.127955094 0.09123176401 + 23 48 889.0559462 -555.5406596 -555.488929 0.001077721414 7.195160551 7.050223459 0.08747135986 + 24 48 889.0559462 -556.0330633 -556.027926 0.0001070272218 6.009103539 5.611881174 0.08935441647 + 25 48 889.0559462 -555.9945281 -555.968399 0.0005443553218 6.212902066 5.979217189 0.081244274 + 26 48 889.0559462 -555.9554151 -556.047132 0.001910769529 6.012019145 5.544452585 0.09545132709 + 27 48 889.0559462 -555.7366233 -555.747848 0.0002338482448 6.764939057 6.47892568 0.1011665243 # Elastic_BCC.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 28 2 36.40799882 -23.68590704 -23.689367 0.00172998215 0.0005857469368 0.0006222748589 9.806537259e-06 - 29 2 36.47727251 -23.68481169 -23.689888 0.00253815748 0.0005821264538 0.0006166052222 8.79731916e-06 - 30 2 36.47184897 -23.68494784 -23.689996 0.002524079261 0.0008240616648 0.0008810425642 2.03742847e-05 - 31 2 36.62078348 -23.68225087 -23.690957 0.004353066251 9.422546454e-07 0 3.770200691e-07 - 32 2 36.71197042 -23.67989944 -23.690521 0.005310779897 0.0005669504778 0.0005982273815 8.158760457e-06 - 33 2 36.77593928 -23.67819051 -23.69038 0.006094744726 0.0005635032271 0.0005925723585 7.849373754e-06 - 34 2 36.36547558 -23.68676383 -23.689202 0.001219083907 0.0005885128317 0.0006279363025 1.053580552e-05 - 35 2 36.55974375 -23.68319963 -23.690482 0.003641183767 0.0008154648836 0.0008640138888 1.662920457e-05 - 36 2 36.46414346 -23.68507116 -23.689902 0.002415420446 0.0005812774046 0.0006152154094 9.669301885e-06 - 37 2 36.63368821 -23.6817672 -23.690563 0.004397900764 0.0005717456258 0.0006038725031 8.311567333e-06 - 38 2 36.45345189 -23.68547117 -23.690207 0.002367914685 0.001009744332 0.00107369735 2.610693761e-05 - 39 2 36.38484847 -23.68616091 -23.689285 0.001562044857 0.0008322058885 0.000890013483 1.991679731e-05 - 40 2 36.43347895 -23.68567207 -23.689768 0.00204796728 0.001012061034 0.001080249045 2.782864047e-05 - 41 2 36.50220719 -23.68411383 -23.68968 0.00278308616 0.0008199315614 0.0008680034562 1.637343483e-05 - 42 2 36.50719109 -23.68445604 -23.690074 0.002808981706 0.001296718436 0.001373818765 2.641479743e-05 - 43 2 36.28428565 -23.68777598 -23.688108 0.0001660088807 0.0005942219444 0.0006336134468 1.099939523e-05 - 44 2 36.3642236 -23.68663754 -23.689241 0.001301728023 0.0008329159622 0.0008880101351 1.87459351e-05 - 45 2 36.40397469 -23.68626116 -23.68952 0.001629420369 0.0008297070698 0.0008860011287 1.917842761e-05 - 46 2 36.15958616 -23.68901859 -23.686278 0.00137029292 0.0006010646615 0.0006406777661 1.138305668e-05 - 47 2 36.85012426 -23.6762264 -23.690097 0.006935298578 0.0007925625473 0.0008410160522 1.64399889e-05 - 48 2 36.76983294 -23.67871264 -23.690811 0.006049182364 0.0007984019485 0.0008500070588 1.765059232e-05 - 49 2 36.6630398 -23.68078335 -23.690266 0.004741323677 0.0009871892372 0.001044322747 2.331514603e-05 - 50 2 36.55357619 -23.68366573 -23.690597 0.003465633835 0.0009975988325 0.001050833003 2.173211018e-05 - 51 2 36.65271066 -23.68154759 -23.690673 0.00456270493 0.0005710871671 0.0006038907186 8.900573795e-06 - 52 2 36.56222224 -23.68337216 -23.690551 0.00358941935 0.0008144210937 0.0008590064028 1.523928998e-05 - 53 2 36.56679849 -23.68340668 -23.690693 0.003643158713 0.000813797429 0.0008590110593 1.595698281e-05 - 54 2 36.59811665 -23.6823077 -23.69021 0.003951152242 0.0008145831596 0.0008730051546 2.003359235e-05 - 55 2 36.34900278 -23.68697807 -23.688943 0.0009824647708 0.0008322110625 0.0008800306813 1.744870524e-05 - 56 2 36.74034826 -23.67898787 -23.690136 0.005574066952 0.0005652133001 0.000593996633 7.925878102e-06 - 57 2 36.23610366 -23.68828866 -23.687444 0.0004223290506 0.0008436278773 0.000903059245 2.177751294e-05 - 58 2 36.42259639 -23.68591698 -23.689801 0.001942008622 0.0008265155769 0.0008740011442 1.602155172e-05 - 59 2 36.58194 -23.68291534 -23.690408 0.003746329495 7.853116351e-07 0 2.932806602e-07 - 60 2 36.59950783 -23.68250113 -23.690362 0.003930433875 0.0005739954419 0.0006067503605 1.009250374e-05 - 61 2 37.02589653 -23.67131383 -23.688881 0.008783582645 0.0007776878272 0.0008250054545 1.619372939e-05 - 62 2 36.71189602 -23.67982686 -23.690515 0.005344069627 0.001390387168 0.001475779794 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1.390580399e-05 + 125 2 36.58722353 -23.68265657 -23.690145 0.00374421628 0.0008159137665 0.0008740766557 2.136045675e-05 + 126 2 36.79405605 -23.67803714 -23.690482 0.006222430293 0.0005630702013 0.0005939983165 8.85354297e-06 + 127 2 36.45320348 -23.68530353 -23.689864 0.002280236365 0.0008267100988 0.0008860124153 2.061923922e-05 # Elastic_FCC.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 128 4 74.14589882 -46.45131085 -46.437936 0.003343712064 0.0008256457199 0.001265949446 0.0001479290109 - 129 4 74.26852111 -46.45483689 -46.438504 0.004083223321 0.0008748834584 0.001492549497 0.00016699606 - 130 4 74.05957274 -46.44875622 -46.436378 0.00309455541 0.0005424812049 0.000810592376 0.000101580849 - 131 4 74.30647158 -46.45520792 -46.441551 0.003414228955 0.001024641091 0.001283675193 8.610019891e-05 - 132 4 73.40902276 -46.4265266 -46.416957 0.002392400689 0.0008639838485 0.001186145859 9.385947194e-05 - 133 4 74.1804881 -46.45258342 -46.440495 0.003022105394 0.0008837693943 0.001212440514 7.547051692e-05 - 134 4 74.17596744 -46.45191353 -46.437972 0.003485383709 0.001290912736 0.002358226452 0.0002715207183 - 135 4 74.73528136 -46.46363987 -46.44586 0.004444968013 0.001259032114 0.002033949852 0.0002223899696 - 136 4 74.0787509 -46.44925413 -46.435744 0.003377531744 0.0009337469879 0.001690849491 0.0002527014982 - 137 4 74.24609528 -46.45412062 -46.438209 0.003977905975 0.0008183472842 0.001160049999 8.303210772e-05 - 138 4 73.73005434 -46.43863378 -46.42629 0.003085943763 0.0005398665621 0.0005297018029 9.43376107e-06 - 139 4 74.33993289 -46.45634184 -46.443301 0.003260210396 0.001019667937 0.001818421568 0.0002031713802 - 140 4 74.20715045 -46.45310823 -46.439002 0.003526558315 0.001120917957 0.001416973535 8.385488569e-05 - 141 4 73.89686848 -46.44426829 -46.432438 0.002957573131 0.001055104762 0.001010469198 5.761635625e-05 - 142 4 73.27773838 -46.42097353 -46.412654 0.002079881801 0.001288759221 0.001801959766 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-46.43312 0.003053508236 0.0005400988731 0.0007272771136 5.413030856e-05 - 153 4 73.9811119 -46.4471904 -46.434347 0.003210848973 0.000834112345 0.001284451634 0.0001304096064 - 154 4 73.82698041 -46.441812 -46.430573 0.002809749911 0.0008428066761 0.001315746176 0.0001159814784 - 155 4 74.70690467 -46.4633092 -46.445665 0.004411050685 0.001032736606 0.00180789159 0.0002150497821 - 156 4 74.08446722 -46.44922009 -46.435898 0.003330523233 0.0008301152485 0.001869300939 0.0002469789816 - 157 4 74.25274774 -46.45452028 -46.442107 0.003103319562 0.0006221717143 0.0006020930161 2.151287814e-05 - 158 4 74.05043726 -46.44881316 -46.434432 0.003595289873 0.000935394397 0.001092982159 7.589095174e-05 - 159 4 74.16653794 -46.45216047 -46.436308 0.003963116556 0.001165997584 0.001839150891 0.0002017849391 - 160 4 73.62293094 -46.43471139 -46.423938 0.00269334756 0.0009282950983 0.001463463016 0.000180643305 - 161 4 73.74948122 -46.43915588 -46.428115 0.00276021901 0.0006455156692 0.0008584497656 7.55521751e-05 - 162 4 73.70731572 -46.4377108 -46.4269 0.00270269938 0.001146432653 0.001845719914 0.0002177014499 - 163 4 73.59054722 -46.43424498 -46.421142 0.003275744005 0.001070285109 0.001309150106 6.310128542e-05 - 164 4 73.85798892 -46.44313986 -46.432233 0.002726715584 0.0007704427761 0.0007253109678 2.47763448e-05 - 165 4 73.86179419 -46.44300648 -46.429408 0.003399621185 0.0008334574138 0.001068327665 6.682328259e-05 - 166 4 74.58468636 -46.46113881 -46.445145 0.003998453263 0.0009654561972 0.001776038288 0.0002133574022 - 167 4 74.02247797 -46.44776714 -46.435868 0.002974783975 0.001172308374 0.002376074704 0.0003537233153 - 168 4 74.20501804 -46.45335725 -46.439663 0.003423563321 0.0005357336262 0.001119403413 0.0001057860993 - 169 4 73.72492498 -46.43827692 -46.428287 0.002497480771 0.001199172385 0.001277000392 3.442241856e-05 - 170 4 73.62492908 -46.43462391 -46.424584 0.002509977081 0.0006543042661 0.0008032957114 4.113075704e-05 - 171 4 73.28647 -46.42133993 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4 74.58468636 -46.46113881 -46.445145 0.003998452755 0.0009654561253 0.001776038288 0.0002133574173 + 167 4 74.02247797 -46.44776713 -46.435868 0.002974783408 0.001172308278 0.002376074704 0.0003537233362 + 168 4 74.20501804 -46.45335725 -46.439663 0.003423562793 0.0005357335948 0.001119403413 0.0001057861048 + 169 4 73.72492498 -46.43827692 -46.428287 0.00249748019 0.001199172287 0.001277000392 3.442241395e-05 + 170 4 73.62492908 -46.43462391 -46.424584 0.002509976491 0.0006543042024 0.0008032957114 4.113076772e-05 + 171 4 73.28647 -46.42133993 -46.413045 0.002073732867 0.001025290654 0.001248322074 5.004201967e-05 + 172 4 74.01119894 -46.44792434 -46.436994 0.002732584481 0.0009408903639 0.001331939188 0.0001513955587 + 173 4 74.45838911 -46.45890245 -46.443604 0.003824612242 0.0008652237342 0.001177046303 0.0001036876632 + 174 4 74.29439096 -46.45481655 -46.439718 0.003774637959 7.937739607e-07 0 2.16900779e-07 + 175 4 74.12581885 -46.45104078 -46.435527 0.003878446058 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74.36513571 -46.45635746 -46.441993 0.003591113969 0.0008209061886 0.001887735151 0.0002392272687 + 186 4 74.14572274 -46.45131062 -46.439033 0.003069403991 0.0007583547125 0.000821568013 4.304382184e-05 + 187 4 74.11964094 -46.45043541 -46.436967 0.003367101873 0.0009904274689 0.001482323514 0.0001528507492 + 188 4 73.76706483 -46.43970043 -46.427245 0.003113856835 0.001008693047 0.001293885621 8.257978381e-05 + 189 4 74.21830016 -46.45309069 -46.438046 0.003761172827 0.00116354854 0.001627288542 0.0001286952583 + 190 4 73.51075683 -46.43047578 -46.420083 0.00259819585 0.001334826131 0.002395244873 0.0003392003683 + 191 4 74.62704502 -46.46197961 -46.445247 0.004183151461 0.0008490345633 0.001219330964 8.984638543e-05 + 192 4 74.54172989 -46.46048301 -46.446044 0.003609751612 0.0008018136666 0.001305329077 0.0001126246298 + 193 4 74.05152275 -46.4491333 -46.434472 0.003665324806 0.0008288481706 0.0008323340675 5.797426995e-05 + 194 4 74.415732 -46.45806324 -46.44458 0.003370810956 0.0006130004847 0.0009744208536 6.665443495e-05 + 195 4 74.3298536 -46.45570744 -46.441776 0.003482860273 0.001025864906 0.001339231869 0.0001026437813 + 196 4 74.14951222 -46.45110489 -46.436389 0.003678973505 0.00117751644 0.001786741168 0.0001566147507 + 197 4 74.58621137 -46.46129862 -46.446416 0.003720653765 0.0006013410942 0.0006588778339 4.718503395e-05 + 198 4 74.93791818 -46.4668018 -46.449806 0.00424894914 0.001116402603 0.002135055034 0.0002754987197 + 199 4 73.6789527 -46.43686767 -46.427189 0.002419668309 0.0009202462101 0.001050788276 3.832148023e-05 + 200 4 73.72666848 -46.43838466 -46.427857 0.002631914057 0.000916598926 0.001487666629 0.0001502215435 + 201 4 74.38554824 -46.45730744 -46.44004 0.004316858848 0.0006147077527 0.000757202747 3.915525299e-05 + 202 4 74.09024992 -46.45025082 -46.437214 0.003259204623 0.000823112906 0.001505586265 0.0001621804833 + 203 4 73.60013606 -46.433967 -46.422628 0.002834751082 0.0008553071125 0.001601713458 0.000233732131 + 204 4 74.47827164 -46.45874769 -46.443535 0.00380317303 0.001150644704 0.001590304373 0.0001312331936 + 205 4 74.22558703 -46.45321801 -46.439922 0.003324001852 0.001030412749 0.001530493385 0.0001208769886 + 206 4 74.15291432 -46.45141844 -46.437675 0.003435859942 0.001323881965 0.002440246094 0.000351523644 + 207 4 74.50981896 -46.45987915 -46.445558 0.003580287949 0.0008016583891 0.00113392416 9.087921501e-05 + 208 4 74.19814905 -46.45309789 -46.439106 0.003497972207 0.001159709328 0.001830731002 0.0002004464824 + 209 4 74.51720313 -46.45968457 -46.443073 0.004152892794 0.0005327789399 0.0005766870902 1.911195046e-05 + 210 4 74.29924604 -46.45529068 -46.4397 0.003897668752 0.0008203202583 0.001204174406 8.707934353e-05 + 211 4 74.09425795 -46.45003681 -46.436374 0.003415701915 0.0008937039936 0.001461656594 0.0001906816478 + 212 4 73.73717548 -46.43887502 -46.426557 0.003079503833 0.0008473432438 0.001359624213 0.0001078467328 + 213 4 73.99983876 -46.44675075 -46.434009 0.00318543858 0.0009993979373 0.001391131194 0.000126864771 + 214 4 74.07916779 -46.4492147 -46.436262 0.003238173905 0.0012911873 0.002503347159 0.0002946038716 + 215 4 73.94744484 -46.44611874 -46.434505 0.0029034362 0.0009930846846 0.001041637173 1.44560542e-05 + 216 4 74.2021224 -46.45267242 -46.438768 0.003476105557 0.0009790325482 0.001098285027 5.900684038e-05 + 217 4 74.20389194 -46.45287404 -46.440254 0.003155011025 0.0005440222637 0.0006069892915 4.917760806e-05 + 218 4 73.66782167 -46.43682196 -46.42286 0.003490490208 0.0005521691303 0.0007365242698 6.657586723e-05 + 219 4 73.46349993 -46.42843317 -46.418078 0.002588792975 0.001215695483 0.002028412187 0.0002117690174 + 220 4 74.30307454 -46.45509879 -46.440513 0.003646448628 0.0008205757569 0.001158189967 0.000110036346 + 221 4 73.21819832 -46.41838058 -46.409824 0.002139145869 0.000869266353 0.001759573812 0.0002125030952 + 222 4 74.35772636 -46.45658501 -46.440329 0.004064003047 0.0006179175264 0.0009534044263 8.737057714e-05 + 223 4 74.17615527 -46.45177345 -46.43773 0.003510862689 0.0007631781991 0.000926180328 6.446679043e-05 + 224 4 73.43860935 -46.4277585 -46.416525 0.002808375906 0.0006623119965 0.0007573664899 4.251239635e-05 + 225 4 74.31356506 -46.45553467 -46.440293 0.003810416894 0.0008201864367 0.0007725386722 1.244767351e-05 + 226 4 74.25452523 -46.45450406 -46.43839 0.004028515986 0.000624431309 0.0005612022808 1.898088401e-05 + 227 4 74.27331932 -46.45546024 -46.438916 0.004136060657 0.0008098609869 0.001650878554 0.0001889274693 # GSF_110.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 228 24 828.0362386 -278.841059 -279.068761 0.009487584525 2.72614833 1.756353161 0.06344242408 - 229 24 828.0362386 -280.0438878 -279.784296 0.01081632666 1.025836721 0.9057668891 0.03431923951 - 230 24 828.0362386 -280.1389453 -279.901657 0.009887012289 0.3820871277 0.001565946359 0.02063932785 - 231 24 828.0362386 -279.7578636 -279.584238 0.007234401488 1.64648385 1.035572248 0.0631725447 - 232 24 828.0362386 -280.0438906 -279.784283 0.01081698239 1.025825727 0.9056396189 0.03433378444 - 233 24 828.0362386 -279.2779929 -279.302158 0.001006878324 2.597392679 1.771965137 0.07498220005 - 234 24 828.0362386 -279.7119341 -279.55564 0.006512253793 2.085996291 1.405626506 0.06414554104 - 235 24 828.0362386 -279.1342145 -279.246939 0.0046968562 1.71457265 0.4813964151 0.09091187564 - 236 24 828.0362386 -279.2779974 -279.302157 0.001006648695 2.597391427 1.771953347 0.07498197786 - 237 24 828.0362386 -279.1342234 -279.246935 0.004696314982 1.714140478 0.4809484798 0.09087970171 - 238 24 828.0362386 -280.1388645 -279.896025 0.01011831262 0.3833173916 0.01060549839 0.02057247804 - 239 24 828.0362386 -279.7581378 -279.584237 0.007245867803 1.645952076 1.035836121 0.06318595996 - 240 24 828.0362386 -278.9562357 -279.124427 0.007007970806 2.699607312 1.809545887 0.07438805388 - 241 24 828.0362386 -279.4052861 -279.379366 0.001080005822 1.874556379 0.8982692706 0.08646597374 - 242 24 828.0362386 -279.4051598 -279.37937 0.001074576375 1.874858015 0.898081355 0.08649972049 - 243 24 828.0362386 -278.9562335 -279.124427 0.007008064278 2.69960878 1.809523374 0.07438948099 - 244 24 828.0362386 -280.1389453 -279.901657 0.009887012288 0.3820871302 0.001570374478 0.02063719036 - 245 24 828.0362386 -280.0482206 -279.79264 0.01064919009 0.9069086412 0.8392614852 0.03243660465 - 246 24 828.0362386 -280.1388645 -279.896025 0.01011831262 0.3833173892 0.01060243293 0.02057250605 - 247 24 828.0362386 -279.0366629 -279.206496 0.007076380652 1.638514504 0.005326518563 0.08048169608 - 248 24 828.0362386 -279.7119391 -279.55564 0.006512462147 2.085987982 1.4056319 0.06414587415 - 249 24 828.0362386 -280.0482407 -279.79264 0.0106500307 0.9067923341 0.8392625708 0.03242814737 + 228 24 828.0362386 -278.8410589 -279.068761 0.009487586046 2.726148177 1.756353161 0.06344241374 + 229 24 828.0362386 -280.0438878 -279.784296 0.01081632552 1.025836691 0.9057668891 0.03431923408 + 230 24 828.0362386 -280.1389453 -279.901657 0.009887011104 0.3820870056 0.001565946359 0.02063932212 + 231 24 828.0362386 -279.7578636 -279.584238 0.007234400289 1.646483877 1.035572248 0.06317254006 + 232 24 828.0362386 -280.0438905 -279.784283 0.01081698125 1.025825697 0.9056396189 0.03433377902 + 233 24 828.0362386 -279.2779929 -279.302158 0.001006879708 2.597392642 1.771965137 0.07498219236 + 234 24 828.0362386 -279.7119341 -279.55564 0.006512252548 2.085996302 1.405626506 0.06414553539 + 235 24 828.0362386 -279.1342144 -279.246939 0.004696857796 1.7145726 0.4813964151 0.09091186796 + 236 24 828.0362386 -279.2779974 -279.302157 0.001006650079 2.59739139 1.771953347 0.07498197018 + 237 24 828.0362386 -279.1342234 -279.246935 0.004696316576 1.714140427 0.4809484798 0.09087969403 + 238 24 828.0362386 -280.1388645 -279.896025 0.01011831143 0.3833172699 0.01060549839 0.0205724723 + 239 24 828.0362386 -279.7581378 -279.584237 0.007245866604 1.645952103 1.035836121 0.06318595533 + 240 24 828.0362386 -278.9562357 -279.124427 0.007007972259 2.699607205 1.809545887 0.07438804482 + 241 24 828.0362386 -279.4052861 -279.379366 0.00108000439 1.874556392 0.8982692706 0.08646596743 + 242 24 828.0362386 -279.4051598 -279.37937 0.001074574944 1.874858028 0.898081355 0.08649971418 + 243 24 828.0362386 -278.9562334 -279.124427 0.007008065732 2.699608673 1.809523374 0.07438947193 + 244 24 828.0362386 -280.1389453 -279.901657 0.009887011104 0.382087008 0.001570374478 0.02063718463 + 245 24 828.0362386 -280.0482205 -279.79264 0.01064918897 0.9069086057 0.8392614852 0.03243659951 + 246 24 828.0362386 -280.1388645 -279.896025 0.01011831143 0.3833172675 0.01060243293 0.02057250032 + 247 24 828.0362386 -279.0366628 -279.206496 0.007076382361 1.638514407 0.005326518563 0.08048168704 + 248 24 828.0362386 -279.7119391 -279.55564 0.006512460902 2.085987992 1.4056319 0.06414586851 + 249 24 828.0362386 -280.0482407 -279.79264 0.01065002958 0.9067922986 0.8392625708 0.03242814224 # GSF_112.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 250 30 1075.650827 -344.9605862 -345.175835 0.007174959837 2.758670887 1.057395322 0.1516335514 - 251 30 1075.650827 -346.7372372 -346.361714 0.01251743884 1.674795443 1.220284939 0.09596890025 - 252 30 1075.650827 -346.1686185 -345.795524 0.0124364846 2.551456269 2.112860875 0.10755288 - 253 30 1075.650827 -344.7305027 -345.164602 0.01446997792 3.364761799 1.765832199 0.1653996186 - 254 30 1075.650827 -346.8954513 -346.593523 0.01006427501 1.339499116 0.01148867129 0.08728300098 - 255 30 1075.650827 -346.7069529 -346.396186 0.01035889573 1.846653973 0.9954683928 0.0997929511 - 256 30 1075.650827 -344.9126927 -345.319406 0.01355711079 3.783666896 1.772040852 0.183536504 - 257 30 1075.650827 -345.4584504 -345.594794 0.004544785997 3.694055476 1.516014157 0.1747792949 - 258 30 1075.650827 -346.1486771 -345.98566 0.005433902737 2.934925448 1.406252265 0.1397537989 - 259 30 1075.650827 -345.5181007 -345.383994 0.004470222189 2.558293533 0.963574308 0.1353120364 - 260 30 1075.650827 -346.895074 -346.582564 0.0104170008 1.340303189 0.0126740587 0.08735504366 - 261 30 1075.650827 -345.1232455 -345.452139 0.01096311785 4.843836486 2.787719406 0.1587318223 - 262 30 1075.650827 -346.8954616 -346.593523 0.01006462081 1.339471698 0.01148834 0.08728175903 - 263 30 1075.650827 -345.3878123 -345.281949 0.00352877514 3.043883494 1.873142686 0.1266226476 - 264 30 1075.650827 -346.0211337 -345.928661 0.003082421722 3.704012513 2.100874472 0.1385926707 - 265 30 1075.650827 -344.4666474 -345.111657 0.021500321 5.06094108 3.358068319 0.1556709809 - 266 30 1075.650827 -346.7313839 -346.367123 0.01214203028 1.743704873 1.335797131 0.09640035849 - 267 30 1075.650827 -346.8950084 -346.582565 0.01041477963 1.340257775 0.01254743735 0.08735401526 - 268 30 1075.650827 -344.3283906 -344.91356 0.01950564676 4.516603813 3.441834403 0.1385132972 - 269 30 1075.650827 -346.2085632 -345.836703 0.01239534037 2.265804505 1.608769148 0.1081261351 - 270 30 1075.650827 -344.700705 -344.984307 0.00945340055 3.625655523 2.542628782 0.1276641401 - 271 30 1075.650827 -346.7005544 -346.393931 0.01022078085 2.065166533 1.211680725 0.1018842139 + 250 30 1075.650827 -344.9605863 -345.175835 0.007174958242 2.758670703 1.057395322 0.1516335449 + 251 30 1075.650827 -346.7372372 -346.361714 0.01251744041 1.674795336 1.220284939 0.09596889278 + 252 30 1075.650827 -346.1686186 -345.795524 0.0124364868 2.551456187 2.112860875 0.1075528655 + 253 30 1075.650827 -344.7305027 -345.164602 0.01446997708 3.364761651 1.765832199 0.1653996104 + 254 30 1075.650827 -346.8954513 -346.593523 0.01006427628 1.339499001 0.01148867129 0.08728299447 + 255 30 1075.650827 -346.7069529 -346.396186 0.01035889705 1.846653887 0.9954683928 0.09979294451 + 256 30 1075.650827 -344.9126927 -345.319406 0.01355711006 3.783666815 1.772040852 0.1835364962 + 257 30 1075.650827 -345.4584504 -345.594794 0.004544785139 3.694055398 1.516014157 0.1747792869 + 258 30 1075.650827 -346.1486771 -345.98566 0.005433903845 2.934925394 1.406252265 0.1397537934 + 259 30 1075.650827 -345.5181007 -345.383994 0.00447022439 2.558293398 0.963574308 0.1353120293 + 260 30 1075.650827 -346.8950741 -346.582564 0.01041700207 1.340303074 0.0126740587 0.08735503715 + 261 30 1075.650827 -345.1232455 -345.452139 0.01096311715 4.843836394 2.787719406 0.158731815 + 262 30 1075.650827 -346.8954617 -346.593523 0.01006462208 1.339471584 0.01148834 0.08728175252 + 263 30 1075.650827 -345.3878123 -345.281949 0.003528777779 3.04388336 1.873142686 0.1266226401 + 264 30 1075.650827 -346.0211337 -345.928661 0.003082422836 3.704012447 2.100874472 0.1385926656 + 265 30 1075.650827 -344.4666474 -345.111657 0.0215003205 5.060940978 3.358068319 0.1556709723 + 266 30 1075.650827 -346.731384 -346.367123 0.01214203185 1.743704774 1.335797131 0.0964003512 + 267 30 1075.650827 -346.8950084 -346.582565 0.0104147809 1.34025766 0.01254743735 0.08735400875 + 268 30 1075.650827 -344.3283906 -344.91356 0.01950564575 4.516603649 3.441834403 0.1385132929 + 269 30 1075.650827 -346.2085633 -345.836703 0.01239534254 2.265804409 1.608769148 0.108126121 + 270 30 1075.650827 -344.700705 -344.984307 0.009453398382 3.625655349 2.542628782 0.1276641348 + 271 30 1075.650827 -346.7005545 -346.393931 0.01022078221 2.065166442 1.211680725 0.1018842071 # Liquid.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 272 100 2002.996789 -1105.503318 -1105.601723 0.0009840494819 33.67286931 31.39853886 0.5196524452 - 273 100 2002.996789 -1100.916702 -1099.673012 0.01243690338 34.89744975 32.03167218 0.5697884714 - 274 100 2002.996789 -1125.248108 -1121.31506 0.0393304842 23.10428082 20.81076453 0.4236223838 + 272 100 2002.996789 -1105.503318 -1105.601723 0.0009840495195 33.67286942 31.39853886 0.5196524511 + 273 100 2002.996789 -1100.916702 -1099.673012 0.01243689799 34.89745034 32.03167218 0.569788481 + 274 100 2002.996789 -1125.248108 -1121.31506 0.03933048075 23.1042808 20.81076453 0.4236223924 # Surface.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 275 24 828.0362197 -280.1388649 -279.911828 0.009459871579 0.3833166854 0.002753093533 0.02099588504 - 276 48 1756.536679 -551.9765069 -555.359452 0.07047802342 5.695770456 0.003020630398 0.1710474837 - 277 40 1394.433693 -457.8965908 -459.216162 0.03298928103 6.476050258 5.0461364 0.1141155334 - 278 40 1394.433693 -459.4317425 -461.144076 0.04280833672 2.948762274 0.005582740008 0.1122771175 - 279 24 828.0362197 -279.9357878 -279.635146 0.01252674305 2.282528657 1.288799837 0.04892859515 - 280 30 1075.65076 -346.8954518 -346.592525 0.01009755978 1.339498644 0.008446203407 0.08713648041 - 281 30 1075.65076 -345.7511061 -345.744506 0.0002200020602 4.894457811 3.124961367 0.1246204548 + 275 24 828.0362197 -280.1388649 -279.911828 0.009459870394 0.3833165637 0.002753093533 0.0209958793 + 276 48 1756.536679 -551.9765065 -555.359452 0.07047803038 5.695770431 0.003020630398 0.1710474815 + 277 40 1394.433693 -457.8965908 -459.216162 0.03298927919 6.47605009 5.0461364 0.1141155284 + 278 40 1394.433693 -459.4317427 -461.144076 0.04280833158 2.948762022 0.005582740008 0.1122771088 + 279 24 828.0362197 -279.9357878 -279.635146 0.01252674323 2.282528363 1.288799837 0.0489285834 + 280 30 1075.65076 -346.8954518 -346.592525 0.01009756105 1.339498529 0.008446203407 0.08713647389 + 281 30 1075.65076 -345.7511061 -345.744506 0.0002200037964 4.894457614 3.124961367 0.1246204459 # Volume_A15.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 282 8 300.763 -66.50302875 -66.990732 0.06096290654 2.070805005e-14 0 3.631153386e-15 - 283 8 97.336 -72.7500097 -72.957807 0.0259746619 1.511672159e-13 0 2.34376219e-14 - 284 8 140.608 -94.15533159 -94.145745 0.001198324285 4.305382145e-14 0 7.202015931e-15 - 285 8 148.877 -94.40707976 -94.554682 0.01845027963 6.136765249e-14 0 9.639893091e-15 - 286 8 103.823 -79.45083183 -79.438363 0.001558603801 1.609809698e-13 0 2.60299852e-14 - 287 8 287.496 -69.43914663 -69.627817 0.02358379567 1.679738342e-14 0 2.405958061e-15 - 288 8 226.981 -83.07759075 -82.604907 0.05908546842 1.915338855e-14 0 3.19969428e-15 - 289 8 64 14.38834338 14.89048 0.06276707694 2.845182834e-13 0 4.143528619e-14 - 290 8 157.464 -94.12106502 -94.367599 0.03081674698 5.687176521e-14 0 8.093288733e-15 - 291 8 195.112 -89.39236137 -89.248227 0.01801679589 1.96773723e-14 0 2.981507011e-15 - 292 8 205.379 -87.50415026 -87.211997 0.03651915708 1.790014153e-14 0 2.869444878e-15 - 293 8 166.375 -93.42125042 -93.66897 0.03096494702 3.451919285e-14 0 5.078779068e-15 - 294 8 68.921 -8.019333013 -7.989166 0.00377087664 3.170493305e-13 0 5.512970871e-14 - 295 8 216 -85.39060669 -84.982834 0.05097158636 1.480632601e-14 0 2.551713885e-15 - 296 8 175.616 -92.37850184 -92.536373 0.0197338953 4.210923433e-14 0 7.366403503e-15 - 297 8 74.088 -26.52314908 -26.77612 0.03162136555 2.834024822e-13 0 4.449131336e-14 - 298 8 250.047 -77.95455872 -77.544107 0.05130646502 1.025536434e-14 0 1.6376226e-15 - 299 8 238.328 -80.59031989 -80.114217 0.05951286173 2.062607247e-14 0 3.232026083e-15 - 300 8 79.507 -41.81723351 -42.143041 0.04072593647 1.873388141e-13 0 3.220411762e-14 - 301 8 185.193 -91.02736747 -91.040671 0.001662941488 2.121249823e-14 0 3.546388897e-15 - 302 8 110.592 -84.779921 -84.499231 0.0350862494 6.310661738e-14 0 1.028675525e-14 - 303 8 328.509 -60.69292471 -61.825173 0.1415310366 2.084564541e-14 0 3.412598138e-15 - 304 8 125 -91.53133046 -91.156873 0.04680718267 4.773938494e-14 0 7.628169861e-15 - 305 8 85.184 -54.31160005 -54.658744 0.04339299433 2.310159953e-13 0 3.878047002e-14 - 306 8 274.625 -72.3485476 -72.277255 0.008911575333 4.228157489e-15 0 7.178394468e-16 - 307 8 262.144 -75.1975391 -74.923334 0.03427563809 6.697991002e-15 0 1.186384096e-15 - 308 8 91.125 -64.47776052 -64.798066 0.04003818449 1.200414571e-13 0 2.078500884e-14 - 309 8 132.651 -93.23477035 -93.048342 0.02330354336 5.474054227e-14 0 9.286802922e-15 - 310 8 314.432 -63.57553771 -64.38702 0.1014352867 4.52512488e-15 0 7.37955468e-16 - 311 8 117.649 -88.79067691 -88.352871 0.05472573815 7.294269496e-14 0 1.208396102e-14 + 282 8 300.763 -66.50302875 -66.990732 0.06096290674 1.941277332e-14 0 3.37325783e-15 + 283 8 97.336 -72.75000964 -72.957807 0.0259746695 1.351006698e-13 0 2.177344384e-14 + 284 8 140.608 -94.15533163 -94.145745 0.001198328985 4.044529328e-14 0 6.693247629e-15 + 285 8 148.877 -94.40707977 -94.554682 0.01845027858 6.513916874e-14 0 1.052717644e-14 + 286 8 103.823 -79.45083178 -79.438363 0.001558598047 1.722214314e-13 0 2.77785865e-14 + 287 8 287.496 -69.43914664 -69.627817 0.02358379473 1.869801108e-14 0 2.486725909e-15 + 288 8 226.981 -83.07759076 -82.604907 0.05908546939 1.580586786e-14 0 2.506150792e-15 + 289 8 64 14.38834339 14.89048 0.06276707625 3.142551462e-13 0 4.611672661e-14 + 290 8 157.464 -94.121065 -94.367599 0.03081674996 4.627906691e-14 0 7.060581015e-15 + 291 8 195.112 -89.39236133 -89.248227 0.01801679107 2.992297744e-14 0 4.401789389e-15 + 292 8 205.379 -87.50415023 -87.211997 0.03651915426 2.29993221e-14 0 3.752044138e-15 + 293 8 166.375 -93.42125038 -93.66897 0.03096495278 2.907694533e-14 0 4.724788551e-15 + 294 8 68.921 -8.019333034 -7.989166 0.003770879216 3.356694228e-13 0 6.09434176e-14 + 295 8 216 -85.39060668 -84.982834 0.0509715856 9.263122354e-15 0 1.424782104e-15 + 296 8 175.616 -92.37850178 -92.536373 0.01973390211 3.567976799e-14 0 6.038472675e-15 + 297 8 74.088 -26.52314912 -26.77612 0.03162135966 2.830510779e-13 0 4.116147259e-14 + 298 8 250.047 -77.95455874 -77.544107 0.05130646772 1.722828231e-14 0 2.531351199e-15 + 299 8 238.328 -80.59031991 -80.114217 0.05951286389 1.790178605e-14 0 2.961270842e-15 + 300 8 79.507 -41.81723354 -42.143041 0.04072593188 2.017987815e-13 0 3.254206583e-14 + 301 8 185.193 -91.02736742 -91.040671 0.001662947812 2.413722535e-14 0 4.098218376e-15 + 302 8 110.592 -84.77992099 -84.499231 0.035086249 6.257383276e-14 0 9.730565054e-15 + 303 8 328.509 -60.69292469 -61.825173 0.1415310384 2.336487667e-14 0 4.192320181e-15 + 304 8 125 -91.53133052 -91.156873 0.04680718995 4.580314378e-14 0 7.417918736e-15 + 305 8 85.184 -54.31160005 -54.658744 0.04339299436 2.081820808e-13 0 3.494754179e-14 + 306 8 274.625 -72.34854762 -72.277255 0.008911577286 3.722472678e-15 0 6.21411631e-16 + 307 8 262.144 -75.19753913 -74.923334 0.03427564069 1.368884593e-14 0 2.258168709e-15 + 308 8 91.125 -64.47776048 -64.798066 0.04003818964 1.208370656e-13 0 1.995060684e-14 + 309 8 132.651 -93.2347704 -93.048342 0.02330355033 5.798970328e-14 0 9.670321353e-15 + 310 8 314.432 -63.5755377 -64.38702 0.1014352879 7.556804155e-15 0 1.29652209e-15 + 311 8 117.649 -88.79067694 -88.352871 0.05472574302 7.470145864e-14 0 1.29226998e-14 # Volume_BCC.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 312 2 74.088 -16.41904747 -16.763625 0.1722887642 6.280369835e-16 0 1.480297366e-16 - 313 2 13.824 16.22924421 16.314145 0.04245039628 5.418579475e-13 0 1.921425981e-13 - 314 2 27 -21.21097711 -21.209071 0.0009530541749 1.406385731e-20 0 4.926438324e-21 - 315 2 21.952 -15.82599793 -15.780524 0.02273696417 1.519568058e-13 0 5.939693182e-14 - 316 2 24.389 -19.01309058 -19.002205 0.005442788415 1.715070279e-14 0 7.001343949e-15 - 317 2 29.791 -22.67048777 -22.620568 0.0249598862 1.447213082e-14 0 5.773159728e-15 - 318 2 15.625 4.09580239 4.096885 0.000541304822 7.09075162e-14 0 2.460069185e-14 - 319 2 10.648 56.21520102 56.26276 0.0237794897 5.714115892e-13 0 1.989103326e-13 - 320 2 46.656 -22.54194178 -22.585113 0.02158560863 5.178925639e-15 0 2.072416313e-15 - 321 2 50.653 -21.73865047 -21.795501 0.02842526716 1.776356839e-15 0 5.921189465e-16 - 322 2 12.167 33.26085584 33.110078 0.07538892226 1.853008459e-13 0 4.618527782e-14 - 323 2 54.872 -20.80030781 -20.885998 0.04284509578 4.945168153e-15 0 1.776356839e-15 - 324 2 39.304 -23.54386901 -23.601336 0.0287334932 4.615110447e-15 0 1.480297366e-15 - 325 2 42.875 -23.16144783 -23.207313 0.0229325837 1.256073967e-15 0 2.960594732e-16 - 326 2 59.319 -19.76694673 -19.898089 0.06557113644 3.38994561e-14 0 1.376676551e-14 - 327 2 32.768 -23.46365392 -23.405474 0.02908995949 1.404684427e-14 0 5.69914486e-15 - 328 2 17.576 -4.670020201 -4.781324 0.05565189926 7.497614828e-14 0 2.324066865e-14 - 329 2 64 -18.67254284 -18.864936 0.0961965785 8.881784197e-16 0 2.960594732e-16 - 330 2 68.921 -17.54726712 -17.813086 0.132909438 1.986027323e-15 0 5.921189465e-16 - 331 2 19.683 -11.12327166 -11.197201 0.03696466895 2.353149064e-14 0 8.474702421e-15 - 332 2 35.937 -23.68985458 -23.696705 0.003425209136 1.008776768e-14 0 2.664535259e-15 + 312 2 74.088 -16.41904746 -16.763625 0.172288768 8.881784197e-16 0 2.960594732e-16 + 313 2 13.824 16.2292442 16.314145 0.04245040205 6.132313711e-13 0 2.290852693e-13 + 314 2 27 -21.2109771 -21.209071 0.0009530502432 1.123466673e-14 0 3.552712694e-15 + 315 2 21.952 -15.82599793 -15.780524 0.02273696393 2.538428743e-13 0 1.020665034e-13 + 316 2 24.389 -19.01309058 -19.002205 0.005442789013 7.306210466e-15 0 2.50031477e-15 + 317 2 29.791 -22.67048776 -22.620568 0.02495988117 2.031435111e-14 0 8.215650382e-15 + 318 2 15.625 4.095802366 4.096885 0.0005413171271 6.359497134e-14 0 2.069640755e-14 + 319 2 10.648 56.21520101 56.26276 0.0237794968 6.137452342e-13 0 2.262703913e-13 + 320 2 46.656 -22.54194179 -22.585113 0.02158560454 1.006819876e-14 0 3.996802889e-15 + 321 2 50.653 -21.73865048 -21.795501 0.0284252602 1.776356839e-15 0 5.921189465e-16 + 322 2 12.167 33.26085588 33.110078 0.0753889407 1.720476052e-13 0 4.707345624e-14 + 323 2 54.872 -20.80030783 -20.885998 0.04284508708 1.538370149e-15 0 5.921189465e-16 + 324 2 39.304 -23.54386901 -23.601336 0.02873349282 4.528839094e-15 0 1.480297366e-15 + 325 2 42.875 -23.16144784 -23.207313 0.02293258231 2.082963029e-15 0 7.401486831e-16 + 326 2 59.319 -19.76694674 -19.898089 0.06557112796 4.389974022e-14 0 1.776356839e-14 + 327 2 32.768 -23.46365391 -23.405474 0.0290899572 1.331156944e-14 0 5.403085387e-15 + 328 2 17.576 -4.6700202 -4.781324 0.05565189983 4.987657631e-14 0 1.465494393e-14 + 329 2 64 -18.67254286 -18.864936 0.09619657243 8.881784197e-16 0 2.960594732e-16 + 330 2 68.921 -17.54726713 -17.813086 0.1329094363 1.371024298e-15 0 4.440892099e-16 + 331 2 19.683 -11.12327165 -11.197201 0.03696467615 4.343228798e-14 0 1.539509261e-14 + 332 2 35.937 -23.68985458 -23.696705 0.003425208911 8.588276581e-15 0 2.812564996e-15 # Volume_FCC.xyz config # atoms volume energy DFT energy energy error force DFT force force error - 333 4 39.304 -19.04121552 -19.075994 0.008694620252 6.149369336e-14 0 1.428891727e-14 - 334 4 140.608 -35.2532829 -34.873619 0.09491597585 7.957989219e-17 0 1.134599802e-17 - 335 4 97.336 -43.9090385 -43.950003 0.01024112443 7.574797037e-15 0 1.788016838e-15 - 336 4 54.872 -41.05446227 -40.991909 0.01563831745 1.796862215e-14 0 4.435977049e-15 - 337 4 59.319 -43.40999789 -43.453929 0.01098277722 1.046405685e-13 0 2.961707847e-14 - 338 4 103.823 -42.63532355 -42.686077 0.01268836179 3.517805391e-15 0 6.656576249e-16 - 339 4 148.877 -33.58964547 -33.224653 0.09124811866 2.796922432e-17 0 3.296204697e-18 - 340 4 42.875 -26.84997559 -26.862709 0.003183352242 4.993644842e-14 0 1.246283169e-14 - 341 4 195.112 -25.57828561 -25.519883 0.01460065321 6.262788848e-18 0 7.380767439e-19 - 342 4 32.768 3.274215362 3.463071 0.04721390959 9.948372023e-14 0 2.374605142e-14 - 343 4 157.464 -31.91218765 -31.59595 0.07905941145 3.590442174e-17 0 4.231376681e-18 - 344 4 64 -45.05473725 -45.100466 0.01143218814 7.562525825e-15 0 1.666864843e-15 - 345 4 68.921 -46.04331303 -46.052258 0.00223624348 6.855212567e-15 0 1.378349022e-15 - 346 4 166.375 -30.24680982 -30.001189 0.06140520551 2.79275228e-16 0 5.521613788e-17 - 347 4 216 -22.95485573 -22.8504 0.0261139317 8.601683942e-17 0 1.387778781e-17 - 348 4 35.937 -9.215415972 -9.164691 0.01268124304 4.969532234e-14 0 1.263413564e-14 - 349 4 205.379 -24.20645976 -24.150343 0.01402919094 2.781506571e-18 0 3.27803693e-19 - 350 4 74.088 -46.44951294 -46.426795 0.005679485175 2.85713622e-15 0 6.197108218e-16 - 351 4 175.616 -28.6196086 -28.451145 0.04211589966 1.86333623e-14 0 5.371024787e-15 - 352 4 27 40.45415394 40.341566 0.02814698381 1.551476694e-13 0 3.460228053e-14 - 353 4 29.791 19.42166569 19.617912 0.04906157638 1.634591539e-13 0 3.962354174e-14 - 354 4 185.193 -27.05578107 -26.954384 0.02534926785 2.245157412e-16 0 3.780164124e-17 - 355 4 79.507 -46.36425383 -46.323696 0.01013945845 2.859655697e-15 0 5.273443409e-16 - 356 4 85.184 -45.86352273 -45.828947 0.008643931747 2.873384493e-14 0 8.068879454e-15 - 357 4 125 -38.44027502 -38.16029 0.06999625451 1.884407822e-15 0 4.441941036e-16 - 358 4 46.656 -32.9716863 -32.919741 0.01298632582 9.519985681e-14 0 2.466053981e-14 - 359 4 110.592 -41.29864314 -41.272675 0.006492034437 5.006706748e-14 0 1.431785829e-14 - 360 4 117.649 -39.91686354 -39.753322 0.04088538616 6.682640242e-15 0 1.556171529e-15 - 361 4 50.653 -37.65718146 -37.547435 0.02743661618 1.888595639e-14 0 4.827446313e-15 - 362 4 132.651 -36.87810682 -36.52595 0.08803920495 3.379801177e-17 0 3.983133886e-18 - 363 4 91.125 -45.01844386 -45.016087 0.0005892156793 6.396592464e-15 0 1.477601422e-15 + 333 4 39.304 -19.04121551 -19.075994 0.008694621404 9.324046941e-14 0 2.550216982e-14 + 334 4 140.608 -35.2532829 -34.873619 0.09491597439 7.957989483e-17 0 1.134599845e-17 + 335 4 97.336 -43.90903851 -43.950003 0.01024112333 9.677895068e-15 0 2.24135791e-15 + 336 4 54.872 -41.05446227 -40.991909 0.01563831765 1.98280496e-14 0 4.875440329e-15 + 337 4 59.319 -43.40999789 -43.453929 0.01098277702 9.570074295e-14 0 2.719164593e-14 + 338 4 103.823 -42.63532355 -42.686077 0.01268836179 2.539930576e-15 0 4.806204543e-16 + 339 4 148.877 -33.58964546 -33.224653 0.09124811554 2.796923066e-17 0 3.296205444e-18 + 340 4 42.875 -26.8499756 -26.862709 0.003183350784 4.824942051e-14 0 1.148213469e-14 + 341 4 195.112 -25.5782856 -25.519883 0.01460065124 2.683808864e-16 0 5.477307421e-17 + 342 4 32.768 3.274215348 3.463071 0.04721391298 1.751484723e-13 0 4.608697683e-14 + 343 4 157.464 -31.91218763 -31.59595 0.07905940659 3.590442267e-17 0 4.231376791e-18 + 344 4 64 -45.05473725 -45.100466 0.01143218825 7.235555613e-15 0 1.620123306e-15 + 345 4 68.921 -46.04331302 -46.052258 0.002236244179 5.893206675e-15 0 1.299708229e-15 + 346 4 166.375 -30.2468098 -30.001189 0.06140519937 2.820758891e-16 0 5.580616674e-17 + 347 4 216 -22.95485577 -22.8504 0.02611394167 1.164554524e-16 0 2.312964635e-17 + 348 4 35.937 -9.215415964 -9.164691 0.01268124103 4.893101434e-14 0 1.156092005e-14 + 349 4 205.379 -24.20645978 -24.150343 0.01402919404 2.781506505e-18 0 3.278036852e-19 + 350 4 74.088 -46.44951294 -46.426795 0.005679484598 2.411816735e-15 0 4.763070257e-16 + 351 4 175.616 -28.61960857 -28.451145 0.04211589328 1.078338842e-14 0 3.09506759e-15 + 352 4 27 40.45415396 40.341566 0.02814698887 1.556900619e-13 0 3.789568123e-14 + 353 4 29.791 19.42166568 19.617912 0.04906157941 1.398773649e-13 0 3.335786504e-14 + 354 4 185.193 -27.05578105 -26.954384 0.02534926276 2.758936733e-16 0 5.630535877e-17 + 355 4 79.507 -46.36425384 -46.323696 0.01013945879 2.152124725e-15 0 4.437884935e-16 + 356 4 85.184 -45.86352273 -45.828947 0.008643933117 3.448840532e-14 0 9.539924949e-15 + 357 4 125 -38.44027502 -38.16029 0.06999625463 1.884407826e-15 0 4.44194105e-16 + 358 4 46.656 -32.97168631 -32.919741 0.01298632653 1.142146022e-13 0 2.894877625e-14 + 359 4 110.592 -41.29864314 -41.272675 0.006492033936 3.342024128e-14 0 9.358862094e-15 + 360 4 117.649 -39.91686354 -39.753322 0.04088538603 7.303704341e-15 0 1.704201263e-15 + 361 4 50.653 -37.65718147 -37.547435 0.02743661628 2.105764443e-14 0 5.292352205e-15 + 362 4 132.651 -36.87810682 -36.52595 0.08803920465 3.379802923e-17 0 3.983135944e-18 + 363 4 91.125 -45.01844387 -45.016087 0.0005892174087 1.081458604e-14 0 2.513809578e-15 diff --git a/examples/PACKAGES/pod/Ta/in.pod.compute b/examples/PACKAGES/pod/Ta/in.pod.compute index 5f3dddb582..609c794e7f 100644 --- a/examples/PACKAGES/pod/Ta/in.pod.compute +++ b/examples/PACKAGES/pod/Ta/in.pod.compute @@ -37,10 +37,10 @@ compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta # set up compute snap generating global array -compute gdd all pod/gdd Ta_param.pod Ta_coefficients.pod Ta Ta +compute gdd all pod/global Ta_param.pod Ta_coefficients.pod Ta Ta #fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector -compute ldd all pod/ldd Ta_param.pod Ta_coefficients.pod Ta Ta +compute ldd all pod/local Ta_param.pod Ta_coefficients.pod Ta Ta #fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector #dump mydump_ld all custom 1000 dump_ld id c_ld[*] diff --git a/examples/PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 b/examples/PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 new file mode 100644 index 0000000000..6dd2ab946c --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.24June24.fitpod.g++.1 @@ -0,0 +1,119 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-179-g353121c942-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +fitpod Ta_param.pod Ta_data.pod +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Data File **************** +file format: extxyz +file extension: xyz +path to training data set: XYZ +path to test data set: XYZ +path to environment configuration set: XYZ +basename for output files: Ta +training fraction: 1 +test fraction: 1 +randomize training data set: 1 +randomize test data set: 1 +error analysis for training data set: 1 +error analysis for test data set: 0 +energy/force calculation for training data set: 0 +energy/force calculation for test data set: 0 +fitting weight for energy: 100 +fitting weight for force: 1 +fitting weight for stress: 0 +save pod descriptors: 0 +compute pod descriptors: 0 +**************** End of Data File **************** +**************** Begin of Training Data Set **************** +--------------------------------------------------------------- + data file | number of configurations | number of atoms +--------------------------------------------------------------- + Displaced_A15.xyz | 9 | 576 + Displaced_BCC.xyz | 9 | 486 + Displaced_FCC.xyz | 9 | 432 + Elastic_BCC.xyz | 100 | 200 + Elastic_FCC.xyz | 100 | 400 + GSF_110.xyz | 22 | 528 + GSF_112.xyz | 22 | 660 + Liquid.xyz | 3 | 300 + Surface.xyz | 7 | 236 + Volume_A15.xyz | 30 | 240 + Volume_BCC.xyz | 21 | 42 + Volume_FCC.xyz | 31 | 124 +--------------------------------------------------------------- +number of files: 12 +number of configurations in all files: 363 +number of atoms in all files: 4224 +minimum number of atoms: 2 +maximum number of atoms: 100 +**************** End of Training Data Set **************** +**************** Begin of Memory Allocation **************** +maximum number of atoms in periodic domain: 100 +maximum number of atoms in extended domain: 2700 +maximum number of neighbors in extended domain: 270000 +size of double memory: 232128 +size of descriptor matrix: 32 x 32 +**************** End of Memory Allocation **************** +**************** Begin of Least-Squares Fitting **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** Begin of Error Calculation **************** +Configuration: # 1 +Configuration: # 101 +Configuration: # 201 +Configuration: # 301 +**************** End of Error Calculation **************** +**************** Begin of Error Analysis for the Training Data Set **************** +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.015324 0.015365 0.140594 0.184797 +Displaced_BCC.xyz 9 486 0.009486 0.011643 0.249983 0.320375 +Displaced_FCC.xyz 9 432 0.000686 0.000880 0.091420 0.113585 +Elastic_BCC.xyz 100 200 0.003796 0.004379 0.000015 0.000020 +Elastic_FCC.xyz 100 400 0.003332 0.003372 0.000122 0.000178 +GSF_110.xyz 22 528 0.007027 0.007797 0.057637 0.115638 +GSF_112.xyz 22 660 0.010396 0.011347 0.125237 0.198553 +Liquid.xyz 3 300 0.017584 0.023822 0.504354 0.660300 +Surface.xyz 7 236 0.025511 0.034302 0.107190 0.285034 +Volume_A15.xyz 30 240 0.038624 0.048355 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.044423 0.061685 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030062 0.041271 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012618 0.024806 0.125879 0.247229 +--------------------------------------------------------------------------------------------------- +**************** End of Error Analysis for the Training Data Set **************** +Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.24June24.pod.compute.g++.1 b/examples/PACKAGES/pod/Ta/log.24June24.pod.compute.g++.1 new file mode 100644 index 0000000000..f120ddd5e5 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/log.24June24.pod.compute.g++.1 @@ -0,0 +1,293 @@ +LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-179-g353121c942-modified) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) + using 1 OpenMP thread(s) per MPI task +# Demonstrate bispectrum computes + +# initialize simulation + +variable nsteps index 0 +variable nrep equal 2 +variable a equal 2.0 +units metal + +# generate the box and atom positions using a BCC lattice + +variable nx equal ${nrep} +variable nx equal 2 +variable ny equal ${nrep} +variable ny equal 2 +variable nz equal ${nrep} +variable nz equal 2 + +boundary p p p + +atom_modify map hash +lattice bcc $a +lattice bcc 2 +Lattice spacing in x,y,z = 2 2 2 +region box block 0 ${nx} 0 ${ny} 0 ${nz} +region box block 0 2 0 ${ny} 0 ${nz} +region box block 0 2 0 2 0 ${nz} +region box block 0 2 0 2 0 2 +create_box 2 box +Created orthogonal box = (0 0 0) to (4 4 4) + 1 by 1 by 1 MPI processor grid +create_atoms 2 box +Created 16 atoms + using lattice units in orthogonal box = (0 0 0) to (4 4 4) + create_atoms CPU = 0.001 seconds + +mass * 180.88 + +displace_atoms all random 0.1 0.1 0.1 123456 +Displacing atoms ... + +# set up dummy potential to satisfy cutoff +variable rcutfac equal 6.0 +pair_style zero ${rcutfac} +pair_style zero 6 +pair_coeff * * + +# set up per-atom computes + +compute ld all pod/atom Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +compute dd all podd/atom Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + + +# set up compute snap generating global array + +compute gdd all pod/global Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +#fix gdd all ave/time 1 1 1 c_gdd[*] file pod.gdd.dat mode vector + +compute ldd all pod/local Ta_param.pod Ta_coefficients.pod Ta Ta +**************** Begin of POD Potentials **************** +species: Ta +periodic boundary conditions: 1 1 1 +number of environment clusters: 1 +number of principal compoments: 2 +inner cut-off radius: 1 +outer cut-off radius: 5 +bessel polynomial degree: 3 +inverse polynomial degree: 6 +one-body potential: 1 +two-body radial basis functions: 6 +three-body radial basis functions: 5 +three-body angular degree: 4 +four-body radial basis functions: 0 +four-body angular degree: 0 +five-body radial basis functions: 0 +five-body angular degree: 0 +six-body radial basis functions: 0 +six-body angular degree: 0 +seven-body radial basis functions: 0 +seven-body angular degree: 0 +number of local descriptors per element for one-body potential: 1 +number of local descriptors per element for two-body potential: 6 +number of local descriptors per element for three-body potential: 25 +number of local descriptors per element for four-body potential: 0 +number of local descriptors per element for five-body potential: 0 +number of local descriptors per element for six-body potential: 0 +number of local descriptors per element for seven-body potential: 0 +number of local descriptors per element for all potentials: 32 +number of global descriptors: 32 +**************** End of POD Potentials **************** + +**************** Begin of Model Coefficients **************** +total number of coefficients for POD potential: 32 +total number of elements for PCA projection matrix: 0 +total number of elements for PCA centroids: 0 +**************** End of Model Coefficients **************** + +#fix ldd all ave/time 1 1 1 c_ldd[*] file pod.ldd.dat mode vector + +#dump mydump_ld all custom 1000 dump_ld id c_ld[*] +#dump mydump_dd all custom 1000 dump_dd id c_dd[*] + +variable sample_ld1 equal C_ld[1][10] # Arbitrary local descriptor +fix ldprint all print 1 "${sample_ld1}" + +run ${nsteps} +run 0 +WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60) +Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule +WARNING: More than one compute pod (src/ML-POD/compute_pod_atom.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_podd_atom.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_pod_global.cpp:87) +WARNING: More than one compute pod (src/ML-POD/compute_pod_local.cpp:89) +Neighbor list info ... + update: every = 1 steps, delay = 0 steps, check = yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 8 + ghost atom cutoff = 8 + binsize = 4, bins = 1 1 1 + 5 neighbor lists, perpetual/occasional/extra = 1 4 0 + (1) pair zero, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d + bin: standard + (2) compute pod/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) compute podd/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (4) compute pod/global, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (5) compute pod/local, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +0.344594831165384 +Per MPI rank memory allocation (min/avg/max) = 6.326 | 6.326 | 6.326 Mbytes + Step Temp E_pair E_mol TotEng Press + 0 0 0 0 0 0 +Loop time of 1.23e-06 on 1 procs for 0 steps with 16 atoms + +243.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0 | 0 | 0 | 0.0 | 0.00 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0 | 0 | 0 | 0.0 | 0.00 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 1.23e-06 | | |100.00 + +Nlocal: 16 ave 16 max 16 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1984 ave 1984 max 1984 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 4311 ave 4311 max 4311 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 8623 ave 8623 max 8623 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 8623 +Ave neighs/atom = 538.9375 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/src/KOKKOS/pair_pod_kokkos.cpp b/src/KOKKOS/pair_pod_kokkos.cpp index f036ac2c57..d9383ec22a 100644 --- a/src/KOKKOS/pair_pod_kokkos.cpp +++ b/src/KOKKOS/pair_pod_kokkos.cpp @@ -644,7 +644,7 @@ void PairPODKokkos::NeighborList(t_pod_1d l_rij, t_pod_1i l_numij, template void PairPODKokkos::radialbasis(t_pod_1d rbft, t_pod_1d rbftx, t_pod_1d rbfty, t_pod_1d rbftz, t_pod_1d l_rij, t_pod_1d l_besselparams, double l_rin, double l_rmax, int l_besseldegree, - int l_inversedegree, int l_nbesselpars, int l_ns, int Nij) + int l_inversedegree, int l_nbesselpars, int Nij) { Kokkos::parallel_for("ComputeRadialBasis", Nij, KOKKOS_LAMBDA(int n) { double xij1 = l_rij(0+3*n); @@ -1111,7 +1111,7 @@ void PairPODKokkos::fourbodydesc(t_pod_1d d4, t_pod_1d l_sumU, t_po template void PairPODKokkos::fourbody_forces(t_pod_1d fij, t_pod_1d cb4, t_pod_1d l_rbf, t_pod_1d l_rbfx, t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, - t_pod_1d l_sumU, t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, t_pod_1i l_elemindex, + t_pod_1d l_sumU, t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni, int Nij) { int totalIterations = l_nrbf4 * Nij; @@ -1332,7 +1332,7 @@ void PairPODKokkos::fourbody_forcecoeff(t_pod_1d fb4, t_pod_1d cb4, template void PairPODKokkos::allbody_forces(t_pod_1d fij, t_pod_1d l_forcecoeff, t_pod_1d l_rbf, t_pod_1d l_rbfx, t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, - t_pod_1i l_idxi, t_pod_1i l_tj, int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, int Nij) + t_pod_1i l_idxi, t_pod_1i l_tj, int l_nelements, int l_nrbf3, int l_K3, int Nij) { int totalIterations = l_nrbf3 * Nij; Kokkos::parallel_for("allbody_forces", totalIterations, KOKKOS_LAMBDA(int idx) { @@ -1419,7 +1419,7 @@ void PairPODKokkos::blockatom_base_descriptors(t_pod_1d bd, int Ni, begin = std::chrono::high_resolution_clock::now(); radialbasis(abf, abfx, abfy, abfz, rij, besselparams, rin, rmax, - besseldegree, inversedegree, nbesselpars, ns, Nij); + besseldegree, inversedegree, nbesselpars, Nij); Kokkos::fence(); end = std::chrono::high_resolution_clock::now(); comptime[10] += std::chrono::duration_cast(end-begin).count()/1e6; @@ -1687,7 +1687,7 @@ void PairPODKokkos::blockatom_energyforce(t_pod_1d l_ei, t_pod_1d l_ if ((nl4 > 0) && (Nij>2)) fourbody_forcecoeff(forcecoeff, cb4, sumU, pa4, pb4, pc4, nelements, nrbf3, nrbf4, nabf4, K3, Q4, Ni); if ((nl3 > 0) && (Nij>1)) allbody_forces(l_fij, forcecoeff, rbf, rbfx, rbfy, rbfz, abf, abfx, abfy, abfz, - idxi, tj, nelements, nrbf3, nabf3, K3, Nij); + idxi, tj, nelements, nrbf3, K3, Nij); // begin = std::chrono::high_resolution_clock::now(); // if ((nl3 > 0) && (Nij>1)) threebody_forces(l_fij, cb3, rbf, rbfx, rbfy, rbfz, abf, abfx, abfy, abfz, sumU, @@ -1698,7 +1698,7 @@ void PairPODKokkos::blockatom_energyforce(t_pod_1d l_ei, t_pod_1d l_ // // begin = std::chrono::high_resolution_clock::now(); // if ((nl4 > 0) && (Nij>2)) fourbody_forces(l_fij, cb4, rbf, rbfx, rbfy, rbfz, abf, abfx, abfy, abfz, sumU, idxi, tj, -// pa4, pb4, pc4, elemindex, nelements, nrbf3, nrbf4, nabf4, K3, Q4, Ni, Nij); +// pa4, pb4, pc4, nelements, nrbf3, nrbf4, nabf4, K3, Q4, Ni, Nij); // Kokkos::fence(); // end = std::chrono::high_resolution_clock::now(); // comptime[9] += std::chrono::duration_cast(end-begin).count()/1e6; diff --git a/src/KOKKOS/pair_pod_kokkos.h b/src/KOKKOS/pair_pod_kokkos.h index ab6cd3f827..8fc8e219eb 100644 --- a/src/KOKKOS/pair_pod_kokkos.h +++ b/src/KOKKOS/pair_pod_kokkos.h @@ -168,7 +168,7 @@ class PairPODKokkos : public PairPOD { void radialbasis(t_pod_1d rbft, t_pod_1d rbftx, t_pod_1d rbfty, t_pod_1d rbftz, t_pod_1d rij, t_pod_1d l_besselparams, double l_rin, double l_rmax, int l_besseldegree, - int l_inversedegree, int l_nbesselpars, int l_ns, int Nij); + int l_inversedegree, int l_nbesselpars, int Nij); void matrixMultiply(t_pod_1d a, t_pod_1d b, t_pod_1d c, int r1, int c1, int c2); @@ -202,7 +202,7 @@ class PairPODKokkos : public PairPOD { int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, int Ni, int Nij); void fourbody_forces(t_pod_1d fij, t_pod_1d cb4, t_pod_1d l_rbf, t_pod_1d l_rbfx, t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, t_pod_1d l_sumU, - t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, t_pod_1i l_elemindex, + t_pod_1i l_idxi, t_pod_1i l_tj, t_pod_1i l_pa4, t_pod_1i l_pb4, t_pod_1i l_pc4, int l_nelements, int l_nrbf3, int l_nrbf4, int l_nabf4, int l_K3, int l_Q4, int Ni, int Nij); void threebody_forcecoeff(t_pod_1d fb3, t_pod_1d cb3, t_pod_1d l_sumU, t_pod_1i l_pc3, @@ -213,7 +213,7 @@ class PairPODKokkos : public PairPOD { void allbody_forces(t_pod_1d fij, t_pod_1d l_forcecoeff, t_pod_1d l_rbf, t_pod_1d l_rbfx, t_pod_1d l_rbfy, t_pod_1d l_rbfz, t_pod_1d l_abf, t_pod_1d l_abfx, t_pod_1d l_abfy, t_pod_1d l_abfz, - t_pod_1i l_idxi, t_pod_1i l_tj, int l_nelements, int l_nrbf3, int l_nabf3, int l_K3, int Nij); + t_pod_1i l_idxi, t_pod_1i l_tj, int l_nelements, int l_nrbf3, int l_K3, int Nij); void blockatom_energyforce(t_pod_1d l_ei, t_pod_1d l_fij, int Ni, int Nij); void tallyenergy(t_pod_1d l_ei, int istart, int Ni); diff --git a/src/ML-POD/compute_pod_atom.cpp b/src/ML-POD/compute_pod_atom.cpp index 566811cc31..5a0d83e426 100644 --- a/src/ML-POD/compute_pod_atom.cpp +++ b/src/ML-POD/compute_pod_atom.cpp @@ -155,7 +155,7 @@ void ComputePODAtom::compute_peratom() // peratom base descriptors double *bd = &podptr->bd[0]; double *bdd = &podptr->bdd[0]; - podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, ti, tj, nij); + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); if (nClusters>1) { // peratom env descriptors diff --git a/src/ML-POD/compute_pod_global.cpp b/src/ML-POD/compute_pod_global.cpp index fceca7a0ff..a3dd95ccbd 100644 --- a/src/ML-POD/compute_pod_global.cpp +++ b/src/ML-POD/compute_pod_global.cpp @@ -153,7 +153,7 @@ void ComputePODGlobal::compute_array() // peratom base descriptors double *bd = &podptr->bd[0]; double *bdd = &podptr->bdd[0]; - podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, ti, tj, nij); + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); pod[0][nCoeffPerElement*(ti[0]-1)] += 1.0; // one-body descriptor diff --git a/src/ML-POD/compute_pod_global.h b/src/ML-POD/compute_pod_global.h index f6753811bb..9b0da8e5dc 100644 --- a/src/ML-POD/compute_pod_global.h +++ b/src/ML-POD/compute_pod_global.h @@ -13,7 +13,7 @@ #ifdef COMPUTE_CLASS // clang-format off -ComputeStyle(pod/gdd,ComputePODGlobal); +ComputeStyle(pod/global,ComputePODGlobal); // clang-format on #else diff --git a/src/ML-POD/compute_pod_local.cpp b/src/ML-POD/compute_pod_local.cpp index ab9a02238b..33a9936a76 100644 --- a/src/ML-POD/compute_pod_local.cpp +++ b/src/ML-POD/compute_pod_local.cpp @@ -154,7 +154,7 @@ void ComputePODLocal::compute_array() // peratom base descriptors double *bd = &podptr->bd[0]; double *bdd = &podptr->bdd[0]; - podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, ti, tj, nij); + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); if (nClusters>1) { // peratom env descriptors diff --git a/src/ML-POD/compute_pod_local.h b/src/ML-POD/compute_pod_local.h index 93a7215c73..7fad8f1151 100644 --- a/src/ML-POD/compute_pod_local.h +++ b/src/ML-POD/compute_pod_local.h @@ -13,7 +13,7 @@ #ifdef COMPUTE_CLASS // clang-format off -ComputeStyle(pod/ldd,ComputePODLocal); +ComputeStyle(pod/local,ComputePODLocal); // clang-format on #else diff --git a/src/ML-POD/compute_podd_atom.cpp b/src/ML-POD/compute_podd_atom.cpp index 37b28f5e4d..d4c508794a 100644 --- a/src/ML-POD/compute_podd_atom.cpp +++ b/src/ML-POD/compute_podd_atom.cpp @@ -155,7 +155,7 @@ void ComputePODDAtom::compute_peratom() // peratom base descriptors double *bd = &podptr->bd[0]; double *bdd = &podptr->bdd[0]; - podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, ti, tj, nij); + podptr->peratombase_descriptors(bd, bdd, rij, tmpmem, tj, nij); if (nClusters>1) { // peratom env descriptors diff --git a/src/ML-POD/eapod.cpp b/src/ML-POD/eapod.cpp index f6d771eb83..2eaa4a1206 100644 --- a/src/ML-POD/eapod.cpp +++ b/src/ML-POD/eapod.cpp @@ -852,7 +852,7 @@ int EAPOD::read_centroids(std::string centroids_file) void EAPOD::peratombase_descriptors(double *bd1, double *bdd1, double *rij, double *temp, - int *ti, int *tj, int Nj) + int *tj, int Nj) { for (int i=0; i 1) { // multi-environment descriptors // calculate multi-environment descriptors and their derivatives with respect to atom coordinates @@ -1491,7 +1491,7 @@ void EAPOD::base_descriptors(double *basedesc, double *x, myneighbors(rij, x, ai, aj, ti, tj, jlist, pairnumsum, atomtype, alist, i); // many-body descriptors - peratombase_descriptors(bd, bdd, rij, &tmpmem[3*Nj], ti, tj, Nj); + peratombase_descriptors(bd, bdd, rij, &tmpmem[3*Nj], tj, Nj); for (int m=0; mdestroy(envdata.we); memory->destroy(envdata.wf); } - + if (compute_descriptors==0) { // compute POD coefficients using least-squares method @@ -127,7 +127,7 @@ void FitPOD::command(int narg, char **arg) // calculate energy and force for the training data set if ((traindata.training_calculation) && ((int) traindata.data_path.size() > 1) ) - energyforce_calculation(traindata, desc.c); + energyforce_calculation(traindata); if (!((testdata.data_path == traindata.data_path) && (testdata.fraction == 1.0) && (traindata.fraction == 1.0))) { @@ -140,7 +140,7 @@ void FitPOD::command(int narg, char **arg) // calculate energy and force for the test data set if ((testdata.test_analysis) && (testdata.test_calculation) && ((int) testdata.data_path.size() > 1) && (testdata.fraction > 0) ) - energyforce_calculation(testdata, desc.c); + energyforce_calculation(testdata); // deallocate testing data @@ -380,7 +380,7 @@ void FitPOD::get_exyz_files(std::vector& files, std::vector 0) && (Nij>1)) { angularbasis(abftm, &abftm[K3], &abftm[2*K3], &abftm[3*K3], Nij); - radialangularsum2(Ni, Nij); + radialangularsum2(Ni); threebodydesc(d3, Ni); if ((nl33>0) && (Nij>3)) { @@ -1843,10 +1843,10 @@ void PairPOD::blockatombase_descriptors(double *bd1, double *bdd1, int Ni, int N if ((nl3 > 0) && (Nij>1)) { angularbasis(abftm, &abftm[K3], &abftm[2*K3], &abftm[3*K3], Nij); - radialangularsum2(Ni, Nij); + radialangularsum2(Ni); threebodydesc(d3, Ni); - threebodydescderiv(dd3, Ni, Nij); + threebodydescderiv(dd3, Nij); if ((nl33>0) && (Nij>3)) { crossdesc(d33, d3, d3, ind33l, ind33r, nl33, Ni); @@ -1856,7 +1856,7 @@ void PairPOD::blockatombase_descriptors(double *bd1, double *bdd1, int Ni, int N if ((nl4 > 0) && (Nij>2)) { if (K4 < K3) { fourbodydesc(d4, Ni); - fourbodydescderiv(dd4, Ni, Nij); + fourbodydescderiv(dd4, Nij); } if ((nl34>0) && (Nij>4)) { @@ -2026,13 +2026,13 @@ void PairPOD::blockatom_forces(double *fij, int Ni, int Nij) // double *dd34 = &bdd[3*Nij*(nl2+nl3+nl4+nl33)]; // 3*Nj*nl34 // double *dd44 = &bdd[3*Nij*(nl2+nl3+nl4+nl33+nl34)]; // 3*Nj*nl44 - if ((nl2 > 0) && (Nij>0)) twobodydescderiv(dd2, Ni, Nij); - if ((nl3 > 0) && (Nij>1)) threebodydescderiv(dd3, Ni, Nij); - if ((nl4 > 0) && (Nij>2)) fourbodydescderiv(dd4, Ni, Nij); + if ((nl2 > 0) && (Nij>0)) twobodydescderiv(dd2, Nij); + if ((nl3 > 0) && (Nij>1)) threebodydescderiv(dd3, Nij); + if ((nl4 > 0) && (Nij>2)) fourbodydescderiv(dd4, Nij); double *d3 = &bd[Ni*nl2]; // nl3 double *d4 = &bd[Ni*(nl2 + nl3)]; // nl4 - double *cb2 = &cb[0]; // nl3 + //double *cb2 = &cb[0]; // nl2 double *cb3 = &cb[Ni*nl2]; // nl3 double *cb4 = &cb[Ni*(nl2 + nl3)]; // nl4 double *cb33 = &cb[Ni*(nl2 + nl3 + nl4)]; // nl33 diff --git a/src/ML-POD/pair_pod.h b/src/ML-POD/pair_pod.h index 00a0f32564..c41de91e9e 100644 --- a/src/ML-POD/pair_pod.h +++ b/src/ML-POD/pair_pod.h @@ -38,9 +38,9 @@ public: void lammpsNeighborList(double *rij1, int *ai1, int *aj1, int *ti1, int *tj1, double **x, int **firstneigh, int *atomtype, int *map, int *numneigh, double rcutsq, int i); - void NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq, int i1, int i2); + void NeighborCount(double **x, int **firstneigh, int *ilist, int *numneigh, double rcutsq, int i1); void NeighborList(double **x, int **firstneigh, int *atomtype, int *map, int *ilist, int *numneigh, - double rcutsq, int i1, int i2); + double rcutsq, int i1); void tallyenergy(double *ei, int istart, int Ni); void tallystress(double *fij, double *rij, int *ai, int *aj, int nlocal, int N); void tallyforce(double **force, double *fij, int *ai, int *aj, int N); @@ -53,15 +53,15 @@ public: void orthogonalradialbasis(int Nij); void angularbasis(double *tm, double *tmu, double *tmv, double *tmw, int N); void radialangularsum(int Ni, int Nij); - void radialangularsum2(int Ni, int Nij); + void radialangularsum2(int Ni); void twobodydesc(double *d2, int Ni, int Nij); - void twobodydescderiv(double *dd2, int Ni, int Nij); + void twobodydescderiv(double *dd2, int Nij); void twobodydescderiv(double *d2, double *dd2, int Ni, int Nij); void threebodydesc(double *d3, int Ni); - void threebodydescderiv(double *dd3, int Ni, int Nij); + void threebodydescderiv(double *dd3, int Nij); void extractsumU(int Ni); void fourbodydesc(double *d4, int Ni); - void fourbodydescderiv(double *dd4, int Ni, int Nij); + void fourbodydescderiv(double *dd4, int Nij); void crossdesc(double *d12, double *d1, double *d2, int *ind1, int *ind2, int n12, int Ni); void crossdescderiv(double *dd12, double *d1, double *d2, double *dd1, double *dd2, int *ind1, int *ind2, int *idxi, int n12, int Ni, int Nij);