Will write log file to "o04-r2scan-md.md.log". Command line: /app1/ebapps/arches/flat-avx2/software/ORCA/6.1.0-gompi-2023b-avx2/bin/orca_md -orca o04-r2scan-md ------------------------------------------------------------------------------------------- _____ ___ _ _ _ ______ ______ _____ ___ / ___| / _ \ | \ | | | | _ / __ \| ___ \/ __ \ / _ \ \ `--. / /_\ \ | \| | __| | _ _ _| |_ | | | || |_/ /| / \// /_\ \ `--. \ | _ | | . ` | / _` || | | | |_ _| | | | || / | | | _ | /\__/ / | | | | | |\ | | (_| || |_| | |_| | \__/ || |\ \ | \__/\| | | | \____/ \_| |_/ \_| \_/ \__,_| \__, | \____/ \_| \_| \____/\_| |_/ __/ | |___/ #################################################################### ######## Scriptable Nuclear Dynamics (SANdy) + ORCA ######## ######## (c) Martin Brehm, 2016 - 2025 ######## ######## Paderborn University, Germany ######## ######## https://sanscript.org/orcamd ######## #################################################################### * Compiled as ORCA module. Called from ORCA. * ORCA base name: "o04-r2scan-md" * Source code version: Jun 07 2025, compiled at Jun 12 2025 07:48:10. * Enabled features: SAN_MD, SAN_INTERPRETER * Libraries: KISS_FFT, LBFGSBC * Executable name: "/app1/ebapps/arches/flat-avx2/software/ORCA/6.1.0-gompi-2023b-avx2/bin/orca_md" * Messages are redirected, Errors are redirected, Output is redirected, Input is redirected * Running on IN-006 at Tue Sep 29 00:31:21 2026 (PID 260725) * Running in /nfs/home/svu/e1075536/guide-runs/xtb-md/o04-r2scan-md ----------------------------------------------- Technical information: * Compiler: LLVM, CLANG 20.1.6, "Clang 20.1.6 (/home/frankw/CompEnv/src/llvm2016/llvm-project/clang 47addd4540b4c393e478ba92bea2589e330c57fb)", Linux, __cplusplus=201103L * Compile host: x86_64, Little Endian, char=8bits, int=4b, long=8b, ll=8b, addr=8b, 0x01020304=4,3,2,1. * Class sizes: InputElem=248, ValuePair=112, Type=96, Value=8, VMToken=8, VMInst=8 * Compile flags: MMX, SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2, POPCNT, FMA3, AVX, AVX2 * Local machine: Intel(R) Xeon(R) Gold 6438N (GenuineIntel), Family 6, Model 143, Stepping 8 2 CPUs, 64 cores, 64 threads, Uptime 60d 13h 02m 43s MMX, SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2, POPCNT, AES, FMA3, AVX, AVX2, AVX512F, SHA Caches: 64x L1d (3072 KiB), 64x L1i (2048 KiB), 64x L2 (128 MiB), 2x L3 (120 MiB) * Op. System: Red Hat Enterprise Linux 9.4 (Plow), Linux version 5.14.0-427.125.1.el9_4.x86_64 * Phys. Memory: 503.40 GiB total, 205.19 GiB free * Stack size: infinite The following libraries are included: * KISS FFT, Version 131.1.0 (02/2021), License: BSD 3-clause (c) 2003-2010 Mark Borgerding, see https://github.com/mborgerding/kissfft * L-BFGS-B-C, Version 3.0 (04/2011), License: BSD 3-clause (c) Stephen Becker, see https://github.com/stephenbeckr/L-BFGS-B-C * MT19937 Pseudo Random Number Gen., License: Custom (permissive) (c) 1997-2005 Makoto Matsumoto, Takuji Nishimura, Mutsuo Saito, see https://github.com/clibs/mt19937ar Initializing SAN engine... 24 physical quantities and 49 units added. Initialized SAN language: 97 operators, 57 keywords, 4 namespaces, 35 types, 183 flags Done. >>> Reading Input File >>> Reading input file "o04-r2scan-md.mdinput" ... 142 bytes read. 5 lines. Tokenizing input... Found 21 tokens in file. ( 14 identifiers, 6 numeric literals, 1 string literals ) Line endings are uniform: 5 x \n <<< Finished Reading Input File (took 0.001 seconds) <<< Using the following settings: Interpret: true Execution: SAN-VM Parser verbose level: 1 Execute verbose level: 2 Syntax highlighting: 0 Static vars: false Dynamic types: true Max. recursion depth: 200 Max. nesting depth: 1000 Max. argument count: 100 Only parse: false >>> Parsing Input Script >>> Handled 4 underscore identifiers. Handling module imports... Importing module "Math" to global namespace. Importing module "MD" to global namespace. Handled 2 module imports. Handled 7 variable occurrences. Assigned 6 identifiers. Handling functions, iteration 1... iteration 2... iteration 3... Handling "FOR" loops... Handling AutoDecl, iteration 1... No auto declarations. Assigned 4 flags, re-doing function handling... Handling functions ( 2), iteration 1... Moving "Void" argument 2 ("Thermostat") of function "Initvel" up 1 levels to "ROOT". iteration 2... Handling "FOR" loops... Handling AutoDecl, iteration 1... No auto declarations. Handling functions, final pass... Moving "Void" argument 5 ("Dump") of function "Thermostat" up 1 levels to "ROOT". Function handling done (2 macro-iterations, 0.001 seconds). Handling keywords, iteration 1... Prepared 5 argument lists. Assigned 12 read-only flags. Assigned 19 simple VP flags. Assigned 18 tree IDs. <<< Finished Parsing Input Script (took 0.002 seconds) <<< SAN-VM: Compiling... Optimization level: Not specified. Using default ("-O2"). Done (took 0.000 seconds). Part # Tokens # Registers # Shortcuts # Optimizations --------------------------------------------------------------------------- Main Program 44 0 0 0 ------------------------------------------------------------------------------------------- >>> Initializing MD engine with interface "ORCA" >>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>> Output of System Information (from ORCA) >>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> (the output of geometry and basis set information is missing in the MD log file, as it is written to the screen directly by ORCA.) ############################################ Total Atom Count: 22 Total System Mass: 144.174 a.m.u. Total Basis Dimension: 270 Total Electron Number: 78 Total Charge: 0 Total Multiplicity: 1 Spin Treatment: Restricted ------------------------------------------ ReducePrint: true Print Mulliken Pop: 1 Print Loewdin Pop: 1 Print Mayer Pop: 1 Print Orbital Energies: 1 ############################################ <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< <<< End of System Information <<< <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<< Initializing regions... Defined regions: All: 22 atoms, 144.174 a.m.u. QM: All Active: All ### System Geometry ### * Region "All" = "Active" = "QM": Bounding box: from ( -3.598 | -3.182 | -1.599 ) to ( 3.268 | 2.770 | 2.073 ) Angstrom System extent: ( 6.866 | 5.952 | 3.672 ) Angstrom Center of mass: ( -0.079 | -0.014 | -0.221 ) Angstrom Total mass: 144.174 a.m.u. Moment of inertia: ( 357.11 | -86.99 | -89.14 ) ( -86.99 | 484.38 | 6.33 ) a.m.u. Angstrom^2 ( -89.14 | 6.33 | 683.47 ) Singular values: ( 709.91 | 297.39 | 517.66 ) a.m.u. Angstrom^2 Smallest interatomic distance from active region: 1.010412 Angstrom (atoms 3 - 13). <<< MD engine initialization done (took 0.621 seconds) <<< ############################################################### ######## Executing Input Script (SAN-VM) ######## ############################################################### Execution verbose level is 2. ------------------------------------------------------------------------------------------- >>>>>> Timestep( 0.5_fs ) Setting integration time step to 0.50 fs. The lightest element in the active region has an atomic mass of 1.008 a.m.u. Recommending time step not larger than 0.50 .. 1.00 fs. --> choice seems reasonable >>>>>> Initvel( 300_K ) Old temperature of the total system is 0.000 K. Initializing atom velocities for region "all" to 300.000 K: Creating Maxwell-Boltzmann distribution... Temperature after random initialization is 408.418 K. Rescaling velocities to match desired initial temperature (factor 0.857054)... Removing initial center of mass movement... Temperature after center of mass movement removal is 295.486 K. Removing initial angular velocity... Angular momentum before: ( 0.39452144 | -0.23460160 | 0.27216727 ) a.m.u. Angstrom^2 fs^-1 Angular velocity before: ( 0.00117471 | -0.00028060 | 0.00055402 ) fs^-1 Angular momentum after: ( 0.00000000 | -0.00000000 | 0.00000000 ) a.m.u. Angstrom^2 fs^-1 Angular velocity after: ( 0.00000000 | -0.00000000 | 0.00000000 ) fs^-1 Temperature after angular velocity removal is 283.093 K. Rescaling velocities to match desired initial temperature (factor 1.029428)... Done. New temperature of the total system is 300.000 K. >>>>>> Thermostat( NHC, 300_K, Timecon, 50_fs ) Note: No NHC chain length specified. Using 3 as default (nothing to worry about). Note: No MTS count specified. Using 2 as default (nothing to worry about). Note: No Yoshida order specified. Using 3 as default (nothing to worry about). Switching on thermostat for region "All": Type NHC, temperature 300.00 K, time constant 50.00 fs, global, chain length 3, MTS 2, Yoshida order 3. >>>>>> Dump( Position, Stride, 1, Filename, "o04-r2scan-md.traj.xyz" ) Modified writing position trajectory for region "all": Format XYZ, stride 1, filename "o04-r2scan-md.traj.xyz", append. >>>>>> Run( 200 ) *************************************************** **** Starting MD loop for 200 steps **** *************************************************** Defined regions: All: 22 atoms, 144.174 a.m.u. QM: All Active: All Dump: Will write Position data of region "All" in XYZ format with stride 1 to "o04-r2scan-md.traj.xyz" (append). Hint: To compute properties (dipole, etc.) in each step, specify "dump properties" before run. Active Thermostats: (*) Region "All": Type NHC, temperature 300.00 K, time constant 50.00 fs, chain length 3, MTS 2, Yoshida order 3, global. NHC potential energy 0.0000 kJ mol^-1, kinetic energy 1.8708 kJ mol^-1, temperature 300.000 K. Will write restart file to "o04-r2scan-md.mdrestart" after each step. Will write energy statistics to "o04-r2scan-md-md-ener.csv" after each step. The system contains 66 active degrees of freedom (22 active atoms * 3). Smallest interatomic distance from active region: 1.010412 Angstrom (atoms 3 - 13). Step | Sim. Time | Iter | t_Ener | t_Grad | Temp | E_Kin | E_Pot | E_Tot | Cons.Qty | E.Drift | [fs] | | [s] | [s] | [K] | [Hartree] | [Hartree] | [Hartree] | [Hartree] | [K] ------------|------------|------|---------|---------|----------|-----------|---------------|---------------|---------------|----------- 0 0.0 10 22.34 300.00 0.031351 -495.775841 -495.744489 1 0.5 6 15.61 4.09 294.91 0.030820 -495.775330 -495.744511 -495.744481 0.00 2 1.0 6 15.47 3.96 281.41 0.029408 -495.773926 -495.744518 -495.744460 0.10 3 1.5 6 15.05 3.88 262.62 0.027445 -495.771961 -495.744517 -495.744432 0.23 4 2.0 4 13.20 4.03 242.51 0.025343 -495.769859 -495.744516 -495.744408 0.35 5 2.5 4 17.85 3.74 224.46 0.023457 -495.767983 -495.744526 -495.744396 0.41 6 3.0 4 12.84 3.96 210.20 0.021967 -495.766515 -495.744547 -495.744399 0.39 7 3.5 5 14.05 3.81 199.54 0.020853 -495.765432 -495.744579 -495.744414 0.32 8 4.0 6 15.23 3.86 190.94 0.019954 -495.764567 -495.744613 -495.744432 0.24 9 4.5 6 15.61 3.85 182.43 0.019065 -495.763702 -495.744637 -495.744442 0.19 10 5.0 6 15.26 3.86 172.38 0.018014 -495.762667 -495.744653 -495.744446 0.17 11 5.5 6 15.17 3.88 160.15 0.016736 -495.761396 -495.744660 -495.744442 0.19 12 6.0 6 14.92 3.88 146.30 0.015289 -495.759946 -495.744657 -495.744430 0.24 13 6.5 6 15.37 3.92 132.52 0.013849 -495.758497 -495.744648 -495.744414 0.32 14 7.0 4 13.36 3.90 121.20 0.012666 -495.757303 -495.744637 -495.744397 0.40 15 7.5 5 14.97 3.79 114.79 0.011996 -495.756628 -495.744632 -495.744387 0.45 16 8.0 3 12.25 3.73 114.97 0.012015 -495.756647 -495.744632 -495.744383 0.47 17 8.5 5 14.66 3.85 121.81 0.012729 -495.757374 -495.744644 -495.744393 0.42 18 9.0 6 15.51 3.89 133.53 0.013954 -495.758623 -495.744669 -495.744414 0.32 19 9.5 6 15.42 3.86 147.15 0.015378 -495.760071 -495.744693 -495.744436 0.21 20 10.0 6 15.06 3.72 159.43 0.016662 -495.761371 -495.744709 -495.744452 0.14 21 10.5 6 15.20 3.89 168.04 0.017561 -495.762276 -495.744714 -495.744456 0.12 22 11.0 6 15.47 4.01 172.24 0.018000 -495.762709 -495.744708 -495.744450 0.15 23 11.5 6 15.94 3.78 172.74 0.018052 -495.762748 -495.744697 -495.744440 0.20 24 12.0 6 15.57 3.87 171.00 0.017870 -495.762555 -495.744685 -495.744429 0.25 25 12.5 5 14.20 3.87 168.51 0.017610 -495.762287 -495.744676 -495.744423 0.28 26 13.0 3 12.47 3.73 166.42 0.017392 -495.762056 -495.744664 -495.744414 0.32 27 13.5 6 19.21 3.77 165.24 0.017268 -495.761924 -495.744656 -495.744410 0.34 28 14.0 6 15.11 3.87 164.97 0.017240 -495.761893 -495.744653 -495.744412 0.33 29 14.5 4 12.80 3.56 165.37 0.017282 -495.761933 -495.744651 -495.744415 0.32 30 15.0 5 13.73 3.72 165.86 0.017333 -495.761986 -495.744652 -495.744422 0.28 31 15.5 5 13.85 3.88 165.80 0.017327 -495.761981 -495.744654 -495.744431 0.24 32 16.0 5 13.81 3.77 164.62 0.017203 -495.761856 -495.744653 -495.744437 0.21 33 16.5 6 15.14 3.67 161.97 0.016927 -495.761574 -495.744647 -495.744439 0.20 34 17.0 6 14.79 3.85 157.88 0.016499 -495.761135 -495.744636 -495.744436 0.21 35 17.5 6 14.68 3.74 152.74 0.015962 -495.760583 -495.744621 -495.744431 0.24 36 18.0 6 15.14 3.64 147.44 0.015408 -495.760012 -495.744603 -495.744422 0.28 37 18.5 6 15.30 3.86 143.18 0.014963 -495.759548 -495.744585 -495.744414 0.32 38 19.0 6 15.15 4.03 141.19 0.014755 -495.759323 -495.744569 -495.744408 0.35 39 19.5 6 15.07 3.94 142.35 0.014876 -495.759432 -495.744556 -495.744407 0.36 40 20.0 5 13.99 4.00 146.84 0.015345 -495.759895 -495.744550 -495.744412 0.33 41 20.5 5 14.29 3.81 153.98 0.016092 -495.760640 -495.744548 -495.744424 0.28 42 21.0 5 14.47 4.03 162.29 0.016960 -495.761510 -495.744550 -495.744440 0.20 43 21.5 6 15.87 3.81 169.85 0.017750 -495.762298 -495.744548 -495.744453 0.13 44 22.0 4 13.75 3.83 174.87 0.018275 -495.762812 -495.744537 -495.744459 0.10 45 22.5 4 13.64 3.81 176.38 0.018433 -495.762950 -495.744518 -495.744458 0.11 46 23.0 6 16.04 3.74 174.64 0.018251 -495.762740 -495.744489 -495.744448 0.16 47 23.5 6 15.53 4.00 171.03 0.017874 -495.762330 -495.744457 -495.744434 0.22 48 24.0 5 14.15 3.76 167.51 0.017506 -495.761933 -495.744427 -495.744424 0.28 49 24.5 5 14.93 3.97 165.87 0.017334 -495.761738 -495.744404 -495.744420 0.29 50 25.0 5 14.51 3.86 167.11 0.017464 -495.761853 -495.744389 -495.744425 0.27 51 25.5 6 14.79 3.86 171.19 0.017891 -495.762267 -495.744377 -495.744434 0.23 52 26.0 5 20.20 2.96 176.97 0.018494 -495.762864 -495.744369 -495.744449 0.16 53 26.5 5 12.98 2.94 182.64 0.019087 -495.763452 -495.744365 -495.744468 0.06 54 27.0 4 12.28 3.00 186.29 0.019468 -495.763822 -495.744354 -495.744482 -0.00 55 27.5 4 11.99 2.95 186.35 0.019475 -495.763807 -495.744333 -495.744486 -0.02 56 28.0 4 12.55 3.02 182.24 0.019045 -495.763347 -495.744302 -495.744481 0.00 57 28.5 4 12.24 2.95 174.82 0.018270 -495.762531 -495.744261 -495.744466 0.07 58 29.0 5 12.78 2.98 166.37 0.017386 -495.761604 -495.744217 -495.744447 0.17 59 29.5 5 12.77 2.83 159.86 0.016707 -495.760886 -495.744179 -495.744433 0.23 60 30.0 5 17.80 3.88 157.84 0.016496 -495.760648 -495.744153 -495.744431 0.24 61 30.5 3 11.41 3.65 161.24 0.016851 -495.760982 -495.744131 -495.744434 0.22 62 31.0 5 13.94 3.67 168.67 0.017627 -495.761748 -495.744121 -495.744451 0.15 63 31.5 5 13.92 3.65 177.12 0.018510 -495.762629 -495.744119 -495.744477 0.02 64 32.0 6 15.44 3.84 183.51 0.019178 -495.763283 -495.744105 -495.744493 -0.06 65 32.5 6 15.62 3.93 185.63 0.019400 -495.763475 -495.744075 -495.744495 -0.07 66 33.0 6 15.58 4.00 183.04 0.019128 -495.763162 -495.744034 -495.744485 -0.02 67 33.5 7 16.09 3.89 177.01 0.018499 -495.762484 -495.743985 -495.744469 0.06 68 34.0 5 14.61 3.85 169.98 0.017763 -495.761700 -495.743937 -495.744451 0.14 69 34.5 5 13.85 3.89 164.57 0.017198 -495.761093 -495.743895 -495.744440 0.20 70 35.0 5 14.69 3.89 162.76 0.017009 -495.760872 -495.743863 -495.744438 0.21 71 35.5 5 14.39 3.79 165.22 0.017266 -495.761108 -495.743842 -495.744448 0.16 72 36.0 5 12.84 3.69 171.11 0.017882 -495.761710 -495.743828 -495.744466 0.07 73 36.5 5 12.82 3.78 178.34 0.018637 -495.762453 -495.743815 -495.744488 -0.03 74 37.0 6 13.68 3.81 184.30 0.019261 -495.763057 -495.743796 -495.744505 -0.11 75 37.5 8 16.76 3.78 186.73 0.019515 -495.763281 -495.743766 -495.744512 -0.15 76 38.0 7 16.30 4.02 184.51 0.019282 -495.763008 -495.743725 -495.744509 -0.13 77 38.5 7 20.42 3.81 178.08 0.018610 -495.762286 -495.743676 -495.744497 -0.07 78 39.0 6 15.05 3.78 169.24 0.017686 -495.761309 -495.743623 -495.744480 0.01 79 39.5 4 13.72 3.89 160.41 0.016764 -495.760336 -495.743573 -495.744465 0.08 80 40.0 4 13.42 3.76 153.77 0.016070 -495.759601 -495.743531 -495.744457 0.12 81 40.5 4 13.01 3.78 150.57 0.015735 -495.759233 -495.743498 -495.744457 0.11 82 41.0 6 15.24 3.75 150.77 0.015756 -495.759228 -495.743472 -495.744465 0.08 83 41.5 4 13.04 3.81 153.24 0.016014 -495.759464 -495.743450 -495.744478 0.02 84 42.0 4 13.04 3.83 156.18 0.016321 -495.759748 -495.743427 -495.744490 -0.04 85 42.5 5 14.21 3.81 157.73 0.016483 -495.759884 -495.743401 -495.744501 -0.09 86 43.0 4 13.13 3.67 156.74 0.016380 -495.759747 -495.743367 -495.744504 -0.11 87 43.5 4 13.48 3.82 153.13 0.016003 -495.759326 -495.743323 -495.744498 -0.08 88 44.0 4 13.44 4.00 147.83 0.015449 -495.758724 -495.743275 -495.744486 -0.02 89 44.5 4 13.80 3.88 142.43 0.014884 -495.758113 -495.743228 -495.744475 0.03 90 45.0 5 13.95 3.83 138.52 0.014476 -495.757663 -495.743188 -495.744470 0.05 91 45.5 3 11.84 3.74 137.11 0.014328 -495.757478 -495.743150 -495.744468 0.07 92 46.0 6 15.26 3.75 138.20 0.014442 -495.757560 -495.743118 -495.744470 0.05 93 46.5 6 15.18 3.85 140.94 0.014729 -495.757818 -495.743089 -495.744478 0.01 94 47.0 6 15.16 3.84 144.24 0.015074 -495.758131 -495.743056 -495.744484 -0.01 95 47.5 5 13.92 3.70 147.18 0.015381 -495.758401 -495.743021 -495.744487 -0.03 96 48.0 5 14.32 3.72 149.36 0.015609 -495.758592 -495.742983 -495.744490 -0.04 97 48.5 5 14.00 3.84 150.83 0.015762 -495.758707 -495.742945 -495.744493 -0.06 98 49.0 6 15.09 3.98 151.60 0.015843 -495.758749 -495.742906 -495.744497 -0.07 99 49.5 6 15.78 3.94 151.49 0.015831 -495.758695 -495.742864 -495.744498 -0.08 100 50.0 6 15.92 3.83 150.27 0.015704 -495.758524 -495.742819 -495.744496 -0.07 101 50.5 8 16.67 4.00 148.19 0.015486 -495.758257 -495.742770 -495.744490 -0.04 102 51.0 8 20.12 3.88 146.09 0.015267 -495.757985 -495.742718 -495.744481 -0.00 103 51.5 6 14.83 3.71 145.17 0.015171 -495.757840 -495.742668 -495.744474 0.03 104 52.0 7 15.83 3.79 146.40 0.015300 -495.757923 -495.742624 -495.744473 0.04 105 52.5 5 13.73 3.81 149.94 0.015670 -495.758254 -495.742584 -495.744478 0.01 106 53.0 5 12.94 2.88 155.12 0.016211 -495.758759 -495.742548 -495.744488 -0.03 107 53.5 5 12.97 3.11 160.72 0.016796 -495.759306 -495.742510 -495.744499 -0.09 108 54.0 4 12.20 2.96 165.53 0.017298 -495.759766 -495.742468 -495.744507 -0.12 109 54.5 4 12.26 2.98 168.64 0.017623 -495.760042 -495.742418 -495.744510 -0.14 110 55.0 6 14.11 2.90 169.61 0.017725 -495.760091 -495.742365 -495.744509 -0.13 111 55.5 6 13.61 2.98 168.47 0.017606 -495.759914 -495.742308 -495.744506 -0.12 112 56.0 6 13.51 3.05 165.65 0.017311 -495.759560 -495.742249 -495.744500 -0.09 113 56.5 6 13.89 3.00 162.03 0.016933 -495.759121 -495.742188 -495.744491 -0.05 114 57.0 5 12.72 2.94 158.84 0.016600 -495.758728 -495.742128 -495.744483 -0.01 115 57.5 5 12.48 2.85 157.33 0.016442 -495.758515 -495.742073 -495.744479 0.01 116 58.0 5 13.60 3.80 158.24 0.016537 -495.758563 -495.742026 -495.744483 -0.01 117 58.5 6 15.02 3.77 161.34 0.016861 -495.758845 -495.741984 -495.744493 -0.06 118 59.0 5 13.52 3.71 165.27 0.017271 -495.759216 -495.741945 -495.744508 -0.13 119 59.5 6 14.65 3.65 168.16 0.017573 -495.759477 -495.741904 -495.744522 -0.20 120 60.0 6 15.39 3.80 168.48 0.017607 -495.759458 -495.741851 -495.744525 -0.21 121 60.5 6 15.22 3.59 165.66 0.017313 -495.759102 -495.741789 -495.744519 -0.18 122 61.0 6 14.84 3.74 160.51 0.016774 -495.758495 -495.741721 -495.744506 -0.12 123 61.5 5 14.02 3.88 154.97 0.016195 -495.757847 -495.741652 -495.744490 -0.04 124 62.0 3 11.87 3.70 151.54 0.015837 -495.757419 -495.741582 -495.744472 0.04 125 62.5 5 13.52 3.77 152.29 0.015915 -495.757436 -495.741522 -495.744464 0.08 126 63.0 5 14.27 3.78 158.03 0.016515 -495.757993 -495.741477 -495.744473 0.04 127 63.5 5 14.22 3.69 168.10 0.017567 -495.759008 -495.741441 -495.744492 -0.05 128 64.0 5 13.98 3.82 180.30 0.018842 -495.760247 -495.741404 -495.744516 -0.17 129 64.5 6 14.88 3.87 191.80 0.020044 -495.761403 -495.741359 -495.744535 -0.26 130 65.0 6 19.13 3.83 200.11 0.020912 -495.762211 -495.741299 -495.744542 -0.29 131 65.5 8 16.70 3.71 203.94 0.021312 -495.762538 -495.741226 -495.744539 -0.28 132 66.0 8 16.87 3.82 203.66 0.021284 -495.762427 -495.741143 -495.744527 -0.22 133 66.5 6 14.89 3.67 201.03 0.021009 -495.762065 -495.741056 -495.744510 -0.14 134 67.0 7 16.12 3.69 198.37 0.020730 -495.761704 -495.740974 -495.744496 -0.07 135 67.5 7 15.82 3.66 197.54 0.020643 -495.761545 -495.740901 -495.744492 -0.05 136 68.0 6 14.97 3.78 199.14 0.020811 -495.761650 -495.740839 -495.744497 -0.08 137 68.5 6 15.49 3.87 202.35 0.021146 -495.761928 -495.740782 -495.744510 -0.14 138 69.0 6 15.40 3.61 205.35 0.021460 -495.762185 -495.740725 -495.744523 -0.20 139 69.5 6 15.18 3.72 206.24 0.021553 -495.762216 -495.740663 -495.744531 -0.24 140 70.0 6 15.07 3.77 203.71 0.021288 -495.761883 -495.740595 -495.744533 -0.25 141 70.5 5 13.95 3.86 197.44 0.020633 -495.761155 -495.740522 -495.744529 -0.23 142 71.0 6 15.18 3.80 188.19 0.019667 -495.760114 -495.740447 -495.744519 -0.18 143 71.5 6 15.01 3.87 177.54 0.018554 -495.758925 -495.740371 -495.744505 -0.11 144 72.0 5 13.90 3.84 167.49 0.017503 -495.757803 -495.740300 -495.744493 -0.05 145 72.5 3 12.15 3.70 160.03 0.016724 -495.756954 -495.740230 -495.744479 0.01 146 73.0 5 13.95 3.88 156.46 0.016351 -495.756524 -495.740173 -495.744475 0.03 147 73.5 6 14.86 3.67 156.96 0.016403 -495.756530 -495.740127 -495.744483 -0.01 148 74.0 6 14.60 3.68 160.58 0.016781 -495.756866 -495.740085 -495.744495 -0.07 149 74.5 6 14.11 3.73 165.51 0.017297 -495.757338 -495.740041 -495.744507 -0.12 150 75.0 6 14.56 3.67 169.96 0.017762 -495.757752 -495.739990 -495.744513 -0.15 151 75.5 6 14.96 3.74 173.01 0.018081 -495.758009 -495.739928 -495.744510 -0.14 152 76.0 6 14.62 3.70 174.93 0.018281 -495.758141 -495.739860 -495.744501 -0.10 153 76.5 6 14.94 3.71 176.80 0.018476 -495.758268 -495.739792 -495.744493 -0.06 154 77.0 6 14.48 3.66 179.69 0.018778 -495.758507 -495.739729 -495.744491 -0.05 155 77.5 6 15.27 3.75 183.94 0.019223 -495.758894 -495.739671 -495.744495 -0.07 156 78.0 6 14.79 3.83 189.05 0.019757 -495.759371 -495.739614 -495.744502 -0.10 157 78.5 6 15.07 3.76 194.01 0.020275 -495.759831 -495.739556 -495.744508 -0.13 158 79.0 6 19.80 3.87 197.84 0.020675 -495.760169 -495.739494 -495.744512 -0.15 159 79.5 6 15.42 3.71 199.85 0.020886 -495.760314 -495.739428 -495.744513 -0.15 160 80.0 5 13.89 3.86 199.75 0.020875 -495.760237 -495.739362 -495.744514 -0.16 161 80.5 5 13.84 3.95 197.59 0.020649 -495.759948 -495.739299 -495.744517 -0.17 162 81.0 5 14.04 3.69 193.73 0.020245 -495.759483 -495.739237 -495.744521 -0.19 163 81.5 5 14.34 3.82 188.56 0.019705 -495.758883 -495.739178 -495.744524 -0.21 164 82.0 6 15.18 3.73 182.40 0.019061 -495.758179 -495.739118 -495.744526 -0.21 165 82.5 7 16.21 3.82 175.36 0.018326 -495.757385 -495.739059 -495.744526 -0.21 166 83.0 7 16.37 3.78 167.46 0.017500 -495.756502 -495.739002 -495.744525 -0.21 167 83.5 8 17.29 3.78 158.87 0.016602 -495.755548 -495.738946 -495.744522 -0.19 168 84.0 8 17.16 3.83 150.11 0.015687 -495.754576 -495.738889 -495.744515 -0.16 169 84.5 8 17.13 3.80 142.13 0.014853 -495.753686 -495.738833 -495.744507 -0.13 170 85.0 7 15.74 3.75 136.10 0.014223 -495.753003 -495.738781 -495.744501 -0.09 171 85.5 3 11.84 3.67 133.04 0.013903 -495.752632 -495.738729 -495.744494 -0.06 172 86.0 5 14.31 3.82 133.24 0.013924 -495.752612 -495.738688 -495.744495 -0.07 173 86.5 5 14.10 3.93 136.16 0.014230 -495.752883 -495.738653 -495.744505 -0.11 174 87.0 5 13.89 3.75 140.69 0.014703 -495.753320 -495.738617 -495.744515 -0.16 175 87.5 6 14.74 3.88 145.55 0.015211 -495.753786 -495.738576 -495.744521 -0.19 176 88.0 7 16.38 3.76 149.90 0.015665 -495.754193 -495.738527 -495.744521 -0.19 177 88.5 7 16.31 3.95 153.62 0.016054 -495.754527 -495.738473 -495.744517 -0.17 178 89.0 7 15.75 3.78 157.27 0.016436 -495.754851 -495.738415 -495.744510 -0.14 179 89.5 7 15.70 3.65 161.78 0.016907 -495.755264 -495.738357 -495.744504 -0.11 180 90.0 7 16.52 3.68 167.97 0.017554 -495.755854 -495.738300 -495.744502 -0.10 181 90.5 7 16.56 3.73 176.16 0.018409 -495.756656 -495.738246 -495.744504 -0.11 182 91.0 3 12.14 3.70 185.98 0.019436 -495.757623 -495.738187 -495.744504 -0.11 183 91.5 7 16.77 3.80 196.20 0.020504 -495.758636 -495.738132 -495.744510 -0.14 184 92.0 6 14.78 3.70 205.10 0.021434 -495.759513 -495.738079 -495.744521 -0.19 185 92.5 6 14.92 3.66 211.02 0.022053 -495.760072 -495.738019 -495.744529 -0.23 186 93.0 6 19.35 3.73 212.81 0.022239 -495.760192 -495.737952 -495.744529 -0.23 187 93.5 6 14.61 3.73 210.38 0.021986 -495.759863 -495.737877 -495.744520 -0.19 188 94.0 3 11.97 3.71 205.01 0.021424 -495.759215 -495.737790 -495.744499 -0.09 189 94.5 7 16.42 3.71 198.75 0.020771 -495.758479 -495.737709 -495.744480 0.01 190 95.0 5 14.18 3.69 193.68 0.020240 -495.757883 -495.737642 -495.744474 0.03 191 95.5 4 13.03 3.85 190.96 0.019956 -495.757545 -495.737589 -495.744480 0.01 192 96.0 4 12.96 3.72 190.23 0.019880 -495.757421 -495.737541 -495.744490 -0.04 193 96.5 6 14.78 3.76 189.97 0.019853 -495.757347 -495.737494 -495.744501 -0.10 194 97.0 6 14.66 3.63 188.56 0.019705 -495.757148 -495.737443 -495.744507 -0.12 195 97.5 6 14.87 3.76 185.14 0.019348 -495.756732 -495.737384 -495.744505 -0.11 196 98.0 6 15.19 3.56 179.95 0.018806 -495.756127 -495.737321 -495.744497 -0.08 197 98.5 5 13.82 3.70 174.06 0.018190 -495.755450 -495.737260 -495.744489 -0.04 198 99.0 5 14.16 3.72 168.89 0.017650 -495.754854 -495.737204 -495.744484 -0.01 199 99.5 3 12.30 3.69 165.88 0.017335 -495.754477 -495.737142 -495.744472 0.04 200 100.0 5 14.91 3.67 165.85 0.017332 -495.754420 -495.737088 -495.744467 0.07 ------------|------------|------|---------|---------|----------|-----------|---------------|---------------|---------------|----------- Step | Sim. Time | Iter | t_Ener | t_Grad | Temp | E_Kin | E_Pot | E_Tot | Cons.Qty | E.Drift | [fs] | | [s] | [s] | [K] | [Hartree] | [Hartree] | [Hartree] | [Hartree] | [K] Finished MD run of 200 steps. The average temperature during this run was 171.18571 K. Smallest interatomic distance from active region: 0.997601 Angstrom (atoms 8 - 18). >>> Invariance Statistics >>> The maximal deviation of the gradient from translational invariance was 2.293e-08 kJ mol^-1 Angstrom^-1. This would introduce a center of mass drift of 0.000 Kelvin within 1.0 ps. The maximal deviation of the gradient from rotational invariance (torque) was 3.048e+00 kJ mol^-1 rad^-1. This would introduce an overall rotation of 0.253 Kelvin within 1.0 ps. <<< Invariance Statistics <<< ### System Geometry ### * Region "All" = "Active" = "QM": Bounding box: from ( -3.760 | -2.917 | -1.918 ) to ( 3.561 | 2.564 | 2.193 ) Angstrom System extent: ( 7.321 | 5.481 | 4.111 ) Angstrom Center of mass: ( -0.079 | -0.014 | -0.221 ) Angstrom Angular momentum: ( 0.00097036 | 0.01083748 | 0.00305549 ) a.m.u. Angstrom^2 fs^-1 Angular velocity: ( 0.00001204 | 0.00002034 | 0.00000577 ) fs^-1 Moment of inertia: ( 328.57 | -115.27 | -111.07 ) ( -115.27 | 599.29 | 6.10 ) a.m.u. Angstrom^2 ( -111.07 | 6.10 | 740.03 ) Singular values: ( 263.99 | 775.82 | 628.07 ) a.m.u. Angstrom^2 Thermostat Summary: (*) Region "All": Injected 19.37 kJ mol^-1 of energy into the system (equivalent to 70.61 K). NHC potential energy 3.7621 kJ mol^-1, kinetic energy 5.5346 kJ mol^-1, temperature 887.550 K. >>> Timing data >>> MD loop was running for 3707.404 seconds (1h 01m 47.404s) Performance: 18.537 seconds/step, 97.103 fs/hour. Average SCF iterations/step: 5.512 Time spent within the MD module (overhead): 0.910 seconds (0.0246 % of total time). <<< Timing data <<< Finished MD loop. ------------------------------------------------------------------------------------------- ####################################################################### ######## Finished Executing Input Script (SAN-VM) ######## ####################################################################### Total execution time: 3707.404 seconds (1h 01m 47.404s) 22 instructions executed 5 function calls Timings for individual modules during the MD run: Startup calculation ... 595.186 sec (= 9.920 min) 16.3 % SCF iterations ... 2325.001 sec (= 38.750 min) 63.5 % SCF gradient evaluation ... 739.359 sec (= 12.323 min) 20.2 % ORCA initialization ... 0.619 sec (= 0.010 min) 0.0 % Self time inside of MD module ... 0.958 sec (= 0.016 min) 0.0 % ------------------------------------------------------------------------------ Sum of individual times ... 3661.123 sec (= 61.019 min) 100.0 % Total wall time of MD module ... 3708.025 sec (= 61.800 min) --> "dark time" ... 46.902 sec (= 0.782 min) 1.3 % ( The "dark time" is spent in the ORCA-internal routines for energy and gradient calculation, but not inside of the sub-programs which do so. It contains operating system overhead for spawning new processes in each MD step and some file I/O time. ) ########################################################### #### ORCA ab initio Molecular Dynamics leaving #### #### Scriptable Nuclear Dynamics (SANdy) + ORCA #### #### (c) Martin Brehm, 2016 - 2025 #### #### https://sanscript.org/orcamd #### ###########################################################