diff --git a/doc/src/fitpod_command.rst b/doc/src/fitpod_command.rst index e86a48a315..6718af8eac 100644 --- a/doc/src/fitpod_command.rst +++ b/doc/src/fitpod_command.rst @@ -27,54 +27,145 @@ Description Fit a machine-learning interatomic potential (ML-IAP) based on proper orthogonal descriptors (POD). Two input files are required for this -command. The first input file describes a POD potential, while the -second input file specifies the DFT data. +command. The first input file describes a POD potential parameter +settings, while the second input file specifies the DFT data used for +the fitting procedure. -Below is a one-line description of all the keywords that can be assigned -in the first input file (``Ta_param.pod``): +The table below has one-line descriptions of all the keywords that can +be used in the first input file (i.e. ``Ta_param.pod`` in the example +above): -* species (STRING): Chemical symbols for all elements in the system and have to match XYZ training files. -* pbc 1 1 1 (INT): three integer constants specify boundary conditions -* rin 1.0 (REAL): a real number specifies the inner cut-off radius -* rcut 5.0 (REAL): a real number specifies the outer cut-off radius -* bessel_polynomial_degree 3 (INT): the maximum degree of Bessel polynomials -* inverse_polynomial_degree 6 (INT): the maximum degree of inverse radial basis functions -* onebody 1 (BOOL): turns on/off one-body potential -* twobody_number_radial_basis_functions 6 (INT): number of radial basis functions for two-body potential -* threebody_number_radial_basis_functions 5 (INT): number of radial basis functions for three-body potential -* threebody_number_angular_basis_functions 5 (INT): number of angular basis functions for three-body potential -* fourbody_snap_twojmax 0 (INT): band limit for SNAP bispectrum components (0,2,4,6,8... allowed) -* fourbody_snap_chemflag 0 (BOOL): turns on/off the explicit multi-element variant of the SNAP bispectrum components -* quadratic_pod_potential 0 (BOOL): turns on/off quadratic POD potential -* basename_for_output_files pod (STRING): a basename string added to the output files +.. list-table:: + :header-rows: 1 + :widths: auto -All keywords except species have default values. If keywords are not set -in the input file, their defaults are used. Next, we describe all the -keywords that can be assigned in the second input file (``Ta_data.pod``): + * - Keyword + - Default + - Type + - Description + * - species + - (none) + - STRING + - Chemical symbols for all elements in the system and have to match XYZ training files. + * - pbc + - 1 1 1 + - INT + - three integer constants specify boundary conditions + * - rin + - 1.0 + - REAL + - a real number specifies the inner cut-off radius + * - rcut + - 5.0 + - REAL + - a real number specifies the outer cut-off radius + * - bessel_polynomial_degree + - 3 + - INT + - the maximum degree of Bessel polynomials + * - inverse_polynomial_degree + - 6 + - INT + - the maximum degree of inverse radial basis functions + * - onebody + - 1 + - BOOL + - turns on/off one-body potential + * - twobody_number_radial_basis_functions + - 6 + - INT + - number of radial basis functions for two-body potential + * - threebody_number_radial_basis_functions + - 5 + - INT + - number of radial basis functions for three-body potential + * - threebody_number_angular_basis_functions + - 5 + - INT + - number of angular basis functions for three-body potential + * - fourbody_snap_twojmax + - 0 + - INT + - band limit for SNAP bispectrum components (0,2,4,6,8... allowed) + * - fourbody_snap_chemflag + - 0 + - BOOL + - turns on/off the explicit multi-element variant of the SNAP bispectrum components + * - quadratic_pod_potential + - 0 + - BOOL + - turns on/off quadratic POD potential + * - basename_for_output_files + - pod + - STRING + - a basename string added to the output files -* file_format extxyz (STRING): only extended xyz format is currently supported -* file_extension xyz (STRING): extension of the data files -* path_to_training_data_set (STRING): specifies the path to training data files in double quotes -* path_to_test_data_set "" (STRING): specifies the path to test data files in double quotes -* fraction_training_data_set 1.0 (REAL): a real number (<= 1.0) specifies the fraction of the training set used to fit POD -* randomize_training_data_set 0 (BOOL): turns on/off randomization of the training set -* fitting_weight_energy 100.0 (REAL): a real constant specifies the weight for energy in the least-squares fit -* fitting_weight_force 1.0 (REAL): a real constant specifies the weight for force in the least-squares fit -* error_analysis_for_training_data_set 0 (BOOL): turns on/off error analysis for the training data set -* error_analysis_for_test_data_set 0 (BOOL): turns on/off error analysis for the test data set +All keywords except *species* have default values. If a keyword is not +set in the input file, its default value is used. The next table +describes all keywords that can be used in the second input file +(i.e. ``Ta_data.pod`` in the example above): -All keywords except path_to_training_data_set have default values. If -keywords are not set in the input file, their defaults are used. On -successful training, it produces a number of output files: +.. list-table:: + :header-rows: 1 + :widths: auto -* ``basename_training_errors.pod`` reports the errors in energy and forces for the training data set -* ``basename_training_analysis.pod`` reports detailed errors for all training configurations -* ``basename_test_errors.pod`` reports errors for the test data set -* ``basename_test_analysis.pod`` reports detailed errors for all test configurations -* ``basename_coefficients.pod`` contains the coefficients of the POD potential + * - Keyword + - Default + - Type + - Description + * - file_format + - extxyz + - STRING + - only the extended xyz format (extxyz) is currently supported + * - file_extension + - xyz + - STRING + - extension of the data files + * - path_to_training_data_set + - (none) + - STRING + - specifies the path to training data files in double quotes + * - path_to_test_data_set + - "" + - STRING + - specifies the path to test data files in double quotes + * - fraction_training_data_set + - 1.0 + - REAL + - a real number (<= 1.0) specifies the fraction of the training set used to fit POD + * - randomize_training_data_set + - 0 + - BOOL + - turns on/off randomization of the training set + * - fitting_weight_energy + - 100.0 + - REAL + - a real constant specifies the weight for energy in the least-squares fit + * - fitting_weight_force + - 1.0 + - REAL + - a real constant specifies the weight for force in the least-squares fit + * - error_analysis_for_training_data_set + - 0 + - BOOL + - turns on/off error analysis for the training data set + * - error_analysis_for_test_data_set + - 0 + - BOOL + - turns on/off error analysis for the test data set -After training the POD potential, ``Ta_param.pod`` and ``basename_coefficients.pod`` -are two files needed to use the POD potential in LAMMPS. See +All keywords except *path_to_training_data_set* have default values. If +a keyword is not set in the input file, its default value is used. After +successful training, a number of output files are produced, if enabled: + +* ``_training_errors.pod`` reports the errors in energy and forces for the training data set +* ``_training_analysis.pod`` reports detailed errors for all training configurations +* ``_test_errors.pod`` reports errors for the test data set +* ``_test_analysis.pod`` reports detailed errors for all test configurations +* ``_coefficients.pod`` contains the coefficients of the POD potential + +After training the POD potential, ``Ta_param.pod`` and ``_coefficients.pod`` +are the two files needed to use the POD potential in LAMMPS. See :doc:`pair_style pod ` for using the POD potential. Examples about training and using POD potentials are found in the directory lammps/examples/PACKAGES/pod. diff --git a/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod b/examples/PACKAGES/pod/Ta/Ta_training_analysis.pod index 2cc92f8eb9..199758e400 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 | energy | DFT energy | energy error | force | DFT force | force error | - 1 64 -753.4390371883142 -754.220443 0.012209465807591968 7.735924624311095 8.398670476926332 0.11471486425390308 - 2 64 -752.9893805956235 -753.865255 0.01368553756838331 8.849199813515922 9.134430544814492 0.1287092094838365 - 3 64 -753.3208522383574 -754.0221 0.010956996275666597 8.322448690052669 9.01726110188127 0.11543646534139868 - 4 64 -753.5955479873617 -754.279613 0.010688515822474542 7.708631396481507 8.381725091649153 0.10577524248581281 - 5 64 -753.0525448626341 -753.777209 0.01132287714634117 8.902153447393834 9.478314476700007 0.11903245162926333 - 6 64 -753.3492631141221 -754.048643 0.01092781071684179 7.810233094328555 8.465317937559755 0.11274191144517283 - 7 64 -753.6490826341914 -754.317603 0.010445630715759435 7.444807429875485 8.127690490502268 0.10226834483132667 - 8 64 -753.32753515846 -753.969161 0.010025403774061914 8.52920112993267 9.425464951766411 0.10637303034619959 - 9 64 -753.3951654908428 -754.141988 0.011669101705580331 8.169917991973906 8.821346913268911 0.1139580361198143 + 1 64 -753.4390371883142 -754.220443 0.012209465807591968 7.735924624311095 8.398670476926332 0.11471486425390308 + 2 64 -752.9893805956235 -753.865255 0.01368553756838331 8.849199813515922 9.134430544814492 0.1287092094838365 + 3 64 -753.3208522383574 -754.0221 0.010956996275666597 8.322448690052669 9.01726110188127 0.11543646534139868 + 4 64 -753.5955479873617 -754.279613 0.010688515822474542 7.708631396481507 8.381725091649153 0.10577524248581281 + 5 64 -753.0525448626341 -753.777209 0.01132287714634117 8.902153447393834 9.478314476700007 0.11903245162926333 + 6 64 -753.3492631141221 -754.048643 0.01092781071684179 7.810233094328555 8.465317937559755 0.11274191144517283 + 7 64 -753.6490826341914 -754.317603 0.010445630715759435 7.444807429875485 8.127690490502268 0.10226834483132667 + 8 64 -753.32753515846 -753.969161 0.010025403774061914 8.52920112993267 9.425464951766411 0.10637303034619959 + 9 64 -753.3951654908428 -754.141988 0.011669101705580331 8.169917991973906 8.821346913268911 0.1139580361198143 # Displaced_BCC.xyz | config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | - 10 54 -631.7256314067248 -631.019667 0.013073414939347676 15.43137976831244 16.625876002911852 0.2644440995180555 - 11 54 -632.2717820737765 -631.719595 0.010225686551416823 14.520227658943742 15.58666626272206 0.2234292007779398 - 12 54 -631.9433981955067 -631.386255 0.010317466583457089 15.214742440749932 15.923788831679882 0.22596574544494924 - 13 54 -633.0715327033122 -632.575826 0.009179753765040375 13.387222633512346 14.55977161807516 0.204686057337303 - 14 54 -630.8934956969555 -630.450212 0.008208957351028116 16.55208943682467 16.963407263806737 0.23634113203777507 - 15 54 -632.0720278107077 -631.669379 0.007456459457549264 15.243544753110454 16.057573148572235 0.22775532118460526 - 16 54 -632.802645523698 -632.431277 0.006877194883294898 14.2114664258239 14.698107183802986 0.20251384204702003 - 17 54 -631.680208998728 -630.960068 0.013335944420888339 14.712341546525474 15.9907314848333 0.2281495621651289 - 18 54 -625.0384776587186 -623.378198 0.030745919605900934 23.40214754435865 24.67640432462571 0.3498682765920348 + 10 54 -631.7256314067248 -631.019667 0.013073414939347676 15.43137976831244 16.625876002911852 0.2644440995180555 + 11 54 -632.2717820737765 -631.719595 0.010225686551416823 14.520227658943742 15.58666626272206 0.2234292007779398 + 12 54 -631.9433981955067 -631.386255 0.010317466583457089 15.214742440749932 15.923788831679882 0.22596574544494924 + 13 54 -633.0715327033122 -632.575826 0.009179753765040375 13.387222633512346 14.55977161807516 0.204686057337303 + 14 54 -630.8934956969555 -630.450212 0.008208957351028116 16.55208943682467 16.963407263806737 0.23634113203777507 + 15 54 -632.0720278107077 -631.669379 0.007456459457549264 15.243544753110454 16.057573148572235 0.22775532118460526 + 16 54 -632.802645523698 -632.431277 0.006877194883294898 14.2114664258239 14.698107183802986 0.20251384204702003 + 17 54 -631.680208998728 -630.960068 0.013335944420888339 14.712341546525474 15.9907314848333 0.2281495621651289 + 18 54 -625.0384776587186 -623.378198 0.030745919605900934 23.40214754435865 24.67640432462571 0.3498682765920348 # Displaced_FCC.xyz | config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | 19 48 -555.969904815311 -555.899463 0.0014675378189797546 6.076723564568183 6.084617062577644 0.07097225533172778 - 20 48 -555.9513725474736 -555.922478 0.0006019697390347764 6.276808110532802 6.297071211051453 0.09304007759688171 - 21 48 -555.8352575479919 -555.800269 0.000728928083165196 6.149373534090429 6.021098635803518 0.08156835087195236 - 22 48 -556.2646335350813 -556.196151 0.0014267194808610384 5.061971950438771 5.127955094071613 0.08671676174522915 - 23 48 -555.6280533651646 -555.488929 0.002898424274263789 6.842691153020981 7.050223458554702 0.08140861877545956 - 24 48 -556.1096232717318 -556.027926 0.0017020264944136443 5.657586162368862 5.611881174158804 0.07972132595721448 - 25 48 -556.0586145384509 -555.968399 0.0018794903843944628 5.8765172187696 5.9792171885302 0.07481336528039453 - 26 48 -556.0087786423783 -556.047132 0.0007990282837866403 5.74973736848915 5.544452585448 0.08230729051939972 - 27 48 -555.8257619324029 -555.747848 0.0016232069250605718 6.360724172500975 6.478925680043952 0.09531889945060759 + 20 48 -555.9513725474736 -555.922478 0.0006019697390347764 6.276808110532802 6.297071211051453 0.09304007759688171 + 21 48 -555.8352575479919 -555.800269 0.000728928083165196 6.149373534090429 6.021098635803518 0.08156835087195236 + 22 48 -556.2646335350813 -556.196151 0.0014267194808610384 5.061971950438771 5.127955094071613 0.08671676174522915 + 23 48 -555.6280533651646 -555.488929 0.002898424274263789 6.842691153020981 7.050223458554702 0.08140861877545956 + 24 48 -556.1096232717318 -556.027926 0.0017020264944136443 5.657586162368862 5.611881174158804 0.07972132595721448 + 25 48 -556.0586145384509 -555.968399 0.0018794903843944628 5.8765172187696 5.9792171885302 0.07481336528039453 + 26 48 -556.0087786423783 -556.047132 0.0007990282837866403 5.74973736848915 5.544452585448 0.08230729051939972 + 27 48 -555.8257619324029 -555.747848 0.0016232069250605718 6.360724172500975 6.478925680043952 0.09531889945060759 # Elastic_BCC.xyz | config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | - 28 2 -23.683550425737614 -23.689367 0.002908287131193177 0.0006476690654891145 0.0006222748588847215 7.473204313680527e-06 - 29 2 -23.682831250858055 -23.689888 0.003528374570972659 0.000643276149049826 0.0006166052221640683 7.1271217620395385e-06 - 30 2 -23.68295261398044 -23.689996 0.0035216930097803356 0.0009101925776760112 0.0008810425642385276 1.137157330071999e-05 - 31 2 -23.68109878546453 -23.690957 0.004929107267734878 1.0425659459469606e-06 0 4.159514932622835e-07 - 32 2 -23.679217057072705 -23.690521 0.005651971463647598 0.0006251577956327515 0.0005982273815197694 7.343258080746786e-06 - 33 2 -23.677874583378518 -23.69038 0.006252708310741539 0.0006209549872866152 0.0005925723584508478 7.867521622667099e-06 - 34 2 -23.684170458769703 -23.689202 0.002515770615149293 0.0006510533206477159 0.000627936302502093 6.902840555390397e-06 - 35 2 -23.6817142271379 -23.690482 0.0043838864310501435 0.0009007679091664014 0.0008640138887772579 1.2830088200696247e-05 - 36 2 -23.683028429384336 -23.689902 0.003436785307831869 0.0006422803191510104 0.0006152154094299004 8.366794318520534e-06 - 37 2 -23.680657088615856 -23.690563 0.004952955692072436 0.0006308861644473481 0.0006038725030997851 7.233701491974039e-06 - 38 2 -23.683393925876146 -23.690207 0.003406537061927395 0.0011163849318186075 0.001073697350280795 1.742887299793318e-05 - 39 2 -23.683710082445202 -23.689285 0.0027874587773997206 0.0009201854955894811 0.0008900134830439369 1.0813707654398404e-05 - 40 2 -23.68346034101502 -23.689768 0.00315382949248999 0.0011184689906517506 0.0010802490453594485 1.5612634593006028e-05 - 41 2 -23.68226028413025 -23.68968 0.0037098579348739946 0.0009056805415750813 0.0008680034562143172 1.2942261574573714e-05 - 42 2 -23.68261525325416 -23.690074 0.0037293733729200085 0.0014343132477624152 0.001373818765339883 2.3643108498040922e-05 - 43 2 -23.68471120323133 -23.688108 0.0016983983843346095 0.0006578004864109103 0.0006336134468270066 7.710526622407554e-06 - 44 2 -23.684069319352503 -23.689241 0.002585840323748201 0.0009210090641231295 0.0008880101350772974 1.1437396055538247e-05 - 45 2 -23.683864034166927 -23.68952 0.002827982916537408 0.0009167488520226046 0.0008860011286674525 1.0705800766461788e-05 - 46 2 -23.68526333130852 -23.686278 0.0005073343457411283 0.0006658873064479383 0.0006406777661195993 8.368568053270062e-06 - 47 2 -23.676313172280313 -23.690097 0.006891913859844223 0.0008723081634423558 0.0008410160521654744 1.0770086672601711e-05 - 48 2 -23.67837071762589 -23.690811 0.006220141187055717 0.0008799687221560049 0.0008500070587942196 1.056363950480386e-05 - 49 2 -23.679834898397225 -23.690266 0.005215550801388247 0.0010902204435188458 0.0010443227470470994 1.8746540560027915e-05 - 50 2 -23.68211557119403 -23.690597 0.004240714402985901 0.001104089135016636 0.0010508330029076933 2.1742368843564736e-05 - 51 2 -23.680523087762776 -23.690673 0.005074956118612306 0.0006301839900262931 0.0006038907185907066 7.629836622010858e-06 - 52 2 -23.681873678397167 -23.690551 0.004338660801415983 0.0009009015657311293 0.0008590064027700842 1.4407741198563606e-05 - 53 2 -23.68193367037301 -23.690693 0.004379664813495054 0.0008999859846277528 0.00085901105930017 1.4706473059153044e-05 - 54 2 -23.68099077069971 -23.69021 0.004609614650144422 0.0008986014473961344 0.0008730051546239576 9.195535228627245e-06 - 55 2 -23.68428236213968 -23.688943 0.0023303189301593363 0.000921865410437537 0.0008800306812833288 1.57508642566642e-05 - 56 2 -23.67844250054911 -23.690136 0.005846749725444411 0.0006229280953914929 0.0005939966329870902 8.16500915370181e-06 - 57 2 -23.68495916599319 -23.687444 0.001242417003403773 0.0009334481799494286 0.0009030592450110901 1.2459664528827797e-05 - 58 2 -23.683650087749008 -23.689801 0.003075456125495535 0.0009146886953764765 0.0008740011441640107 1.3790683045878437e-05 - 59 2 -23.681502954525868 -23.690408 0.004452522737066644 8.676768102810234e-07 0 3.2406803953440727e-07 - 60 2 -23.68117698949833 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0.038529203820796276 2.922898525526559e-14 0 4.818527239180944e-15 + 301 8 -91.02064653125733 -91.040671 0.002503058592834506 4.6028526522736476e-15 0 7.778789186859333e-16 + 302 8 -84.76860696166544 -84.499231 0.03367199520818076 3.49763114084807e-14 0 6.588805022411659e-15 + 303 8 -60.71230661032912 -61.825173 0.13910829870885966 1.530720137730772e-14 0 2.761896614189574e-15 + 304 8 -91.58119532861612 -91.156873 0.053040291077014246 3.2622415413251937e-15 0 5.122674564631927e-16 + 305 8 -54.28632783805454 -54.658744 0.04655202024318239 9.354138791509743e-14 0 1.6318068863355815e-14 + 306 8 -72.29250987603558 -72.277255 0.0019068595044480219 2.2054578681329044e-15 0 3.9045734238444635e-16 + 307 8 -75.14362522461471 -74.923334 0.027536403076839022 3.701535352368937e-15 0 6.225037123506564e-16 + 308 8 -64.41770166542021 -64.798066 0.04754554182247439 1.1277642648437778e-14 0 1.8028113724088968e-15 + 309 8 -93.30049446378375 -93.048342 0.031519057972968056 7.681702714531972e-15 0 1.3818667731539263e-15 + 310 8 -63.56337379391148 -64.38702 0.10295577576106574 4.650514188810416e-15 0 7.119955666712308e-16 + 311 8 -88.81213088911828 -88.352871 0.057407486139785746 1.0602241395926366e-14 0 1.834397795700641e-15 # Volume_BCC.xyz | config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | - 312 2 -16.3892152416096 -16.763625 0.18720487919519968 1.0914154436343227e-15 0 3.5388358909926865e-16 - 313 2 16.19624648530409 16.314145 0.05894925734795464 1.173445821789704e-13 0 4.6233271840575206e-14 - 314 2 -21.242304450409645 -21.209071 0.016616725204821492 3.585227660155614e-15 0 1.3207030506352358e-15 - 315 2 -15.805603050124574 -15.780524 0.012539525062287282 2.124997331316811e-14 0 8.053381457077494e-15 - 316 2 -19.055415660702145 -19.002205 0.02660533035107271 6.0759336543043874e-15 0 2.014708381453664e-15 - 317 2 -22.674158244740266 -22.620568 0.026795122370133484 1.1014496902801007e-15 0 3.642919299551295e-16 - 318 2 4.042473604766646 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-19.002205 0.02660533035107271 6.0759336543043874e-15 0 2.014708381453664e-15 + 317 2 -22.674158244740266 -22.620568 0.026795122370133484 1.1014496902801007e-15 0 3.642919299551295e-16 + 318 2 4.042473604766646 4.096885 0.027205697616677238 1.9902433980058767e-14 0 6.92732908073405e-15 + 319 2 56.21038668042891 56.26276 0.026186659785544464 2.330055887092146e-13 0 7.460626360632925e-14 + 320 2 -22.55810416908498 -22.585113 0.013504415457509467 3.0904185144113253e-15 0 1.1287267417022424e-15 + 321 2 -21.7599764107913 -21.795501 0.01776229460435097 1.2337969962857226e-15 0 3.885780586188048e-16 + 322 2 33.30762744801588 33.110078 0.09877472400793863 3.266445464915648e-14 0 1.196323133149472e-14 + 323 2 -20.821568981956375 -20.885998 0.03221450902181289 1.5242840565028428e-15 0 5.181040781584064e-16 + 324 2 -23.552386060429054 -23.601336 0.024474969785472922 1.3371099358483885e-15 0 4.861878767058644e-16 + 325 2 -23.171474216335454 -23.207313 0.017919391832272424 1.137777477464038e-15 0 3.4230199656986815e-16 + 326 2 -19.781756814356513 -19.898089 0.05816609282174312 4.6546920595778824e-15 0 1.886222659545448e-15 + 327 2 -23.450283635840197 -23.405474 0.02240481792009774 9.704285623149953e-16 0 2.4864369822334237e-16 + 328 2 -4.653024677012454 -4.781324 0.06414966149377266 5.862363434730624e-15 0 2.0874505827587577e-15 + 329 2 -18.675358792981537 -18.864936 0.09478860350923135 8.772694031921661e-16 0 3.191891195797325e-16 + 330 2 -17.534418109269176 -17.813086 0.13933394536541144 9.231597913640693e-16 0 3.307539427529112e-16 + 331 2 -11.04838015128553 -11.197201 0.074410424357235 7.148644112374603e-15 0 2.1024848528838902e-15 + 332 2 -23.684909655784992 -23.696705 0.005897672107504803 1.1541863724315294e-15 0 3.7007434154171886e-16 # Volume_FCC.xyz | config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | - 333 4 -19.133479224563946 -19.075994 0.014371306140986029 6.826739107542361e-15 0 1.496343558319661e-15 - 334 4 -35.26070620882045 -34.873619 0.09677180220511339 1.160828264504475e-15 0 2.6311779722602385e-16 - 335 4 -43.93366452519817 -43.950003 0.00408461870045862 1.4096280136020593e-15 0 3.30320261883917e-16 - 336 4 -41.036904813057575 -40.991909 0.01124895326439379 4.635916537527408e-15 0 1.16208402854238e-15 - 337 4 -43.42242783004628 -43.453929 0.007875292488430219 2.3180935053065633e-14 0 6.67345043655236e-15 - 338 4 -42.6738078081144 -42.686077 0.0030672979714001514 1.3611779986936563e-15 0 2.9569807250921326e-16 - 339 4 -33.588538118360724 -33.224653 0.09097127959018003 5.518847641566371e-16 0 1.082756569588857e-16 - 340 4 -27.011636581354555 -26.862709 0.03723189533863902 4.70436898786898e-15 0 9.857137632111491e-16 - 341 4 -25.590091470966968 -25.519883 0.017552117741741924 1.130986492708506e-15 0 2.856511323775142e-16 - 342 4 3.4418818005448313 3.463071 0.0052972998637921265 1.9899840382671654e-14 0 4.603297678298114e-15 - 343 4 -31.907218212756142 -31.59595 0.07781705318903587 1.3234700975501595e-15 0 3.293083398562639e-16 - 344 4 -45.06026255265113 -45.100466 0.010050861837216374 2.919646616711383e-15 0 6.914582488239601e-16 - 345 4 -46.03951745154122 -46.052258 0.0031851371146949248 1.1193147801545848e-15 0 2.6309972718981573e-16 - 346 4 -30.24296845260136 -30.001189 0.060444863150340034 7.064926245034658e-16 0 1.5944999950020153e-16 - 347 4 -22.95808404422531 -22.8504 0.02692101105632716 5.437085264345896e-16 0 1.2598429244281562e-16 - 348 4 -9.12980646179386 -9.164691 0.008721134551534782 1.523379765970025e-14 0 3.5449074231586053e-15 - 349 4 -24.21762173701387 -24.150343 0.016819684253468026 4.2549906208422197e-16 0 7.777343583962686e-17 - 350 4 -46.447572433321874 -46.426795 0.0051943583304687735 1.723920676012659e-15 0 4.706883031483736e-16 - 351 4 -28.620710205803768 -28.451145 0.04239130145094183 5.5425292592552055e-15 0 1.5819955299460158e-15 - 352 4 40.31514224418573 40.341566 0.006605938953567758 4.8281769263871373e-14 0 9.961761651490169e-15 - 353 4 19.5120051209587 19.617912 0.02647671976032484 4.841735199518895e-14 0 1.1033397101170717e-14 - 354 4 -27.063172316161314 -26.954384 0.027197079040328198 1.2255793734759726e-15 0 2.795796002115954e-16 - 355 4 -46.36817163420157 -46.323696 0.011118908550393769 3.349394815419411e-15 0 8.662052556710856e-16 - 356 4 -45.87280132105037 -45.828947 0.010963580262592032 1.3893911369761706e-15 0 2.723515857283587e-16 - 357 4 -38.47137850859525 -38.16029 0.07777212714881188 3.373832020143023e-15 0 7.929131888110655e-16 - 358 4 -33.067647343769835 -32.919741 0.03697658594245823 1.702490142868649e-14 0 4.757190012287064e-15 - 359 4 -41.345129542746605 -41.272675 0.018113635686651364 7.698716676911266e-15 0 2.185584431895852e-15 - 360 4 -39.95828655599284 -39.753322 0.051241138998211255 7.845705937569456e-16 0 2.0193623907474627e-16 - 361 4 -37.661968987638765 -37.547435 0.028633496909691303 3.873442428527344e-15 0 9.32630708772031e-16 - 362 4 -36.89708070433085 -36.52595 0.09278267608271129 1.5087220775411117e-15 0 3.701466216865512e-16 - 363 4 -45.03333641831445 -45.016087 0.004312354578612343 1.937613905884688e-15 0 4.039014493232666e-16 + 333 4 -19.133479224563946 -19.075994 0.014371306140986029 6.826739107542361e-15 0 1.496343558319661e-15 + 334 4 -35.26070620882045 -34.873619 0.09677180220511339 1.160828264504475e-15 0 2.6311779722602385e-16 + 335 4 -43.93366452519817 -43.950003 0.00408461870045862 1.4096280136020593e-15 0 3.30320261883917e-16 + 336 4 -41.036904813057575 -40.991909 0.01124895326439379 4.635916537527408e-15 0 1.16208402854238e-15 + 337 4 -43.42242783004628 -43.453929 0.007875292488430219 2.3180935053065633e-14 0 6.67345043655236e-15 + 338 4 -42.6738078081144 -42.686077 0.0030672979714001514 1.3611779986936563e-15 0 2.9569807250921326e-16 + 339 4 -33.588538118360724 -33.224653 0.09097127959018003 5.518847641566371e-16 0 1.082756569588857e-16 + 340 4 -27.011636581354555 -26.862709 0.03723189533863902 4.70436898786898e-15 0 9.857137632111491e-16 + 341 4 -25.590091470966968 -25.519883 0.017552117741741924 1.130986492708506e-15 0 2.856511323775142e-16 + 342 4 3.4418818005448313 3.463071 0.0052972998637921265 1.9899840382671654e-14 0 4.603297678298114e-15 + 343 4 -31.907218212756142 -31.59595 0.07781705318903587 1.3234700975501595e-15 0 3.293083398562639e-16 + 344 4 -45.06026255265113 -45.100466 0.010050861837216374 2.919646616711383e-15 0 6.914582488239601e-16 + 345 4 -46.03951745154122 -46.052258 0.0031851371146949248 1.1193147801545848e-15 0 2.6309972718981573e-16 + 346 4 -30.24296845260136 -30.001189 0.060444863150340034 7.064926245034658e-16 0 1.5944999950020153e-16 + 347 4 -22.95808404422531 -22.8504 0.02692101105632716 5.437085264345896e-16 0 1.2598429244281562e-16 + 348 4 -9.12980646179386 -9.164691 0.008721134551534782 1.523379765970025e-14 0 3.5449074231586053e-15 + 349 4 -24.21762173701387 -24.150343 0.016819684253468026 4.2549906208422197e-16 0 7.777343583962686e-17 + 350 4 -46.447572433321874 -46.426795 0.0051943583304687735 1.723920676012659e-15 0 4.706883031483736e-16 + 351 4 -28.620710205803768 -28.451145 0.04239130145094183 5.5425292592552055e-15 0 1.5819955299460158e-15 + 352 4 40.31514224418573 40.341566 0.006605938953567758 4.8281769263871373e-14 0 9.961761651490169e-15 + 353 4 19.5120051209587 19.617912 0.02647671976032484 4.841735199518895e-14 0 1.1033397101170717e-14 + 354 4 -27.063172316161314 -26.954384 0.027197079040328198 1.2255793734759726e-15 0 2.795796002115954e-16 + 355 4 -46.36817163420157 -46.323696 0.011118908550393769 3.349394815419411e-15 0 8.662052556710856e-16 + 356 4 -45.87280132105037 -45.828947 0.010963580262592032 1.3893911369761706e-15 0 2.723515857283587e-16 + 357 4 -38.47137850859525 -38.16029 0.07777212714881188 3.373832020143023e-15 0 7.929131888110655e-16 + 358 4 -33.067647343769835 -32.919741 0.03697658594245823 1.702490142868649e-14 0 4.757190012287064e-15 + 359 4 -41.345129542746605 -41.272675 0.018113635686651364 7.698716676911266e-15 0 2.185584431895852e-15 + 360 4 -39.95828655599284 -39.753322 0.051241138998211255 7.845705937569456e-16 0 2.0193623907474627e-16 + 361 4 -37.661968987638765 -37.547435 0.028633496909691303 3.873442428527344e-15 0 9.32630708772031e-16 + 362 4 -36.89708070433085 -36.52595 0.09278267608271129 1.5087220775411117e-15 0 3.701466216865512e-16 + 363 4 -45.03333641831445 -45.016087 0.004312354578612343 1.937613905884688e-15 0 4.039014493232666e-16 diff --git a/examples/PACKAGES/pod/Ta/Ta_training_errors.pod b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod index 7237003522..120aa5fb57 100644 --- a/examples/PACKAGES/pod/Ta/Ta_training_errors.pod +++ b/examples/PACKAGES/pod/Ta/Ta_training_errors.pod @@ -1,20 +1,20 @@ **************** 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 0.011326 0.011373 0.113223 0.141496 -Displaced_BCC.xyz 9 486 0.012158 0.013983 0.240350 0.311834 -Displaced_FCC.xyz 9 432 0.001459 0.001605 0.082874 0.104038 -Elastic_BCC.xyz 100 200 0.004442 0.004774 0.000010 0.000013 -Elastic_FCC.xyz 100 400 0.002855 0.002914 0.000147 0.000208 -GSF_110.xyz 22 528 0.005794 0.006857 0.047304 0.097750 -GSF_112.xyz 22 660 0.010592 0.011566 0.123316 0.191078 -Liquid.xyz 3 300 0.013230 0.015407 0.567180 0.757188 -Surface.xyz 7 236 0.025392 0.037556 0.096037 0.295185 -Volume_A15.xyz 30 240 0.039262 0.048655 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.049805 0.067608 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.030071 0.041758 0.000000 0.000000 ----------------------------------------------------------------------------------------- -All files 363 4224 0.012915 0.025804 0.122413 0.259832 ----------------------------------------------------------------------------------------- +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011326 0.011373 0.113223 0.141496 +Displaced_BCC.xyz 9 486 0.012158 0.013983 0.240350 0.311834 +Displaced_FCC.xyz 9 432 0.001459 0.001605 0.082874 0.104038 +Elastic_BCC.xyz 100 200 0.004442 0.004774 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002855 0.002914 0.000147 0.000208 +GSF_110.xyz 22 528 0.005794 0.006857 0.047304 0.097750 +GSF_112.xyz 22 660 0.010592 0.011566 0.123316 0.191078 +Liquid.xyz 3 300 0.013230 0.015407 0.567180 0.757188 +Surface.xyz 7 236 0.025392 0.037556 0.096037 0.295185 +Volume_A15.xyz 30 240 0.039262 0.048655 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049805 0.067608 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030071 0.041758 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012915 0.025804 0.122413 0.259832 +--------------------------------------------------------------------------------------------------- **************** End of Error Analysis for the Training Data Set **************** diff --git a/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.1 b/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.1 index bcebbc8819..7405d036e4 100644 --- a/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.1 +++ b/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.1 @@ -50,7 +50,7 @@ fitting weight for stress: 0 **************** 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 @@ -91,24 +91,24 @@ 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 0.011326 0.011373 0.113223 0.141496 -Displaced_BCC.xyz 9 486 0.012158 0.013983 0.240350 0.311834 -Displaced_FCC.xyz 9 432 0.001459 0.001605 0.082874 0.104038 -Elastic_BCC.xyz 100 200 0.004442 0.004774 0.000010 0.000013 -Elastic_FCC.xyz 100 400 0.002855 0.002914 0.000147 0.000208 -GSF_110.xyz 22 528 0.005794 0.006857 0.047304 0.097750 -GSF_112.xyz 22 660 0.010592 0.011566 0.123316 0.191078 -Liquid.xyz 3 300 0.013230 0.015407 0.567180 0.757188 -Surface.xyz 7 236 0.025392 0.037556 0.096037 0.295185 -Volume_A15.xyz 30 240 0.039262 0.048655 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.049805 0.067608 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.030071 0.041758 0.000000 0.000000 ----------------------------------------------------------------------------------------- -All files 363 4224 0.012915 0.025804 0.122413 0.259832 ----------------------------------------------------------------------------------------- +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011326 0.011373 0.113223 0.141496 +Displaced_BCC.xyz 9 486 0.012158 0.013983 0.240350 0.311834 +Displaced_FCC.xyz 9 432 0.001459 0.001605 0.082874 0.104038 +Elastic_BCC.xyz 100 200 0.004442 0.004774 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002855 0.002914 0.000147 0.000208 +GSF_110.xyz 22 528 0.005794 0.006857 0.047304 0.097750 +GSF_112.xyz 22 660 0.010592 0.011566 0.123316 0.191078 +Liquid.xyz 3 300 0.013230 0.015407 0.567180 0.757188 +Surface.xyz 7 236 0.025392 0.037556 0.096037 0.295185 +Volume_A15.xyz 30 240 0.039262 0.048655 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049805 0.067608 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030071 0.041758 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012915 0.025804 0.122413 0.259832 +--------------------------------------------------------------------------------------------------- **************** End of Error Analysis for the Training Data Set **************** Total wall time: 0:00:01 diff --git a/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.4 b/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.4 index 4aedd71b10..01888f8ddd 100644 --- a/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.4 +++ b/examples/PACKAGES/pod/Ta/log.30Nov22.fitpod.g++.4 @@ -50,7 +50,7 @@ fitting weight for stress: 0 **************** 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 @@ -91,24 +91,24 @@ 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 0.011326 0.011373 0.113223 0.141496 -Displaced_BCC.xyz 9 486 0.012158 0.013983 0.240350 0.311834 -Displaced_FCC.xyz 9 432 0.001459 0.001605 0.082874 0.104038 -Elastic_BCC.xyz 100 200 0.004442 0.004774 0.000010 0.000013 -Elastic_FCC.xyz 100 400 0.002855 0.002914 0.000147 0.000208 -GSF_110.xyz 22 528 0.005794 0.006857 0.047304 0.097750 -GSF_112.xyz 22 660 0.010592 0.011566 0.123316 0.191078 -Liquid.xyz 3 300 0.013230 0.015407 0.567180 0.757188 -Surface.xyz 7 236 0.025392 0.037556 0.096037 0.295185 -Volume_A15.xyz 30 240 0.039262 0.048655 0.000000 0.000000 -Volume_BCC.xyz 21 42 0.049805 0.067608 0.000000 0.000000 -Volume_FCC.xyz 31 124 0.030071 0.041758 0.000000 0.000000 ----------------------------------------------------------------------------------------- -All files 363 4224 0.012915 0.025804 0.122413 0.259832 ----------------------------------------------------------------------------------------- +--------------------------------------------------------------------------------------------------- + File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force +--------------------------------------------------------------------------------------------------- +Displaced_A15.xyz 9 576 0.011326 0.011373 0.113223 0.141496 +Displaced_BCC.xyz 9 486 0.012158 0.013983 0.240350 0.311834 +Displaced_FCC.xyz 9 432 0.001459 0.001605 0.082874 0.104038 +Elastic_BCC.xyz 100 200 0.004442 0.004774 0.000010 0.000013 +Elastic_FCC.xyz 100 400 0.002855 0.002914 0.000147 0.000208 +GSF_110.xyz 22 528 0.005794 0.006857 0.047304 0.097750 +GSF_112.xyz 22 660 0.010592 0.011566 0.123316 0.191078 +Liquid.xyz 3 300 0.013230 0.015407 0.567180 0.757188 +Surface.xyz 7 236 0.025392 0.037556 0.096037 0.295185 +Volume_A15.xyz 30 240 0.039262 0.048655 0.000000 0.000000 +Volume_BCC.xyz 21 42 0.049805 0.067608 0.000000 0.000000 +Volume_FCC.xyz 31 124 0.030071 0.041758 0.000000 0.000000 +--------------------------------------------------------------------------------------------------- +All files 363 4224 0.012915 0.025804 0.122413 0.259832 +--------------------------------------------------------------------------------------------------- **************** End of Error Analysis for the Training Data Set **************** Total wall time: 0:00:00 diff --git a/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.1 b/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.1 index 311fff00ac..1402ba9387 100644 --- a/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.1 +++ b/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.1 @@ -99,31 +99,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 3.082 | 3.082 | 3.082 Mbytes Step Temp E_pair E_mol TotEng Press - 0 300 -11.841653 0 -11.803178 -15932.81 - 10 296.91627 -11.841257 0 -11.803178 -15691.292 - 20 287.83193 -11.840092 0 -11.803178 -14982.943 - 30 273.2481 -11.838222 0 -11.803177 -13854.289 - 40 253.97579 -11.83575 0 -11.803177 -12377.385 - 50 231.08941 -11.832815 0 -11.803177 -10642.841 - 60 205.86307 -11.829579 0 -11.803177 -8751.3479 - 70 179.69197 -11.826223 0 -11.803177 -6804.808 - 80 154.00241 -11.822928 0 -11.803177 -4898.2688 - 90 130.15527 -11.819869 0 -11.803177 -3113.7145 - 100 109.34992 -11.817201 0 -11.803177 -1516.1852 -Loop time of 2.33037 on 1 procs for 100 steps with 128 atoms + 0 300 -11.841652 0 -11.803177 -15932.736 + 10 296.91627 -11.841257 0 -11.803177 -15691.219 + 20 287.83193 -11.840092 0 -11.803177 -14982.869 + 30 273.2481 -11.838221 0 -11.803177 -13854.215 + 40 253.97579 -11.835749 0 -11.803177 -12377.312 + 50 231.08941 -11.832814 0 -11.803177 -10642.767 + 60 205.86306 -11.829579 0 -11.803177 -8751.2744 + 70 179.69196 -11.826222 0 -11.803177 -6804.7346 + 80 154.0024 -11.822927 0 -11.803177 -4898.1954 + 90 130.15526 -11.819869 0 -11.803176 -3113.6412 + 100 109.34991 -11.8172 0 -11.803176 -1516.1119 +Loop time of 2.21891 on 1 procs for 100 steps with 128 atoms -Performance: 1.854 ns/day, 12.947 hours/ns, 42.912 timesteps/s, 5.493 katom-step/s -99.8% CPU use with 1 MPI tasks x 1 OpenMP threads +Performance: 1.947 ns/day, 12.327 hours/ns, 45.067 timesteps/s, 5.769 katom-step/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.3293 | 2.3293 | 2.3293 | 0.0 | 99.95 +Pair | 2.2179 | 2.2179 | 2.2179 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00039757 | 0.00039757 | 0.00039757 | 0.0 | 0.02 -Output | 0.00023376 | 0.00023376 | 0.00023376 | 0.0 | 0.01 -Modify | 0.00017018 | 0.00017018 | 0.00017018 | 0.0 | 0.01 -Other | | 0.0003112 | | | 0.01 +Comm | 0.00038894 | 0.00038894 | 0.00038894 | 0.0 | 0.02 +Output | 0.00020551 | 0.00020551 | 0.00020551 | 0.0 | 0.01 +Modify | 0.00016188 | 0.00016188 | 0.00016188 | 0.0 | 0.01 +Other | | 0.0002651 | | | 0.01 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.4 b/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.4 index e6bf640186..899cc74050 100644 --- a/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.4 +++ b/examples/PACKAGES/pod/Ta/log.30Nov22.pod.g++.4 @@ -99,31 +99,31 @@ Neighbor list info ... bin: standard Per MPI rank memory allocation (min/avg/max) = 3.062 | 3.062 | 3.062 Mbytes Step Temp E_pair E_mol TotEng Press - 0 300 -11.841653 0 -11.803178 -15932.81 - 10 296.91627 -11.841257 0 -11.803178 -15691.292 - 20 287.83193 -11.840092 0 -11.803178 -14982.943 - 30 273.2481 -11.838222 0 -11.803177 -13854.289 - 40 253.97579 -11.83575 0 -11.803177 -12377.385 - 50 231.08941 -11.832815 0 -11.803177 -10642.841 - 60 205.86307 -11.829579 0 -11.803177 -8751.3479 - 70 179.69197 -11.826223 0 -11.803177 -6804.808 - 80 154.00241 -11.822928 0 -11.803177 -4898.2688 - 90 130.15527 -11.819869 0 -11.803177 -3113.7145 - 100 109.34992 -11.817201 0 -11.803177 -1516.1852 -Loop time of 0.615992 on 4 procs for 100 steps with 128 atoms + 0 300 -11.841652 0 -11.803177 -15932.736 + 10 296.91627 -11.841257 0 -11.803177 -15691.219 + 20 287.83193 -11.840092 0 -11.803177 -14982.869 + 30 273.2481 -11.838221 0 -11.803177 -13854.215 + 40 253.97579 -11.835749 0 -11.803177 -12377.312 + 50 231.08941 -11.832814 0 -11.803177 -10642.767 + 60 205.86306 -11.829579 0 -11.803177 -8751.2744 + 70 179.69196 -11.826222 0 -11.803177 -6804.7346 + 80 154.0024 -11.822927 0 -11.803177 -4898.1954 + 90 130.15526 -11.819869 0 -11.803176 -3113.6412 + 100 109.34991 -11.8172 0 -11.803176 -1516.1119 +Loop time of 0.593779 on 4 procs for 100 steps with 128 atoms -Performance: 7.013 ns/day, 3.422 hours/ns, 162.340 timesteps/s, 20.779 katom-step/s +Performance: 7.275 ns/day, 3.299 hours/ns, 168.413 timesteps/s, 21.557 katom-step/s 99.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.59266 | 0.5987 | 0.60449 | 0.6 | 97.19 +Pair | 0.57816 | 0.58286 | 0.58797 | 0.5 | 98.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.010733 | 0.016433 | 0.022459 | 3.7 | 2.67 -Output | 0.00020418 | 0.00021619 | 0.00025121 | 0.0 | 0.04 -Modify | 9.9553e-05 | 0.00010738 | 0.0001217 | 0.0 | 0.02 -Other | | 0.000532 | | | 0.09 +Comm | 0.0049949 | 0.010104 | 0.01481 | 3.5 | 1.70 +Output | 0.00018367 | 0.00020879 | 0.00024911 | 0.0 | 0.04 +Modify | 9.0609e-05 | 0.00010382 | 0.00012125 | 0.0 | 0.02 +Other | | 0.0005076 | | | 0.09 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 diff --git a/src/ML-POD/fitpod_command.cpp b/src/ML-POD/fitpod_command.cpp index 028609be44..e9a669092b 100644 --- a/src/ML-POD/fitpod_command.cpp +++ b/src/ML-POD/fitpod_command.cpp @@ -453,20 +453,21 @@ void FitPOD::get_data(datastruct &data, std::vector species) size_t maxname = 9; for (auto fname : data.data_files) maxname = MAX(maxname,fname.size()); maxname -= data.data_path.size()+1; + const std::string sepline(maxname+46, '-'); if (comm->me == 0) - utils::logmesg(lmp, "{:-<{}}\n {:^{}} | number of configurations | number of atoms\n{:=<{}}\n", - "", maxname+46, "data file", maxname, "", maxname+46); + utils::logmesg(lmp, "{}\n {:^{}} | number of configurations | number of atoms\n{}\n", + sepline, "data file", maxname, sepline); int i = 0; for (auto fname : data.data_files) { std::string filename = fname.substr(data.data_path.size()+1); data.filenames.push_back(filename); if (comm->me == 0) utils::logmesg(lmp, " {:<{}} | {:>10} | {:>8}\n", - filename, maxname, data.num_config[i], data.num_atom_each_file[i]); + filename, maxname, data.num_config[i], data.num_atom_each_file[i]); ++i; } if (comm->me == 0) { - utils::logmesg(lmp, "{:-<{}}\n", "", maxname+46); + utils::logmesg(lmp, "{}\n", sepline); utils::logmesg(lmp, "number of files: {}\n", data.data_files.size()); utils::logmesg(lmp, "number of configurations in all files: {}\n", data.num_config_sum); utils::logmesg(lmp, "number of atoms in all files: {}\n", data.num_atom_sum); @@ -1316,54 +1317,46 @@ double FitPOD::energyforce_calculation(double *force, double *coeff, datastruct void FitPOD::print_analysis(datastruct data, double *outarray, double *errors) { - std::string s = "All files"; int nfiles = data.data_files.size(); // number of files - int lm = s.size(); + int lm = 10; for (int i = 0; i < nfiles; i++) lm = MAX(lm, (int) data.filenames[i].size()); lm = lm + 2; - std::string filename_errors = (data.training ? "training_errors" : "test_errors"); - std::string filename_analysis = (data.training ? "training_analysis" : "test_analysis"); - - filename_errors = podptr->pod.filenametag + "_" + filename_errors + ".pod"; - filename_analysis = podptr->pod.filenametag + "_" + filename_analysis + ".pod"; + std::string filename_errors = fmt::format("{}_{}_errors.pod", podptr->pod.filenametag, data.training ? "training" : "test"); + std::string filename_analysis = fmt::format("{}_{}_analysis.pod", podptr->pod.filenametag, data.training ? "training" : "test"); FILE *fp_errors = nullptr; FILE *fp_analysis = nullptr; fp_errors = fopen(filename_errors.c_str(), "w"); fp_analysis = fopen(filename_analysis.c_str(), "w"); - std::string sa = "**************** Begin of Error Analysis for the Training Data Set ****************"; - std::string sb = "**************** Begin of Error Analysis for the Test Data Set ****************"; - std::string mystr = (data.training) ? sa : sb; + std::string mystr = fmt::format("**************** Begin of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); - utils::logmesg(lmp, "{}\n", mystr); - fmt::print(fp_errors, mystr + "\n"); + utils::logmesg(lmp, mystr); + fmt::print(fp_errors, mystr); - sa = "----------------------------------------------------------------------------------------\n"; - sb = " File | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force |\n"; - - utils::logmesg(lmp, "{}", sa); - utils::logmesg(lmp, "{}", sb); - utils::logmesg(lmp, "{}", sa); - fmt::print(fp_errors, sa); - fmt::print(fp_errors, sb); - fmt::print(fp_errors, sa); + std::string sa(lm+80,'-'); + sa += '\n'; + std::string sb = fmt::format(" {:^{}} | # configs | # atoms | MAE energy | RMSE energy | MAE force | RMSE force\n", + "File", lm); + utils::logmesg(lmp, sa + sb + sa); + fmt::print(fp_errors, sa + sb + sa); int ci=0, m=8, nc=0, nf=0; for (int file = 0; file < nfiles; file++) { fmt::print(fp_analysis, "# {}\n", data.filenames[file]); - sb = "| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error |\n"; - fmt::print(fp_analysis, sb); + fmt::print(fp_analysis, " config # atoms energy DFT energy energy error " + " force DFT force force error\n"); int nforceall = 0; int nconfigs = data.num_config[file]; nc += nconfigs; for (int ii=0; ii < nconfigs; ii++) { // loop over each configuration in a file - fmt::print(fp_analysis, " "); - for(int count = 0; count < m; count ++) - fmt::print(fp_analysis, "{} ", outarray[count + m*ci]); + fmt::print(fp_analysis, "{:6} {:8} ", outarray[m*ci], outarray[1 + m*ci]); + for(int count = 2; count < m; count ++) + fmt::print(fp_analysis, "{:<15.10} ", outarray[count + m*ci]); fmt::print(fp_analysis, "\n"); nforceall += 3*data.num_atom[ci]; @@ -1372,63 +1365,25 @@ void FitPOD::print_analysis(datastruct data, double *outarray, double *errors) nf += nforceall; int q = file+1; - std::string s = data.filenames[file]; - s = s + std::string(lm-s.size(), ' '); - std::string s1 = std::to_string(nconfigs); - s1 = s1 + std::string(MAX(6- (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(nforceall/3); - s1 = s1 + std::string(MAX(7 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[0 + 4*q]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[1 + 4*q]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[2 + 4*q]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[3 + 4*q]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1 + "\n"; - utils::logmesg(lmp, "{}", s); - fmt::print(fp_errors, "{}", s); + auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + data.filenames[file], lm, nconfigs, nforceall/3, + errors[0 + 4*q], errors[1 + 4*q], errors[2 + 4*q], errors[3 + 4*q]); + utils::logmesg(lmp, s); + fmt::print(fp_errors, s); } + utils::logmesg(lmp, sa); + fmt::print(fp_errors, sa); - utils::logmesg(lmp, "{}", sa); - fmt::print(fp_errors, "{}", sa); + auto s = fmt::format("{:<{}} {:>10} {:>11} {:<10.6f} {:<10.6f} {:<10.6f} {:<10.6f}\n", + "All files", lm, nc, nf/3, errors[0], errors[1], errors[2], errors[3]); + utils::logmesg(lmp, s + sa); + fmt::print(fp_errors, "{}", s + sa); - s = s + std::string(MAX(lm - (int) s.size(),1), ' '); - std::string s1 = std::to_string(nc); - s1 = s1 + std::string(MAX(6- (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(nf/3); - s1 = s1 + std::string(MAX(7 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[0]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[1]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[2]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1; - s1 = std::to_string(errors[3]); - s1 = s1 + std::string(MAX(10 - (int) s1.size(),1), ' '); - s = s + " " + s1 + "\n"; - utils::logmesg(lmp, "{}", s); - utils::logmesg(lmp, "{}", sa); - fmt::print(fp_errors, "{}", s); - fmt::print(fp_errors, "{}", sa); + mystr = fmt::format("**************** End of Error Analysis for the {} Data Set ****************\n", + data.training ? "Training" : "Test"); - sa = "**************** End of Error Analysis for the Training Data Set ****************"; - sb = "**************** End of Error Analysis for the Test Data Set ****************"; - mystr = (data.training) ? sa : sb; - - utils::logmesg(lmp, "{}\n", mystr); - fmt::print(fp_errors, "{}\n", mystr); + utils::logmesg(lmp, mystr); + fmt::print(fp_errors, mystr); fclose(fp_errors); fclose(fp_analysis); diff --git a/src/ML-POD/pair_pod.cpp b/src/ML-POD/pair_pod.cpp index 19a16c06a4..aaf8f730a4 100644 --- a/src/ML-POD/pair_pod.cpp +++ b/src/ML-POD/pair_pod.cpp @@ -78,7 +78,7 @@ PairPOD::~PairPOD() void PairPOD::compute(int eflag, int vflag) { - ev_init(eflag,vflag); + ev_init(eflag, vflag); // we must enforce using F dot r, since we have no energy or stress tally calls. vflag_fdotr = 1; @@ -86,7 +86,7 @@ void PairPOD::compute(int eflag, int vflag) if (peratom_warn && (vflag_atom || eflag_atom)) { peratom_warn = false; if (comm->me == 0) - error->warning(FLERR, "Pair style mlpod does not support per-atom energies or stresses"); + error->warning(FLERR, "Pair style pod does not support per-atom energies or stresses"); } double **x = atom->x; @@ -122,8 +122,8 @@ void PairPOD::compute(int eflag, int vflag) // compute global POD descriptors for atom i - podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nd1234], numneighsum, - typeai, idxi, ti, tj, 1, nij); + podptr->linear_descriptors_ij(gd, tmpmem, rij, &tmpmem[nd1234], numneighsum, typeai, idxi, ti, + tj, 1, nij); } int nd22 = podptr->pod.nd22; @@ -135,11 +135,11 @@ void PairPOD::compute(int eflag, int vflag) int nd = podptr->pod.nd; bigint natom = atom->natoms; - for (int j=nd1234; j<(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); j++) - newpodcoeff[j] = podcoeff[j]/(natom); + for (int j = nd1234; j < (nd1234 + nd22 + nd23 + nd24 + nd33 + nd34 + nd44); j++) + newpodcoeff[j] = podcoeff[j] / (natom); - for (int j=(nd1234+nd22+nd23+nd24+nd33+nd34+nd44); jcalculate_energy(energycoeff, forcecoeff, gd, gdall, newpodcoeff); @@ -153,12 +153,11 @@ void PairPOD::compute(int eflag, int vflag) // compute atomic force for atom i - podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum, - typeai, idxi, ai, aj, ti, tj, 1, nij); + podptr->calculate_force(f, forcecoeff, rij, tmpmem, numneighsum, typeai, idxi, ai, aj, ti, tj, + 1, nij); } if (vflag_fdotr) virial_fdotr_compute(); - } /* ---------------------------------------------------------------------- @@ -167,7 +166,7 @@ void PairPOD::compute(int eflag, int vflag) void PairPOD::settings(int narg, char ** /* arg */) { - if (narg > 0) error->all(FLERR,"Pair style mlpod accepts no arguments"); + if (narg > 0) error->all(FLERR, "Pair style pod accepts no arguments"); } /* ---------------------------------------------------------------------- @@ -176,21 +175,20 @@ void PairPOD::settings(int narg, char ** /* arg */) void PairPOD::coeff(int narg, char **arg) { - int n = atom->ntypes; + const int np1 = atom->ntypes + 1; memory->destroy(setflag); memory->destroy(cutsq); - memory->create(setflag,n+1,n+1,"pair:setflag"); - memory->create(cutsq,n+1,n+1,"pair:cutsq"); + memory->create(setflag, np1, np1, "pair:setflag"); + memory->create(cutsq, np1, np1, "pair:cutsq"); delete[] map; - map = new int[n+1]; + map = new int[np1]; allocated = 1; - if (narg != 4 + atom->ntypes) error->all(FLERR,"Incorrect args for pair coefficients"); + if (narg < 4) utils::missing_cmd_args(FLERR, "pair_coeff", error); + map_element2type(narg - 4, arg + 4); - map_element2type(narg-4,arg+4); - - std::string pod_file = std::string(arg[2]); // pod input file - std::string coeff_file = std::string(arg[3]); // coefficient input file + std::string pod_file = std::string(arg[2]); // pod input file + std::string coeff_file = std::string(arg[3]); // coefficient input file delete podptr; podptr = new MLPOD(lmp, pod_file, coeff_file); @@ -212,9 +210,8 @@ void PairPOD::coeff(int narg, char **arg) podptr->podArrayCopy(newpodcoeff, podptr->pod.coeff, podptr->pod.nd); } - for (int ii = 0; ii < n+1; ii++) - for (int jj = 0; jj < n+1; jj++) - cutsq[ii][jj] = podptr->pod.rcut*podptr->pod.rcut; + for (int ii = 0; ii < np1; ii++) + for (int jj = 0; jj < np1; jj++) cutsq[ii][jj] = podptr->pod.rcut * podptr->pod.rcut; } /* ---------------------------------------------------------------------- @@ -223,7 +220,7 @@ void PairPOD::coeff(int narg, char **arg) void PairPOD::init_style() { - if (force->newton_pair == 0) error->all(FLERR,"Pair style mlpod requires newton pair on"); + if (force->newton_pair == 0) error->all(FLERR, "Pair style pod requires newton pair on"); // need a full neighbor list @@ -239,7 +236,7 @@ void PairPOD::init_style() double PairPOD::init_one(int i, int j) { - if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); + if (setflag[i][j] == 0) error->all(FLERR, "All pair coeffs are not set"); return podptr->pod.rcut; } @@ -268,13 +265,13 @@ void PairPOD::free_tempmemory() void PairPOD::allocate_tempmemory() { - memory->create(rij, dim*nijmax, "pair:rij"); + memory->create(rij, dim * nijmax, "pair:rij"); memory->create(idxi, nijmax, "pair:idxi"); memory->create(ai, nijmax, "pair:ai"); memory->create(aj, nijmax, "pair:aj"); memory->create(ti, nijmax, "pair:ti"); memory->create(tj, nijmax, "pair:tj"); - memory->create(numneighsum, nablockmax+1, "pair:numneighsum"); + memory->create(numneighsum, nablockmax + 1, "pair:numneighsum"); memory->create(typeai, nablockmax, "pair:typeai"); memory->create(tmpmem, szd, "pair:tmpmem"); } @@ -287,43 +284,48 @@ void PairPOD::estimate_tempmemory() int ns2 = podptr->pod.ns2; int ns3 = podptr->pod.ns3; - szd = dim*nijmax+ (1+dim)*nijmax*MAX(nrbf2+ns2,nrbf3+ns3) + (nabf3+1)*7; + szd = dim * nijmax + (1 + dim) * nijmax * MAX(nrbf2 + ns2, nrbf3 + ns3) + (nabf3 + 1) * 7; int szsnap = 0; - if (podptr->sna.twojmax>0) { - szsnap += nijmax*dim; - szsnap += MAX(2*podptr->sna.idxu_max*nijmax, 2*podptr->sna.idxz_max*podptr->sna.ndoubles*nablockmax); // (Ur, Ui) and (Zr, Zi) - szsnap += 2*podptr->sna.idxu_max*dim*nijmax; // dUr, dUi - szsnap += MAX(podptr->sna.idxb_max*podptr->sna.ntriples*dim*nijmax, 2*podptr->sna.idxu_max*podptr->sna.nelements*nablockmax); // dblist and (Utotr, Utoti) + if (podptr->sna.twojmax > 0) { + szsnap += nijmax * dim; + szsnap += MAX(2 * podptr->sna.idxu_max * nijmax, + 2 * podptr->sna.idxz_max * podptr->sna.ndoubles * + nablockmax); // (Ur, Ui) and (Zr, Zi) + szsnap += 2 * podptr->sna.idxu_max * dim * nijmax; // dUr, dUi + szsnap += MAX(podptr->sna.idxb_max * podptr->sna.ntriples * dim * nijmax, + 2 * podptr->sna.idxu_max * podptr->sna.nelements * + nablockmax); // dblist and (Utotr, Utoti) } szd = MAX(szsnap, szd); - szd = nablockmax*(podptr->pod.nd1234) + szd; + szd = nablockmax * (podptr->pod.nd1234) + szd; } -void PairPOD::lammpsNeighPairs(double **x, int **firstneigh, int *atomtypes, int *map, int *numneigh, int gi) +void PairPOD::lammpsNeighPairs(double **x, int **firstneigh, int *atomtypes, int *map, + int *numneigh, int gi) { - double rcutsq = podptr->pod.rcut*podptr->pod.rcut; + double rcutsq = podptr->pod.rcut * podptr->pod.rcut; nij = 0; - int itype = map[atomtypes[gi]]+1; + int itype = map[atomtypes[gi]] + 1; int m = numneigh[gi]; typeai[0] = itype; - for (int l=0; l 1e-20) { - rij[nij*3 + 0] = delx; - rij[nij*3 + 1] = dely; - rij[nij*3 + 2] = delz; - idxi[nij] = 0; - ai[nij] = gi; - aj[nij] = gj; - ti[nij] = itype; - tj[nij] = map[atomtypes[gj]]+1; + rij[nij * 3 + 0] = delx; + rij[nij * 3 + 1] = dely; + rij[nij * 3 + 2] = delz; + idxi[nij] = 0; + ai[nij] = gi; + aj[nij] = gj; + ti[nij] = itype; + tj[nij] = map[atomtypes[gj]] + 1; nij++; } }