diff --git a/examples/mlpod/README.md b/examples/PACKAGES/pod/README.md similarity index 71% rename from examples/mlpod/README.md rename to examples/PACKAGES/pod/README.md index 70c129ed51..2c6db69200 100644 --- a/examples/mlpod/README.md +++ b/examples/PACKAGES/pod/README.md @@ -10,11 +10,11 @@ Go to `lammps` directory and build with the POD package: ### Fit a POD potential for tantalum -Go to `lammps/examples/pod/Ta` directory and run +Go to `lammps/examples/PACKAGES/pod/Ta` directory and run lmp -in in.podfit -See the README in `lammps/examples/pod/Ta` for instructions on how to run MD with the potential. +See the README in `lammps/examples/PACKAGES/pod/Ta` for instructions on how to run MD with the potential. ### Examples for other materials diff --git a/examples/mlpod/Ta/README.md b/examples/PACKAGES/pod/Ta/README.md similarity index 94% rename from examples/mlpod/Ta/README.md rename to examples/PACKAGES/pod/Ta/README.md index fd0ebd698a..b8074f50c9 100644 --- a/examples/mlpod/Ta/README.md +++ b/examples/PACKAGES/pod/Ta/README.md @@ -9,7 +9,7 @@ Fit POD with This creates `coefficients.txt` for the linear model, which we can use to run MD with - lmp -in in.mlpod + lmp -in in.pod diff --git a/examples/PACKAGES/pod/Ta/Ta_coeff.pod b/examples/PACKAGES/pod/Ta/Ta_coeff.pod new file mode 100644 index 0000000000..a71aeebfaf --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_coeff.pod @@ -0,0 +1,33 @@ +POD_coefficients: 32 +-4.443926077098761418 +4.2507783817509592339 +-2.3176356302127896214 +-3.9221278398684784605 +0.83911958461214997129 +-0.79841449734252079029 +0.26378941721655152497 +-21.611634136626200586 +-15.666044232814460457 +-39.29944326792482201 +8.1344792452082685941 +-42.618960929128391513 +2.8389668623167838568 +3.7860858047706988927 +5.3302522869881912015 +0.068458969304951933221 +2.9641410087664388229 +0.093199096723738703019 +-0.18687412923621199434 +-0.24053991546811676061 +-0.16710193675730081186 +0.53880267211977672659 +0.022340165031980874916 +-0.0016838394567211768457 +0.024818837996861804751 +-0.005125945253867680157 +0.076934015079245715585 +-0.058872357353699972249 +-0.055300488883823724351 +-0.12649098515466200565 +0.11729161170526267166 +0.0026962161198949207916 diff --git a/examples/PACKAGES/pod/Ta/Ta_param.pod b/examples/PACKAGES/pod/Ta/Ta_param.pod new file mode 100644 index 0000000000..741050251d --- /dev/null +++ b/examples/PACKAGES/pod/Ta/Ta_param.pod @@ -0,0 +1,32 @@ +# DATE: 2022-11-28 UNITS: metal CONTRIBUTOR: Ngoc Cuong Nguyen, exapde@gmail.com CITATION: https://arxiv.org/abs/2209.02362 +# chemical element symbols +species Ta + +# periodic boundary conditions +pbc 1 1 1 + +# inner cut-off radius +rin 1.0 + +# outer cut-off radius +rcut 5.0 + +# polynomial degrees for radial basis functions +bessel_polynomial_degree 3 +inverse_polynomial_degree 6 + +# one-body potential +onebody 1 + +# two-body linear POD potential +twobody_number_radial_basis_functions 6 + +# three-body linear POD potential +threebody_number_radial_basis_functions 5 +threebody_number_angular_basis_functions 5 + +# four-body linear SNAP potential +fourbody_snap_twojmax 0 + +# quadratic POD potential +quadratic_pod_potential 0 diff --git a/examples/mlpod/Ta/XYZ/Displaced_A15.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Displaced_A15.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Displaced_A15.xyz diff --git a/examples/mlpod/Ta/XYZ/Displaced_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Displaced_BCC.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Displaced_BCC.xyz diff --git a/examples/mlpod/Ta/XYZ/Displaced_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Displaced_FCC.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Displaced_FCC.xyz diff --git a/examples/mlpod/Ta/XYZ/Elastic_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Elastic_BCC.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Elastic_BCC.xyz diff --git a/examples/mlpod/Ta/XYZ/Elastic_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Elastic_FCC.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Elastic_FCC.xyz diff --git a/examples/mlpod/Ta/XYZ/GSF_110.xyz b/examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/GSF_110.xyz rename to examples/PACKAGES/pod/Ta/XYZ/GSF_110.xyz diff --git a/examples/mlpod/Ta/XYZ/GSF_112.xyz b/examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/GSF_112.xyz rename to examples/PACKAGES/pod/Ta/XYZ/GSF_112.xyz diff --git a/examples/mlpod/Ta/XYZ/Liquid.xyz b/examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Liquid.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Liquid.xyz diff --git a/examples/mlpod/Ta/XYZ/Surface.xyz b/examples/PACKAGES/pod/Ta/XYZ/Surface.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Surface.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Surface.xyz diff --git a/examples/mlpod/Ta/XYZ/Volume_A15.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Volume_A15.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Volume_A15.xyz diff --git a/examples/mlpod/Ta/XYZ/Volume_BCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Volume_BCC.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Volume_BCC.xyz diff --git a/examples/mlpod/Ta/XYZ/Volume_FCC.xyz b/examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz similarity index 100% rename from examples/mlpod/Ta/XYZ/Volume_FCC.xyz rename to examples/PACKAGES/pod/Ta/XYZ/Volume_FCC.xyz diff --git a/examples/PACKAGES/pod/Ta/coefficients.txt b/examples/PACKAGES/pod/Ta/coefficients.txt new file mode 100644 index 0000000000..eda41be076 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/coefficients.txt @@ -0,0 +1,33 @@ +POD_coefficients: 32 +-4.4439260834102629616 +4.2507763567856020614 +-2.317636342785090342 +-3.9221278262192456054 +0.83911954670339206075 +-0.79841441570191451493 +0.26378938970293897004 +-21.611635277298233859 +-15.666049364763575014 +-39.299445406813141801 +8.1344752166107472391 +-42.618961366919663192 +2.83896703294615671 +3.7860864488519161419 +5.3302526403343213346 +0.068459467263306622575 +2.9641410566557153672 +0.09319910027211224246 +-0.18687411753164512307 +-0.24053992106031887865 +-0.16710194082955912021 +0.53880267803306791663 +0.022340163868396822888 +-0.0016838382503112482927 +0.024818836492565846119 +-0.0051259416351821613864 +0.076934014636969999534 +-0.058872357370635036711 +-0.055300491475458644908 +-0.12649098472524886172 +0.11729160850571981878 +0.0026962159226454835217 diff --git a/examples/mlpod/Ta/data.txt b/examples/PACKAGES/pod/Ta/data.txt similarity index 100% rename from examples/mlpod/Ta/data.txt rename to examples/PACKAGES/pod/Ta/data.txt diff --git a/examples/mlpod/Ta/in.fitpod b/examples/PACKAGES/pod/Ta/in.fitpod similarity index 100% rename from examples/mlpod/Ta/in.fitpod rename to examples/PACKAGES/pod/Ta/in.fitpod diff --git a/examples/mlpod/Ta/in.mlpod b/examples/PACKAGES/pod/Ta/in.pod similarity index 91% rename from examples/mlpod/Ta/in.mlpod rename to examples/PACKAGES/pod/Ta/in.pod index 9b1fc6ba1e..866ee40549 100644 --- a/examples/mlpod/Ta/in.mlpod +++ b/examples/PACKAGES/pod/Ta/in.pod @@ -24,8 +24,8 @@ mass 1 180.88 # POD potential -pair_style mlpod -pair_coeff * * Ta_param.mlpod Ta_coeff.mlpod Ta +pair_style pod +pair_coeff * * Ta_param.pod Ta_coeff.pod Ta # Setup output diff --git a/examples/mlpod/Ta/original/coefficients.txt b/examples/PACKAGES/pod/Ta/original/coefficients.txt similarity index 100% rename from examples/mlpod/Ta/original/coefficients.txt rename to examples/PACKAGES/pod/Ta/original/coefficients.txt diff --git a/examples/mlpod/Ta/original/data.txt b/examples/PACKAGES/pod/Ta/original/data.txt similarity index 100% rename from examples/mlpod/Ta/original/data.txt rename to examples/PACKAGES/pod/Ta/original/data.txt diff --git a/examples/mlpod/Ta/original/pod.txt b/examples/PACKAGES/pod/Ta/original/pod.txt similarity index 100% rename from examples/mlpod/Ta/original/pod.txt rename to examples/PACKAGES/pod/Ta/original/pod.txt diff --git a/examples/mlpod/Ta/original/test_analysis.txt b/examples/PACKAGES/pod/Ta/original/test_analysis.txt similarity index 100% rename from examples/mlpod/Ta/original/test_analysis.txt rename to examples/PACKAGES/pod/Ta/original/test_analysis.txt diff --git a/examples/mlpod/Ta/original/test_errors.txt b/examples/PACKAGES/pod/Ta/original/test_errors.txt similarity index 100% rename from examples/mlpod/Ta/original/test_errors.txt rename to examples/PACKAGES/pod/Ta/original/test_errors.txt diff --git a/examples/mlpod/Ta/original/training_analysis.txt b/examples/PACKAGES/pod/Ta/original/training_analysis.txt similarity index 100% rename from examples/mlpod/Ta/original/training_analysis.txt rename to examples/PACKAGES/pod/Ta/original/training_analysis.txt diff --git a/examples/mlpod/Ta/original/training_errors.txt b/examples/PACKAGES/pod/Ta/original/training_errors.txt similarity index 100% rename from examples/mlpod/Ta/original/training_errors.txt rename to examples/PACKAGES/pod/Ta/original/training_errors.txt diff --git a/examples/mlpod/Ta/pod.txt b/examples/PACKAGES/pod/Ta/pod.txt similarity index 100% rename from examples/mlpod/Ta/pod.txt rename to examples/PACKAGES/pod/Ta/pod.txt diff --git a/examples/PACKAGES/pod/Ta/training_analysis b/examples/PACKAGES/pod/Ta/training_analysis new file mode 100644 index 0000000000..fec1752e36 --- /dev/null +++ b/examples/PACKAGES/pod/Ta/training_analysis @@ -0,0 +1,387 @@ +# Displaced_A15.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 1 64 -753.4390371641038 -754.220443 0.012209466185879592 7.735924628126515 8.398670476926332 0.11471486403630858 + 2 64 -752.9893805690325 -753.865255 0.013685537983867846 8.849199822743731 9.134430544814492 0.1287092082190108 + 3 64 -753.3208522149914 -754.0221 0.010956996640759442 8.322448690370658 9.01726110188127 0.1154364646232066 + 4 64 -753.5955479674111 -754.279613 0.010688516134202075 7.7086313803157775 8.381725091649153 0.1057752415148796 + 5 64 -753.0525448338192 -753.777209 0.011322877596574799 8.902153463465423 9.478314476700007 0.11903245070754352 + 6 64 -753.3492630869637 -754.048643 0.010927811141192123 7.81023310317775 8.465317937559755 0.11274191058311141 + 7 64 -753.6490826073998 -754.317603 0.010445631134377464 7.444807443112883 8.127690490502268 0.10226834361187016 + 8 64 -753.3275351288926 -753.969161 0.010025404236053248 8.529201152499782 9.425464951766411 0.10637302865372293 + 9 64 -753.3951654622119 -754.141988 0.011669102152938038 8.16991800707869 8.821346913268911 0.11395803476723405 +# Displaced_BCC.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 10 54 -631.7256313896924 -631.019667 0.013073414623931967 15.431379796091193 16.625876002911852 0.264444097524148 + 11 54 -632.2717820636577 -631.719595 0.01022568636403144 14.520227684358721 15.58666626272206 0.22342919931789004 + 12 54 -631.9433981907679 -631.386255 0.010317466495701377 15.214742453159198 15.923788831679882 0.225965745861654 + 13 54 -633.0715326903247 -632.575826 0.00917975352453166 13.38722266334797 14.55977161807516 0.20468605551170418 + 14 54 -630.8934956889983 -630.450212 0.008208957203673132 16.552089448683777 16.963407263806737 0.23634113047281868 + 15 54 -632.0720277940635 -631.669379 0.007456459149323193 15.243544791874637 16.057573148572235 0.22775532002383259 + 16 54 -632.8026455141238 -632.431277 0.006877194705996064 14.211466448872589 14.698107183802986 0.20251384172737405 + 17 54 -631.6802089850705 -630.960068 0.013335944167973022 14.712341577383867 15.9907314848333 0.2281495609720177 + 18 54 -625.0384776341372 -623.378198 0.03074591915068831 23.40214759902482 24.67640432462571 0.34986827372477813 +# Displaced_FCC.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 19 48 -555.9699048113583 -555.899463 0.0014675377366325886 6.076723575154492 6.084617062577644 0.07097225707130976 + 20 48 -555.95137254626 -555.922478 0.0006019697137512973 6.276808111529496 6.297071211051453 0.09304007972961932 + 21 48 -555.8352575474581 -555.800269 0.0007289280720452022 6.149373532323564 6.021098635803518 0.08156835289126887 + 22 48 -556.264633534625 -556.196151 0.0014267194713539766 5.061971944049108 5.127955094071613 0.08671676413684176 + 23 48 -555.628053366446 -555.488929 0.0028984243009588795 6.8426911471013785 7.050223458554702 0.08140862085007508 + 24 48 -556.1096232721641 -556.027926 0.0017020265034185893 5.6575861581871125 5.611881174158804 0.07972132791712566 + 25 48 -556.0586145367726 -555.968399 0.0018794903494286548 5.876517223570426 5.9792171885302 0.07481336674978031 + 26 48 -556.0087786390253 -556.047132 0.0007990283536400966 5.749737375760432 5.544452585448 0.08230729218356654 + 27 48 -555.8257619348691 -555.747848 0.001623206976439917 6.3607241579280185 6.478925680043952 0.09531890226105708 +# Elastic_BCC.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 28 2 -23.683550425836106 -23.689367 0.002908287081947236 0.0006476690606100506 0.0006222748588847215 7.473203179895114e-06 + 29 2 -23.682831250962032 -23.689888 0.003528374518984023 0.0006432761441038811 0.0006166052221640683 7.12712060611385e-06 + 30 2 -23.682952614081657 -23.689996 0.0035216929591719293 0.0009101925705850688 0.0008810425642385276 1.137157094848765e-05 + 31 2 -23.681098785571074 -23.690957 0.004929107214463713 1.0425659377597921e-06 0 4.1595148982290507e-07 + 32 2 -23.679217057190286 -23.690521 0.005651971404857292 0.0006251577904923301 0.0005982273815197694 7.343256880007552e-06 + 33 2 -23.67787458349784 -23.69038 0.0062527082510808185 0.0006209549820895662 0.0005925723584508478 7.867520408564206e-06 + 34 2 -23.68417045886337 -23.689202 0.002515770568315645 0.0006510533157843921 0.000627936302502093 6.902839417182741e-06 + 35 2 -23.681714227242995 -23.690482 0.0043838863785019555 0.0009007679020409553 0.0008640138887772579 1.2830085833770798e-05 + 36 2 -23.683028429485855 -23.689902 0.003436785257072472 0.0006422803142679817 0.0006152154094299004 8.366793181509982e-06 + 37 2 -23.68065708872868 -23.690563 0.004952955635660672 0.0006308861593817567 0.0006038725030997851 7.23370030159855e-06 + 38 2 -23.683393925971956 -23.690207 0.0034065370140226037 0.0011163849232465456 0.001073697350280795 1.7428869498402365e-05 + 39 2 -23.683710082538187 -23.689285 0.002787458730907133 0.0009201854886151864 0.0008900134830439369 1.0813705331575841e-05 + 40 2 -23.68346034111359 -23.689768 0.0031538294432049696 0.001118468982097365 0.0010802490453594485 1.5612631100747896e-05 + 41 2 -23.682260284239348 -23.68968 0.003709857880325629 0.0009056805345809504 0.0008680034562143172 1.294225924427312e-05 + 42 2 -23.68261525336224 -23.690074 0.0037293733188796807 0.0014343132365964954 0.001373818765339883 2.3643105012748138e-05 + 43 2 -23.68471120332157 -23.688108 0.0016983983392151458 0.0006578004816139588 0.0006336134468270066 7.71052550758202e-06 + 44 2 -23.684069319442983 -23.689241 0.002585840278507945 0.0009210090572386523 0.0008880101350772974 1.1437393762551845e-05 + 45 2 -23.683864034265167 -23.68952 0.002827982867417589 0.0009167488450816642 0.0008860011286674525 1.0705798453266074e-05 + 46 2 -23.68526333138765 -23.686278 0.0005073343061763325 0.0006658873018335455 0.0006406777661195993 8.368566979711719e-06 + 47 2 -23.6763131724025 -23.690097 0.006891913798749982 0.0008723081558420834 0.0008410160521654744 1.0770084140311397e-05 + 48 2 -23.678370717741178 -23.690811 0.006220141129411161 0.0008799687146539332 0.0008500070587942196 1.0563637012251327e-05 + 49 2 -23.679834898514077 -23.690266 0.005215550742962094 0.001090220434605017 0.0010443227470470994 1.8746536921041234e-05 + 50 2 -23.68211557129986 -23.690597 0.004240714350070007 0.0011040891263559836 0.0010508330029076933 2.174236530787448e-05 + 51 2 -23.680523087877464 -23.690673 0.0050749560612679545 0.0006301839849079828 0.0006038907185907066 7.6298354322976e-06 + 52 2 -23.681873678503973 -23.690551 0.004338660748013368 0.0009009015586228429 0.0008590064027700842 1.4407738831429123e-05 + 53 2 -23.68193367047911 -23.690693 0.004379664760444157 0.0008999859775073009 0.00085901105930017 1.4706470693579161e-05 + 54 2 -23.68099077081365 -23.69021 0.004609614593174882 0.0008986014400446616 0.0008730051546239576 9.195532781796746e-06 + 55 2 -23.684282362233557 -23.688943 0.002330318883220883 0.0009218654036557117 0.0008800306812833288 1.5750862008591304e-05 + 56 2 -23.67844250067243 -23.690136 0.005846749663785289 0.0006229280902512651 0.0005939966329870902 8.165007953361056e-06 + 57 2 -23.684959166079047 -23.687444 0.0012424169604763335 0.0009334481732756087 0.0009030592450110901 1.2459662318150843e-05 + 58 2 -23.683650087845457 -23.689801 0.0030754560772709993 0.0009146886884842877 0.0008740011441640107 1.3790680750806896e-05 + 59 2 -23.681502954637324 -23.690408 0.0044525226813387775 8.676768027222693e-07 0 3.2406803636593484e-07 + 60 2 -23.681176989612123 -23.690362 0.004592505193938834 0.0006335685070475168 0.0006067503605272931 9.151647656011216e-06 + 61 2 -23.672313219526025 -23.688881 0.008283890236986835 0.0008552029645733772 0.000825005454527423 1.060295873976674e-05 + 62 2 -23.67915431835819 -23.690515 0.005680340820905627 0.0015324336905243176 0.0014757797938717012 2.0299663159082363e-05 + 63 2 -23.67788652758939 -23.690551 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0.0037469996759789126 0.0011105542746956958 0.0010843154522554772 1.0715208168731122e-05 + 72 2 -23.678725752626544 -23.690617 0.005945623686727686 0.0006240186413478946 0.000602468256425183 6.387201431443005e-06 + 73 2 -23.682334352336046 -23.689761 0.003713323831977533 0.0009081453932018793 0.0008790688255193674 1.176612909262191e-05 + 74 2 -23.67675240145185 -23.69027 0.006758799274075855 7.17691402286202e-07 0 2.1257441413519382e-07 + 75 2 -23.68166576351393 -23.690599 0.004466618243034404 0.0006366113391463507 0.0006137752031485143 6.341504138067615e-06 + 76 2 -23.679997159054324 -23.69061 0.005306420472837914 9.68297627904574e-07 0 3.9524897970133417e-07 + 77 2 -23.680105354455197 -23.690603 0.00524882277240124 0.0008909316210346347 0.0008590331774733733 1.2098383000759847e-05 + 78 2 -23.684906304074044 -23.687908 0.0015008479629781135 0.0009326791341411301 0.0009010105437784844 1.1591749518708354e-05 + 79 2 -23.67952847050153 -23.690688 0.005579764749235494 0.0008876851852543994 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0.001482734356294202 0.0007527977994234758 0.0017595738120351758 0.00023929190342972197 + 222 4 -46.45492583800971 -46.440329 0.0036492095024271975 0.0005005573414804818 0.0009534044262536227 0.0001069299129887533 + 223 4 -46.44997363418494 -46.43773 0.003060908546235197 0.0006817503197839165 0.0009261803280139349 7.406594239153779e-05 + 224 4 -46.42531398596522 -46.416525 0.002197246491304483 0.0005574123984829012 0.0007573664898845208 5.999084188670149e-05 + 225 4 -46.45383418835599 -46.440293 0.0033852970889984846 0.0006952778579969145 0.0007725386721711737 1.8967912200650827e-05 + 226 4 -46.45276775293753 -46.43839 0.0035944382343835457 0.0005074067278331188 0.0005612022808221648 1.7048501220182102e-05 + 227 4 -46.45371472608478 -46.438916 0.003699681521196041 0.0006927906710794425 0.0016508785539826967 0.00021608412407982916 +# GSF_110.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 228 24 -278.739448261058 -279.068761 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245 24 -279.9061139309274 -279.79264 0.004728080455308259 0.8363547188863095 0.8392614851641887 0.02424521197795241 + 246 24 -279.99300016527536 -279.896025 0.004040631886473041 0.2807267786231102 0.010602432928342438 0.011261323513793981 + 247 24 -278.89696993514394 -279.206496 0.01289691936900302 1.3891331839743348 0.005326518562813801 0.06646589334290492 + 248 24 -279.589073028376 -279.55564 0.0013930428490003994 1.9510569002456686 1.4056318995939159 0.05372827873849301 + 249 24 -279.90612473550664 -279.79264 0.004728530646109637 0.8363685632634088 0.8392625707893806 0.02424752361721317 +# GSF_112.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 250 30 -345.1450219557288 -345.175835 0.0010271014757070893 2.7173194971821832 1.0573953217004513 0.13920385992256804 + 251 30 -346.8222185522381 -346.361714 0.01535015174126973 1.6322373485613355 1.2202849393785045 0.10106307991224969 + 252 30 -346.3071027507994 -345.795524 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2.2946054778483216e-15 +# Volume_BCC.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 312 2 -16.389215240182413 -16.763625 0.1872048799087942 7.391794945902238e-16 0 2.706168622523819e-16 + 313 2 16.196246482301632 16.314145 0.058949258849184005 4.580372603963489e-14 0 1.5491658881631547e-14 + 314 2 -21.24230444992619 -21.209071 0.016616724963094853 2.2948512556897744e-15 0 8.52330318836443e-16 + 315 2 -15.80560305023002 -15.780524 0.012539525115010441 3.168531795878551e-14 0 1.279380247576345e-14 + 316 2 -19.05541566138774 -19.002205 0.0266053306938705 2.1011350207924772e-15 0 7.175881017054773e-16 + 317 2 -22.674158243817757 -22.620568 0.026795121908879338 1.2479403436383202e-15 0 4.706883031483736e-16 + 318 2 4.0424736011404185 4.096885 0.027205699429790897 1.2123190937582117e-14 0 3.6938045215132815e-15 + 319 2 56.210386679176736 56.26276 0.02618666041163209 1.4388716542864147e-13 0 5.070889793679957e-14 + 320 2 -22.558104170422524 -22.585113 0.013504414788737762 4.059911185733466e-15 0 1.5913196686293911e-15 + 321 2 -21.75997641267593 -21.795501 0.0177622936620363 5.389157964038493e-16 0 1.8041124150158794e-16 + 322 2 33.30762745272851 33.110078 0.09877472636425466 2.3260153819853645e-14 0 8.455620463069616e-15 + 323 2 -20.821568983888593 -20.885998 0.032214508055703917 7.560529131576252e-16 0 2.7755575615628914e-16 + 324 2 -23.552386060591104 -23.601336 0.024474969704447957 6.521564423070088e-16 0 1.8823556717969167e-16 + 325 2 -23.171474216911587 -23.207313 0.017919391544205965 7.678731675328524e-16 0 2.70141730972274e-16 + 326 2 -19.781756815797394 -19.898089 0.058166092101302524 7.937712492470014e-15 0 3.2173338067783184e-15 + 327 2 -23.450283635348274 -23.405474 0.022404817674136268 9.609381656298967e-16 0 3.108046227791779e-16 + 328 2 -4.653024676035037 -4.781324 0.06414966198248129 2.550130858007384e-14 0 7.572067972638763e-15 + 329 2 -18.67535879352914 -18.864936 0.09478860323543081 1.1701040968498854e-15 0 4.1402066959979794e-16 + 330 2 -17.534418108765703 -17.813086 0.13933394561714785 2.309724214262959e-16 0 7.632783294297951e-17 + 331 2 -11.048380148762785 -11.197201 0.07441042561860733 6.754757724254938e-15 0 2.288389385392738e-15 + 332 2 -23.684909655838823 -23.696705 0.0058976720805894445 5.667762650383236e-16 0 1.964574336543734e-16 +# Volume_FCC.xyz +| config | # atoms | energy | DFT energy | energy error | force | DFT force | force error | + 333 4 -19.13347922265706 -19.075994 0.014371305664264256 1.2674587096836563e-14 0 2.8909866941056552e-15 + 334 4 -35.26070620807738 -34.873619 0.09677180201934554 1.9356336902258832e-15 0 4.519677456367906e-16 + 335 4 -43.93366453110218 -43.950003 0.0040846172244553 8.860752879714915e-16 0 2.0469737016526324e-16 + 336 4 -41.03690481092868 -40.991909 0.011248952732170636 3.702031330781809e-15 0 8.94647492662622e-16 + 337 4 -43.42242782737713 -43.453929 0.007875293155718666 3.444429536492223e-14 0 9.89272733691168e-15 + 338 4 -42.67380781365308 -42.686077 0.003067296586729995 1.6593612204935944e-15 0 3.524741262750375e-16 + 339 4 -33.58853811608821 -33.224653 0.09097127902205138 1.006462581706231e-15 0 1.9660199394403813e-16 + 340 4 -27.011636580625847 -26.862709 0.03723189515646208 8.171636482432781e-15 0 2.195515713251763e-15 + 341 4 -25.590091468792146 -25.519883 0.0175521171980364 1.0343986046296224e-15 0 2.301399811462564e-16 + 342 4 3.4418818051531552 3.463071 0.00529729871171114 2.1689862976731427e-14 0 5.2615665098136354e-15 + 343 4 -31.907218209141885 -31.59595 0.07781705228547153 7.670224571430037e-16 0 2.1047978175185259e-16 + 344 4 -45.06026254959207 -45.100466 0.010050862601982402 3.743471296378091e-15 0 9.82447663368852e-16 + 345 4 -46.03951744948016 -46.052258 0.003185137629960977 9.068473334874784e-16 0 2.0816681711721685e-16 + 346 4 -30.242968448077995 -30.001189 0.060444862019498835 1.8511417827596784e-16 0 4.2717565595928875e-17 + 347 4 -22.958084049413888 -22.8504 0.026921012353471774 5.968255550949702e-16 0 1.3010426069826053e-16 + 348 4 -9.129806457248064 -9.164691 0.008721135687983939 1.2718201397438407e-14 0 2.896409963722609e-15 + 349 4 -24.217621737913273 -24.150343 0.016819684478318386 1.3280189137908218e-15 0 2.6917125935573455e-16 + 350 4 -46.44757243313936 -46.426795 0.005194358284839495 2.1097432769115157e-15 0 5.608939238991676e-16 + 351 4 -28.620710201064252 -28.451145 0.04239130026606297 3.807935061595118e-15 0 1.0633132106289504e-15 + 352 4 40.315142241538865 40.341566 0.0066059396152837735 2.6988587583064673e-14 0 5.549690272536343e-15 + 353 4 19.512005124380416 19.617912 0.026476718904896224 4.953963129005879e-14 0 1.0630359936215605e-14 + 354 4 -27.063172312141294 -26.954384 0.02719707803532323 4.2746416544463365e-16 0 1.155036714421224e-16 + 355 4 -46.368171636184556 -46.323696 0.011118909046139436 4.462841737237832e-15 0 1.2819606487468604e-15 + 356 4 -45.872801325008396 -45.828947 0.010963581252099175 4.279559650962984e-15 0 1.2200888447703544e-15 + 357 4 -38.471378510755876 -38.16029 0.07777212768896824 1.6121247356992433e-15 0 3.804826823975797e-16 + 358 4 -33.067647342015434 -32.919741 0.03697658550385796 2.974136765539587e-14 0 8.431768015274935e-15 + 359 4 -41.34512954729189 -41.272675 0.018113636822972623 7.15720788941016e-15 0 2.0560132372657303e-15 + 360 4 -39.958286559381506 -39.753322 0.05124113984537715 3.4005674599510193e-15 0 8.738703457725505e-16 + 361 4 -37.66196898540187 -37.547435 0.028633496350467524 4.931756832922592e-15 0 1.3121014691419575e-15 + 362 4 -36.89708070510661 -36.52595 0.09278267627665215 1.3184309266582198e-15 0 2.859402529568437e-16 + 363 4 -45.03333642367108 -45.016087 0.004312355917770461 7.840566313642486e-16 0 1.9110870293677826e-16 diff --git a/examples/mlpod/Ta/training_analysis.txt b/examples/PACKAGES/pod/Ta/training_analysis.txt similarity index 100% rename from examples/mlpod/Ta/training_analysis.txt rename to examples/PACKAGES/pod/Ta/training_analysis.txt diff --git a/examples/mlpod/Ta/training_errors.txt b/examples/PACKAGES/pod/Ta/training_errors.txt similarity index 100% rename from examples/mlpod/Ta/training_errors.txt rename to examples/PACKAGES/pod/Ta/training_errors.txt diff --git a/examples/mlpod/Ta/Ta_coeff.mlpod b/examples/mlpod/Ta/Ta_coeff.mlpod deleted file mode 120000 index 653050ca21..0000000000 --- a/examples/mlpod/Ta/Ta_coeff.mlpod +++ /dev/null @@ -1 +0,0 @@ -../../../potentials/Ta_coeff.mlpod \ No newline at end of file diff --git a/examples/mlpod/Ta/Ta_param.mlpod b/examples/mlpod/Ta/Ta_param.mlpod deleted file mode 120000 index af3ea6209c..0000000000 --- a/examples/mlpod/Ta/Ta_param.mlpod +++ /dev/null @@ -1 +0,0 @@ -../../../potentials/Ta_param.mlpod \ No newline at end of file diff --git a/examples/mlpod/Ta/coefficients.txt b/examples/mlpod/Ta/coefficients.txt deleted file mode 100644 index 303a6e807c..0000000000 --- a/examples/mlpod/Ta/coefficients.txt +++ /dev/null @@ -1,33 +0,0 @@ -POD_coefficients: 32 --4.4439260833421228014 -4.2507792084373585695 --2.3176353569548382438 --3.9221278452116115076 -0.83911958875384196066 --0.79841451681262742834 -0.26378942428791307684 --21.611635060854631263 --15.666044624950137276 --39.299445394623148786 -8.1344794782934322086 --42.618961100966139099 -2.8389669737584424247 -3.7860858346061583291 -5.3302525591736920063 -0.068458943342773789786 -2.9641410187201997495 -0.093199098324852111541 --0.18687411268203737991 --0.24053991843455554966 --0.1671019331798810903 -0.53880267423258776383 -0.02234016517461668086 --0.0016838416898756938377 -0.024818838088270261943 --0.0051259453100856392643 -0.076934015821388271328 --0.058872357394785461426 --0.055300486774410462232 --0.12649098545625736545 -0.11729161280074705542 -0.0026962163660570193091 diff --git a/examples/mlpod/Ta/log.28Nov22.fitpod.g++.1 b/examples/mlpod/Ta/log.28Nov22.fitpod.g++.1 deleted file mode 100644 index 96095d169d..0000000000 --- a/examples/mlpod/Ta/log.28Nov22.fitpod.g++.1 +++ /dev/null @@ -1,111 +0,0 @@ -LAMMPS (3 Nov 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate fitpod for POD potential - -fitpod pod.txt data.txt -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 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 -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 -**************** 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: 223201 -size of int memory: 14709 -size of descriptor matrix: 32 x 32 -**************** End of Memory Allocation **************** -**************** Begin of Least-Squares Fitting **************** -Configuration: # 1 -Configuration: # 101 -Configuration: # 201 -Configuration: # 301 -**************** End of Least-Squares Fitting **************** -**************** 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 0.011326 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/mlpod/Ta/log.28Nov22.fitpod.g++.4 b/examples/mlpod/Ta/log.28Nov22.fitpod.g++.4 deleted file mode 100644 index 8f39e1bc27..0000000000 --- a/examples/mlpod/Ta/log.28Nov22.fitpod.g++.4 +++ /dev/null @@ -1,111 +0,0 @@ -LAMMPS (3 Nov 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate fitpod for POD potential - -fitpod pod.txt data.txt -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 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 -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 -**************** 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: 223201 -size of int memory: 14709 -size of descriptor matrix: 32 x 32 -**************** End of Memory Allocation **************** -**************** Begin of Least-Squares Fitting **************** -Configuration: # 1 -Configuration: # 101 -Configuration: # 201 -Configuration: # 301 -**************** End of Least-Squares Fitting **************** -**************** 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 0.011326 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/mlpod/Ta/log.28Nov22.mlpod.g++.1 b/examples/mlpod/Ta/log.28Nov22.mlpod.g++.1 deleted file mode 100644 index de2d713e1b..0000000000 --- a/examples/mlpod/Ta/log.28Nov22.mlpod.g++.1 +++ /dev/null @@ -1,142 +0,0 @@ -LAMMPS (3 Nov 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate POD Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 1 by 1 MPI processor grid -create_atoms 1 box -Created 128 atoms - using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) - create_atoms CPU = 0.000 seconds - -mass 1 180.88 - - -# POD potential -pair_style mlpod -pair_coeff * * Ta_param.mlpod Ta_coeff.mlpod Ta -Reading potential file Ta_param.mlpod with DATE: 2022-11-28 -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 32 -**************** End of POD Potentials **************** - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 loop geom -fix 1 all nve -run ${nsteps} -run 100 -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair mlpod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - 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 -6804.8081 - 80 154.00241 -11.822928 0 -11.803177 -4898.2689 - 90 130.15527 -11.819869 0 -11.803177 -3113.7146 - 100 109.34992 -11.817201 0 -11.803177 -1516.1852 -Loop time of 1.90012 on 1 procs for 100 steps with 128 atoms - -Performance: 2.274 ns/day, 10.556 hours/ns, 52.628 timesteps/s, 6.736 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 | 1.8996 | 1.8996 | 1.8996 | 0.0 | 99.97 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.00023259 | 0.00023259 | 0.00023259 | 0.0 | 0.01 -Output | 0.00011278 | 0.00011278 | 0.00011278 | 0.0 | 0.01 -Modify | 9.8013e-05 | 9.8013e-05 | 9.8013e-05 | 0.0 | 0.01 -Other | | 0.0001187 | | | 0.01 - -Nlocal: 128 ave 128 max 128 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 727 ave 727 max 727 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 7424 ave 7424 max 7424 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - - -Total wall time: 0:00:01 diff --git a/examples/mlpod/Ta/log.28Nov22.mlpod.g++.4 b/examples/mlpod/Ta/log.28Nov22.mlpod.g++.4 deleted file mode 100644 index c8b161b771..0000000000 --- a/examples/mlpod/Ta/log.28Nov22.mlpod.g++.4 +++ /dev/null @@ -1,142 +0,0 @@ -LAMMPS (3 Nov 2022) - using 1 OpenMP thread(s) per MPI task -# Demonstrate POD Ta potential - -# Initialize simulation - -variable nsteps index 100 -variable nrep equal 4 -variable a equal 3.316 -units metal - -# generate the box and atom positions using a BCC lattice - -variable nx equal ${nrep} -variable nx equal 4 -variable ny equal ${nrep} -variable ny equal 4 -variable nz equal ${nrep} -variable nz equal 4 - -boundary p p p - -lattice bcc $a -lattice bcc 3.316 -Lattice spacing in x,y,z = 3.316 3.316 3.316 -region box block 0 ${nx} 0 ${ny} 0 ${nz} -region box block 0 4 0 ${ny} 0 ${nz} -region box block 0 4 0 4 0 ${nz} -region box block 0 4 0 4 0 4 -create_box 1 box -Created orthogonal box = (0 0 0) to (13.264 13.264 13.264) - 1 by 2 by 2 MPI processor grid -create_atoms 1 box -Created 128 atoms - using lattice units in orthogonal box = (0 0 0) to (13.264 13.264 13.264) - create_atoms CPU = 0.000 seconds - -mass 1 180.88 - - -# POD potential -pair_style mlpod -pair_coeff * * Ta_param.mlpod Ta_coeff.mlpod Ta -Reading potential file Ta_param.mlpod with DATE: 2022-11-28 -**************** Begin of POD Potentials **************** -species: Ta -periodic boundary conditions: 1 1 1 -inner cut-off radius: 1 -outer cut-off radius: 5 -bessel polynomial degree: 3 -inverse polynomial degree: 6 -one-body potential: 1 -two-body potential: 3 6 6 -three-body potential: 3 6 5 5 -four-body SNAP potential: 0 0 -quadratic POD potential: 0 -number of basis functions for one-body potential: 1 -number of basis functions for two-body potential: 6 -number of basis functions for three-body potential: 25 -number of basis functions for four-body potential: 0 -number of descriptors for one-body potential: 1 -number of descriptors for two-body potential: 6 -number of descriptors for three-body potential: 25 -number of descriptors for four-body potential: 0 -number of descriptors for quadratic POD potential: 0 -total number of descriptors for all potentials: 32 -**************** End of POD Potentials **************** - - -# Setup output - -thermo 10 -thermo_modify norm yes - -# Set up NVE run - -timestep 0.5e-3 -neighbor 1.0 bin -neigh_modify once no every 1 delay 0 check yes - -# Run MD - -velocity all create 300.0 4928459 loop geom -fix 1 all nve -run ${nsteps} -run 100 -Neighbor list info ... - update: every = 1 steps, delay = 0 steps, check = yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 6 - ghost atom cutoff = 6 - binsize = 3, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair mlpod, perpetual - attributes: full, newton on - pair build: full/bin/atomonly - stencil: full/bin/3d - 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 -6804.8081 - 80 154.00241 -11.822928 0 -11.803177 -4898.2689 - 90 130.15527 -11.819869 0 -11.803177 -3113.7146 - 100 109.34992 -11.817201 0 -11.803177 -1516.1852 -Loop time of 0.538333 on 4 procs for 100 steps with 128 atoms - -Performance: 8.025 ns/day, 2.991 hours/ns, 185.759 timesteps/s, 23.777 katom-step/s -97.3% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.51048 | 0.51513 | 0.5254 | 0.8 | 95.69 -Neigh | 0 | 0 | 0 | 0.0 | 0.00 -Comm | 0.011716 | 0.021851 | 0.026365 | 4.1 | 4.06 -Output | 0.00014871 | 0.00025903 | 0.00058806 | 0.0 | 0.05 -Modify | 4.9201e-05 | 5.3229e-05 | 5.8062e-05 | 0.0 | 0.01 -Other | | 0.001041 | | | 0.19 - -Nlocal: 32 ave 32 max 32 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Nghost: 431 ave 431 max 431 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -Neighs: 0 ave 0 max 0 min -Histogram: 4 0 0 0 0 0 0 0 0 0 -FullNghs: 1856 ave 1856 max 1856 min -Histogram: 4 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 7424 -Ave neighs/atom = 58 -Neighbor list builds = 0 -Dangerous builds = 0 - - -Total wall time: 0:00:00 diff --git a/src/ML-POD/fitpod_command.cpp b/src/ML-POD/fitpod.cpp similarity index 99% rename from src/ML-POD/fitpod_command.cpp rename to src/ML-POD/fitpod.cpp index ced3ebd18d..a051b05458 100644 --- a/src/ML-POD/fitpod_command.cpp +++ b/src/ML-POD/fitpod.cpp @@ -15,7 +15,7 @@ Contributing authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) ------------------------------------------------------------------------- */ -#include "fitpod_command.h" +#include "fitpod.h" #include "mlpod.h" diff --git a/src/ML-POD/fitpod_command.h b/src/ML-POD/fitpod.h similarity index 98% rename from src/ML-POD/fitpod_command.h rename to src/ML-POD/fitpod.h index 2bac24e85c..9e42fb2bad 100644 --- a/src/ML-POD/fitpod_command.h +++ b/src/ML-POD/fitpod.h @@ -18,8 +18,8 @@ CommandStyle(fitpod,CFITPOD); // clang-format on #else -#ifndef LMP_FITPOD_COMMAND_H -#define LMP_FITPOD_COMMAND_H +#ifndef LMP_FITPOD_H +#define LMP_FITPOD_H #include "command.h" diff --git a/src/ML-POD/pair_mlpod.cpp b/src/ML-POD/pair_pod.cpp similarity index 94% rename from src/ML-POD/pair_mlpod.cpp rename to src/ML-POD/pair_pod.cpp index 76ab627c58..19a16c06a4 100644 --- a/src/ML-POD/pair_mlpod.cpp +++ b/src/ML-POD/pair_pod.cpp @@ -15,7 +15,7 @@ Contributing authors: Ngoc Cuong Nguyen (MIT) and Andrew Rohskopf (SNL) ------------------------------------------------------------------------- */ -#include "pair_mlpod.h" +#include "pair_pod.h" #include "mlpod.h" @@ -36,7 +36,7 @@ using namespace LAMMPS_NS; /* ---------------------------------------------------------------------- */ -PairMLPOD::PairMLPOD(LAMMPS *lmp) : +PairPOD::PairPOD(LAMMPS *lmp) : Pair(lmp), gd(nullptr), gdall(nullptr), podcoeff(nullptr), newpodcoeff(nullptr), energycoeff(nullptr), forcecoeff(nullptr), podptr(nullptr), tmpmem(nullptr), typeai(nullptr), numneighsum(nullptr), rij(nullptr), idxi(nullptr), ai(nullptr), aj(nullptr), ti(nullptr), @@ -58,7 +58,7 @@ PairMLPOD::PairMLPOD(LAMMPS *lmp) : /* ---------------------------------------------------------------------- */ -PairMLPOD::~PairMLPOD() +PairPOD::~PairPOD() { free_tempmemory(); memory->destroy(podcoeff); @@ -76,7 +76,7 @@ PairMLPOD::~PairMLPOD() } } -void PairMLPOD::compute(int eflag, int vflag) +void PairPOD::compute(int eflag, int vflag) { ev_init(eflag,vflag); @@ -165,7 +165,7 @@ void PairMLPOD::compute(int eflag, int vflag) global settings ------------------------------------------------------------------------- */ -void PairMLPOD::settings(int narg, char ** /* arg */) +void PairPOD::settings(int narg, char ** /* arg */) { if (narg > 0) error->all(FLERR,"Pair style mlpod accepts no arguments"); } @@ -174,7 +174,7 @@ void PairMLPOD::settings(int narg, char ** /* arg */) set coeffs for one or more type pairs ------------------------------------------------------------------------- */ -void PairMLPOD::coeff(int narg, char **arg) +void PairPOD::coeff(int narg, char **arg) { int n = atom->ntypes; memory->destroy(setflag); @@ -221,7 +221,7 @@ void PairMLPOD::coeff(int narg, char **arg) init specific to this pair style ------------------------------------------------------------------------- */ -void PairMLPOD::init_style() +void PairPOD::init_style() { if (force->newton_pair == 0) error->all(FLERR,"Pair style mlpod requires newton pair on"); @@ -237,7 +237,7 @@ void PairMLPOD::init_style() init for one type pair i,j and corresponding j,i ------------------------------------------------------------------------- */ -double PairMLPOD::init_one(int i, int j) +double PairPOD::init_one(int i, int j) { if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set"); return podptr->pod.rcut; @@ -247,13 +247,13 @@ double PairMLPOD::init_one(int i, int j) memory usage ------------------------------------------------------------------------- */ -double PairMLPOD::memory_usage() +double PairPOD::memory_usage() { double bytes = Pair::memory_usage(); return bytes; } -void PairMLPOD::free_tempmemory() +void PairPOD::free_tempmemory() { memory->destroy(rij); memory->destroy(idxi); @@ -266,7 +266,7 @@ void PairMLPOD::free_tempmemory() memory->destroy(tmpmem); } -void PairMLPOD::allocate_tempmemory() +void PairPOD::allocate_tempmemory() { memory->create(rij, dim*nijmax, "pair:rij"); memory->create(idxi, nijmax, "pair:idxi"); @@ -279,7 +279,7 @@ void PairMLPOD::allocate_tempmemory() memory->create(tmpmem, szd, "pair:tmpmem"); } -void PairMLPOD::estimate_tempmemory() +void PairPOD::estimate_tempmemory() { int nrbf2 = podptr->pod.nbf2; int nabf3 = podptr->pod.nabf3; @@ -300,7 +300,7 @@ void PairMLPOD::estimate_tempmemory() szd = nablockmax*(podptr->pod.nd1234) + szd; } -void PairMLPOD::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; diff --git a/src/ML-POD/pair_mlpod.h b/src/ML-POD/pair_pod.h similarity index 93% rename from src/ML-POD/pair_mlpod.h rename to src/ML-POD/pair_pod.h index ef1605b1fe..c47ead1496 100644 --- a/src/ML-POD/pair_mlpod.h +++ b/src/ML-POD/pair_pod.h @@ -13,21 +13,21 @@ #ifdef PAIR_CLASS // clang-format off -PairStyle(mlpod,PairMLPOD); +PairStyle(pod,PairPOD); // clang-format on #else -#ifndef LMP_PAIR_MLPOD_H -#define LMP_PAIR_MLPOD_H +#ifndef LMP_PAIR_POD_H +#define LMP_PAIR_POD_H #include "pair.h" namespace LAMMPS_NS { -class PairMLPOD : public Pair { +class PairPOD : public Pair { public: - PairMLPOD(class LAMMPS *); - ~PairMLPOD() override; + PairPOD(class LAMMPS *); + ~PairPOD() override; void compute(int, int) override; void settings(int, char **) override;