Package evaluation of Packmol on Julia 1.13.0-DEV.449 (8d6b63c3a6*) started at 2025-04-29T05:07:05.900 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 6.82s ################################################################################ # Installation # Installing Packmol... Resolving package versions... Installed Packmol ─ v0.1.12 Updating `~/.julia/environments/v1.13/Project.toml` [6cdf86f9] + Packmol v0.1.12 Updating `~/.julia/environments/v1.13/Manifest.toml` [69e1c6dd] + CellListMap v0.9.8 [ae650224] + ChunkSplitters v3.1.2 [34da2185] + Compat v4.16.0 [187b0558] + ConstructionBase v1.5.8 [ffbed154] + DocStringExtensions v0.9.4 [48062228] + FilePathsBase v0.9.24 [692b3bcd] + JLLWrappers v1.7.0 [1914dd2f] + MacroTools v0.5.16 [e1fe445b] + NativeFileDialog v0.2.1 [bac558e1] + OrderedCollections v1.8.0 [6cdf86f9] + Packmol v0.1.12 [d96e819e] + Parameters v0.12.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [bf97046b] + SPGBox v0.7.2 [efcf1570] + Setfield v1.1.2 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [1c621080] + TestItems v1.0.0 [3a884ed6] + UnPack v1.0.2 ⌃ [7b86fcea] + ATK_jll v2.38.0+0 [6e34b625] + Bzip2_jll v1.0.9+0 ⌃ [83423d85] + Cairo_jll v1.18.4+0 [ee1fde0b] + Dbus_jll v1.16.2+0 [2702e6a9] + EpollShim_jll v0.0.20230411+1 [2e619515] + Expat_jll v2.6.5+0 [a3f928ae] + Fontconfig_jll v2.16.0+0 [d7e528f0] + FreeType2_jll v2.13.4+0 [559328eb] + FriBidi_jll v1.0.17+0 [77ec8976] + GTK3_jll v3.24.31+0 [78b55507] + Gettext_jll v0.21.0+0 ⌃ [7746bdde] + Glib_jll v2.82.4+0 [3b182d85] + Graphite2_jll v1.3.15+0 [2e76f6c2] + HarfBuzz_jll v8.5.0+0 [aacddb02] + JpegTurbo_jll v3.1.1+0 [88015f11] + LERC_jll v4.0.1+0 [1d63c593] + LLVMOpenMP_jll v18.1.8+0 [dd4b983a] + LZO_jll v2.10.3+0 [42c93a91] + Libepoxy_jll v1.5.10+0 ⌅ [e9f186c6] + Libffi_jll v3.2.2+2 [7e76a0d4] + Libglvnd_jll v1.7.1+1 [94ce4f54] + Libiconv_jll v1.18.0+0 [4b2f31a3] + Libmount_jll v2.41.0+0 [89763e89] + Libtiff_jll v4.7.1+0 [38a345b3] + Libuuid_jll v2.41.0+0 [94d9ae2c] + NativeFileDialog_jll v1.1.6+3 [eb89d173] + Packmol_jll v21.0.1+0 [36c8627f] + Pango_jll v1.56.1+0 [30392449] + Pixman_jll v0.44.2+0 ⌃ [a2964d1f] + Wayland_jll v1.21.0+2 [2381bf8a] + Wayland_protocols_jll v1.36.0+0 ⌅ [02c8fc9c] + XML2_jll v2.13.6+1 [ffd25f8a] + XZ_jll v5.8.1+0 [4f6342f7] + Xorg_libX11_jll v1.8.12+0 [0c0b7dd1] + Xorg_libXau_jll v1.0.13+0 [3c9796d7] + Xorg_libXcomposite_jll v0.4.6+0 [935fb764] + Xorg_libXcursor_jll v1.2.4+0 [0aeada51] + Xorg_libXdamage_jll v1.1.6+0 [a3789734] + Xorg_libXdmcp_jll v1.1.6+0 [1082639a] + Xorg_libXext_jll v1.3.7+0 [d091e8ba] + Xorg_libXfixes_jll v6.0.1+0 [a51aa0fd] + Xorg_libXi_jll v1.8.3+0 [d1454406] + Xorg_libXinerama_jll v1.1.6+0 [ec84b674] + Xorg_libXrandr_jll v1.5.5+0 [ea2f1a96] + Xorg_libXrender_jll v0.9.12+0 [b6f176f1] + Xorg_libXtst_jll v1.2.5+0 [c7cfdc94] + Xorg_libxcb_jll v1.17.1+0 [cc61e674] + Xorg_libxkbfile_jll v1.1.3+0 [35661453] + Xorg_xkbcomp_jll v1.4.7+0 [33bec58e] + Xorg_xkeyboard_config_jll v2.44.0+0 [c5fb5394] + Xorg_xtrans_jll v1.6.0+0 [3161d3a3] + Zstd_jll v1.5.7+1 [de012916] + at_spi2_atk_jll v2.34.1+4 [0fc3237b] + at_spi2_core_jll v2.34.0+4 [da03df04] + gdk_pixbuf_jll v2.42.12+0 [bf975903] + iso_codes_jll v4.17.0+0 [b53b4c65] + libpng_jll v1.6.47+0 [d8fb68d0] + xkbcommon_jll v1.4.1+2 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [9fa8497b] + Future v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [efcefdf7] + PCRE2_jll v10.44.0+1 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Installation completed after 4.07s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 81.01s ################################################################################ # Testing # Testing Packmol Status `/tmp/jl_7ZYLcL/Project.toml` [4c88cf16] Aqua v0.8.11 [69e1c6dd] CellListMap v0.9.8 [26cc04aa] FiniteDifferences v0.12.32 ⌅ [f6369f11] ForwardDiff v0.10.38 [e1fe445b] NativeFileDialog v0.2.1 [6cdf86f9] Packmol v0.1.12 [d96e819e] Parameters v0.12.3 [bf97046b] SPGBox v0.7.2 [90137ffa] StaticArrays v1.9.13 [10745b16] Statistics v1.11.1 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [eb89d173] Packmol_jll v21.0.1+0 [37e2e46d] LinearAlgebra v1.12.0 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_7ZYLcL/Manifest.toml` [4c88cf16] Aqua v0.8.11 [69e1c6dd] CellListMap v0.9.8 [d360d2e6] ChainRulesCore v1.25.1 [ae650224] ChunkSplitters v3.1.2 [bbf7d656] CommonSubexpressions v0.3.1 [34da2185] Compat v4.16.0 [187b0558] ConstructionBase v1.5.8 [163ba53b] DiffResults v1.1.0 [b552c78f] DiffRules v1.15.1 [ffbed154] DocStringExtensions v0.9.4 [48062228] FilePathsBase v0.9.24 [26cc04aa] FiniteDifferences v0.12.32 ⌅ [f6369f11] ForwardDiff v0.10.38 [92d709cd] IrrationalConstants v0.2.4 [692b3bcd] JLLWrappers v1.7.0 [2ab3a3ac] LogExpFunctions v0.3.29 [1914dd2f] MacroTools v0.5.16 [77ba4419] NaNMath v1.1.3 [e1fe445b] NativeFileDialog v0.2.1 [bac558e1] OrderedCollections v1.8.0 [6cdf86f9] Packmol v0.1.12 [d96e819e] Parameters v0.12.3 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [92933f4c] ProgressMeter v1.10.4 [708f8203] Richardson v1.4.2 [bf97046b] SPGBox v0.7.2 [efcf1570] Setfield v1.1.2 [276daf66] SpecialFunctions v2.5.1 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [f8b46487] TestItemRunner v1.1.0 [1c621080] TestItems v1.0.0 [3a884ed6] UnPack v1.0.2 ⌃ [7b86fcea] ATK_jll v2.38.0+0 [6e34b625] Bzip2_jll v1.0.9+0 ⌃ [83423d85] Cairo_jll v1.18.4+0 [ee1fde0b] Dbus_jll v1.16.2+0 [2702e6a9] EpollShim_jll v0.0.20230411+1 [2e619515] Expat_jll v2.6.5+0 [a3f928ae] Fontconfig_jll v2.16.0+0 [d7e528f0] FreeType2_jll v2.13.4+0 [559328eb] FriBidi_jll v1.0.17+0 [77ec8976] GTK3_jll v3.24.31+0 [78b55507] Gettext_jll v0.21.0+0 ⌃ [7746bdde] Glib_jll v2.82.4+0 [3b182d85] Graphite2_jll v1.3.15+0 [2e76f6c2] HarfBuzz_jll v8.5.0+0 [aacddb02] JpegTurbo_jll v3.1.1+0 [88015f11] LERC_jll v4.0.1+0 [1d63c593] LLVMOpenMP_jll v18.1.8+0 [dd4b983a] LZO_jll v2.10.3+0 [42c93a91] Libepoxy_jll v1.5.10+0 ⌅ [e9f186c6] Libffi_jll v3.2.2+2 [7e76a0d4] Libglvnd_jll v1.7.1+1 [94ce4f54] Libiconv_jll v1.18.0+0 [4b2f31a3] Libmount_jll v2.41.0+0 [89763e89] Libtiff_jll v4.7.1+0 [38a345b3] Libuuid_jll v2.41.0+0 [94d9ae2c] NativeFileDialog_jll v1.1.6+3 [efe28fd5] OpenSpecFun_jll v0.5.6+0 [eb89d173] Packmol_jll v21.0.1+0 [36c8627f] Pango_jll v1.56.1+0 [30392449] Pixman_jll v0.44.2+0 ⌃ [a2964d1f] Wayland_jll v1.21.0+2 [2381bf8a] Wayland_protocols_jll v1.36.0+0 ⌅ [02c8fc9c] XML2_jll v2.13.6+1 [ffd25f8a] XZ_jll v5.8.1+0 [4f6342f7] Xorg_libX11_jll v1.8.12+0 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v0.8.5+0 [458c3c95] OpenSSL_jll v3.0.16+0 [efcefdf7] PCRE2_jll v10.44.0+1 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. Testing Running tests... Current directory: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol/water_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.0.0 ################################################################################ Packmol must be run with: packmol < inputfile.inp Userguide at: http://m3g.iqm.unicamp.br/packmol Reading input file... (Control-C aborts) Types of coordinate files specified: pdb Seed for random number generator: 1234567 Output file: water_box.pdb Reading coordinate file: water.pdb Number of independent structures: 1 The structures are: Structure 1 :water.pdb( 3 atoms) Maximum number of GENCAN loops for all molecule packing: 200 Distance tolerance: 2.0000000000000000 Warning: Type of residue numbering not set for structure 1 Residue numbering set for structure 1 : 0 Swap chains of molecules of structure 1 : F Number of molecules of type 1 : 1000 Total number of restrictions: 1 Total number of atoms: 3000 Total number of molecules: 1000 Number of fixed molecules: 0 Number of free molecules: 1000 Number of variables: 6000 Total number of fixed atoms: 0 Maximum internal distance of type 1 : 1.6330000000000000 All atoms must be within these coordinates: x: [ -999.24636734693877 , 1000.7536326530612 ] y: [ -998.39999999999998 , 1001.6000000000000 ] z: [ -1000.0000000000000 , 1000.0000000000000 ] If the system is larger than this, increase the sidemax parameter. ################################################################################ Building initial approximation ... ################################################################################ Adjusting initial point to fit the constraints -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Packing:|0 100%| |****************** Restraint-only function value: 1.9249263927764875E-003 Maximum violation of the restraints: 7.6443868798986797E-004 -------------------------------------------------------------------------------- Rescaling maximum and minimum coordinates... Mininum and maximum coordinates after constraint fitting: x: [ -2.7648484370573878E-002 , 40.002258764670991 ] y: [ -2.3521406245318177E-003 , 40.022887838617095 ] z: [ -4.7549945801708127E-003 , 40.000334009267632 ] Computing size of patches... Number of cells in each direction and cell sides: x: 19 cells of size 2.3384161710021880 y: 19 cells of size 2.3381705252232439 z: 19 cells of size 2.3371099475709372 Cell-system length: 44.42991 44.42524 44.40509 Reseting center of mass... -------------------------------------------------------------------------------- Setting initial trial coordinates ... -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Adjusting random positions to fit the constraints. Packing:|0 100%| |*** Restraint-only function value: 8.0763878397168733E-003 Maximum violation of the restraints: 1.8784365349438182E-003 ################################################################################ Objective function at initial point: 8300.7485958682319 ################################################################################ Packing molecules of type: 1 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |****************************** Function value from last GENCAN loop: f = .00000E+00 Best function value before: f = .83007E+04 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 Current structure written to file: water_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 1 Objective function value: 0.0000000000000000 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 0.0000000000000000 -------------------------------------------------------------------------------- ################################################################################ Packing all molecules together ################################################################################ Initial approximation is a solution. Nothing to do. Solution written to file: water_box.pdb ################################################################################ Success! Final objective function value: .94984E+00 Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 -------------------------------------------------------------------------------- Please cite this work if Packmol was useful: L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13) pp. 2157-2164, 2009. https://doi.org/10.1002/jcc.21224 ################################################################################ Running time: 0.430698007 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol/water_box.pdb Current directory: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol/ieee_signaling_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.0.0 ################################################################################ Packmol must be run with: packmol < inputfile.inp Userguide at: http://m3g.iqm.unicamp.br/packmol Reading input file... (Control-C aborts) Types of coordinate files specified: pdb Seed for random number generator: 1234567 Output file: ieee_signaling_box.pdb Reading coordinate file: ieee_signaling.pdb Reading coordinate file: ieee_signaling.pdb Reading coordinate file: ieee_signaling.pdb Reading coordinate file: ieee_signaling.pdb Number of independent structures: 4 The structures are: Structure 1 :ieee_signaling.pdb( 1 atoms) Structure 2 :ieee_signaling.pdb( 1 atoms) Structure 3 :ieee_signaling.pdb( 1 atoms) Structure 4 :ieee_signaling.pdb( 1 atoms) Maximum number of GENCAN loops for all molecule packing: 800 Distance tolerance: 6.0000000000000000 Warning: Type of residue numbering not set for structure 1 Residue numbering set for structure 1 : 0 Swap chains of molecules of structure 1 : F Warning: Type of residue numbering not set for structure 2 Residue numbering set for structure 2 : 0 Swap chains of molecules of structure 2 : F Warning: Type of residue numbering not set for structure 3 Residue numbering set for structure 3 : 0 Swap chains of molecules of structure 3 : F Warning: Type of residue numbering not set for structure 4 Residue numbering set for structure 4 : 0 Swap chains of molecules of structure 4 : F Number of molecules of type 1 : 6916 Number of molecules of type 2 : 7377 Number of molecules of type 3 : 4783 Number of molecules of type 4 : 2766 Total number of restrictions: 8 Total number of atoms: 21842 Total number of molecules: 21842 Number of fixed molecules: 0 Number of free molecules: 21842 Number of variables: 131052 Total number of fixed atoms: 0 Maximum internal distance of type 1 : 0.0000000000000000 Maximum internal distance of type 2 : 0.0000000000000000 Maximum internal distance of type 3 : 0.0000000000000000 Maximum internal distance of type 4 : 0.0000000000000000 All atoms must be within these coordinates: x: [ -1000.0000000000000 , 1000.0000000000000 ] y: [ -1000.0000000000000 , 1000.0000000000000 ] z: [ -1000.0000000000000 , 1000.0000000000000 ] If the system is larger than this, increase the sidemax parameter. ################################################################################ Building initial approximation ... ################################################################################ Adjusting initial point to fit the constraints -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Packing:|0 100%| |*************************** Restraint-only function value: 6.7236466284939321E-009 Maximum violation of the restraints: 6.6377887232484216E-009 -------------------------------------------------------------------------------- Molecules of type: 2 Packing:|0 100%| |****************************** Restraint-only function value: 1.4820668630290202E-011 Maximum violation of the restraints: 1.4820664073159769E-011 -------------------------------------------------------------------------------- Molecules of type: 3 Packing:|0 100%| |*************************** Restraint-only function value: 1.0014096653321234E-009 Maximum violation of the restraints: 2.9583317149944359E-011 -------------------------------------------------------------------------------- Molecules of type: 4 Packing:|0 100%| |*************************** Restraint-only function value: 1.3551002692006912E-005 Maximum violation of the restraints: 1.3540893496853879E-005 -------------------------------------------------------------------------------- Rescaling maximum and minimum coordinates... Mininum and maximum coordinates after constraint fitting: x: [ -384.86635045478602 , 384.83973533048919 ] y: [ -384.85512719106799 , 384.86312013302074 ] z: [ -384.76585932567423 , 384.83310590176524 ] Computing size of patches... Number of cells in each direction and cell sides: x: 117 cells of size 6.6915050067117550 y: 117 cells of size 6.6916089514879378 z: 117 cells of size 6.6905894463883726 Cell-system length: 782.90609 782.91825 782.79897 Reseting center of mass... -------------------------------------------------------------------------------- Setting initial trial coordinates ... -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 1.0326729111041239E-003 Maximum violation of the restraints: 1.0326729093332943E-003 -------------------------------------------------------------------------------- Molecules of type: 2 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 2.1324379608091790E-002 Maximum violation of the restraints: 3.7411489898161038E-003 -------------------------------------------------------------------------------- Molecules of type: 3 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 7.1181333158253264E-004 Maximum violation of the restraints: 6.5502667699360033E-005 -------------------------------------------------------------------------------- Molecules of type: 4 Adjusting random positions to fit the constraints. Packing:|0 100%| |****************** Restraint-only function value: 3.3406665839163477E-002 Maximum violation of the restraints: 7.3165799111741502E-003 ################################################################################ Objective function at initial point: 894719.74759345665 ################################################################################ Packing molecules of type: 1 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |****************** Function value from last GENCAN loop: f = .15978E-06 Best function value before: f = .19668E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .15846E-06 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 1 Objective function value: 1.5977948630680736E-007 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 1.5846032381395894E-007 -------------------------------------------------------------------------------- ################################################################################ Packing molecules of type: 2 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |*************** Function value from last GENCAN loop: f = .10381E-04 Best function value before: f = .32002E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .64917E-05 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 2 Objective function value: 1.0381187324337890E-005 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 6.4917076968170149E-006 -------------------------------------------------------------------------------- ################################################################################ Packing molecules of type: 3 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |********************* Function value from last GENCAN loop: f = .78754E-11 Best function value before: f = .23934E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .78754E-11 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 3 Objective function value: 7.8753958460166788E-012 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 7.8753958460166788E-012 -------------------------------------------------------------------------------- ################################################################################ Packing molecules of type: 4 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |*************************** Function value from last GENCAN loop: f = .61528E-06 Best function value before: f = .13868E+06 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .51013E-06 Current structure written to file: ieee_signaling_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 4 Objective function value: 6.1527984572842272E-007 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 5.1013205062081808E-007 -------------------------------------------------------------------------------- ################################################################################ Packing all molecules together ################################################################################ Initial approximation is a solution. Nothing to do. Solution written to file: ieee_signaling_box.pdb ################################################################################ Success! Final objective function value: .10321E+02 Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .64917E-05 -------------------------------------------------------------------------------- Please cite this work if Packmol was useful: L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13) pp. 2157-2164, 2009. https://doi.org/10.1002/jcc.21224 ################################################################################ Running time: 6.14925528 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol/ieee_signaling_box.pdb Current directory: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol Input file directory: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol Output file: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol/water_box.pdb ################################################################################ PACKMOL - Packing optimization for the automated generation of starting configurations for molecular dynamics simulations. Version 21.0.0 ################################################################################ Packmol must be run with: packmol < inputfile.inp Userguide at: http://m3g.iqm.unicamp.br/packmol Reading input file... (Control-C aborts) Types of coordinate files specified: pdb Seed for random number generator: 1234567 Output file: water_box.pdb Reading coordinate file: water.pdb Number of independent structures: 1 The structures are: Structure 1 :water.pdb( 3 atoms) Maximum number of GENCAN loops for all molecule packing: 200 Distance tolerance: 2.0000000000000000 Warning: Type of residue numbering not set for structure 1 Residue numbering set for structure 1 : 0 Swap chains of molecules of structure 1 : F Number of molecules of type 1 : 1000 Total number of restrictions: 1 Total number of atoms: 3000 Total number of molecules: 1000 Number of fixed molecules: 0 Number of free molecules: 1000 Number of variables: 6000 Total number of fixed atoms: 0 Maximum internal distance of type 1 : 1.6330000000000000 All atoms must be within these coordinates: x: [ -999.24636734693877 , 1000.7536326530612 ] y: [ -998.39999999999998 , 1001.6000000000000 ] z: [ -1000.0000000000000 , 1000.0000000000000 ] If the system is larger than this, increase the sidemax parameter. ################################################################################ Building initial approximation ... ################################################################################ Adjusting initial point to fit the constraints -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Packing:|0 100%| |****************** Restraint-only function value: 1.9249263927764875E-003 Maximum violation of the restraints: 7.6443868798986797E-004 -------------------------------------------------------------------------------- Rescaling maximum and minimum coordinates... Mininum and maximum coordinates after constraint fitting: x: [ -2.7648484370573878E-002 , 40.002258764670991 ] y: [ -2.3521406245318177E-003 , 40.022887838617095 ] z: [ -4.7549945801708127E-003 , 40.000334009267632 ] Computing size of patches... Number of cells in each direction and cell sides: x: 19 cells of size 2.3384161710021880 y: 19 cells of size 2.3381705252232439 z: 19 cells of size 2.3371099475709372 Cell-system length: 44.42991 44.42524 44.40509 Reseting center of mass... -------------------------------------------------------------------------------- Setting initial trial coordinates ... -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Molecules of type: 1 Adjusting random positions to fit the constraints. Packing:|0 100%| |*** Restraint-only function value: 8.0763878397168733E-003 Maximum violation of the restraints: 1.8784365349438182E-003 ################################################################################ Objective function at initial point: 8300.7485958682319 ################################################################################ Packing molecules of type: 1 ################################################################################ -------------------------------------------------------------------------------- Starting GENCAN loop: 0 Scaling radii by: 1.1000000000000001 Packing:|0 100%| |****************************** Function value from last GENCAN loop: f = .00000E+00 Best function value before: f = .83007E+04 Improvement from best function value: 99.99 % Improvement from last loop: 99.99 % Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 Current structure written to file: water_box.pdb -------------------------------------------------------------------------------- Packing solved for molecules of type 1 Objective function value: 0.0000000000000000 Maximum violation of target distance: 0.0000000000000000 Max. constraint violation: 0.0000000000000000 -------------------------------------------------------------------------------- ################################################################################ Packing all molecules together ################################################################################ Initial approximation is a solution. Nothing to do. Solution written to file: water_box.pdb ################################################################################ Success! Final objective function value: .94984E+00 Maximum violation of target distance: 0.000000 Maximum violation of the constraints: .00000E+00 -------------------------------------------------------------------------------- Please cite this work if Packmol was useful: L. Martinez, R. Andrade, E. G. Birgin, J. M. Martinez, PACKMOL: A package for building initial configurations for molecular dynamics simulations. Journal of Computational Chemistry, 30(13) pp. 2157-2164, 2009. https://doi.org/10.1002/jcc.21224 ################################################################################ Running time: 0.451147974 seconds. -------------------------------------------------------------------------------- Wrote output to: /home/pkgeval/.julia/packages/Packmol/b5E9B/test/run_packmol/water_box.pdb Test Summary: | Pass Total Time Package | 57 57 2m58.6s Testing Packmol tests passed Testing completed after 239.92s PkgEval succeeded after 357.74s