├── .gitignore ├── BuildInfo.wl ├── ContentCache.mx ├── DeploymentInfo.m ├── README.md ├── SiteConfig.wl ├── content ├── favicon-16x16.png ├── favicon-32x32.png ├── img │ ├── 11-3313247468270440649.png │ ├── 115errors-611550152511888119.png │ ├── 12-1688074291526202115.png │ ├── 12-5159485901130549445.png │ ├── 12-5405623299749968708.png │ ├── 12-6383125132510836538.png │ ├── 122documentation-5159485901130549445.png │ ├── 123keyboardaliasesandspecialcharacters-5405623299749968708.png │ ├── 123keyboardaliasesandspecialcharacters-6383125132510836538.png │ ├── 13-1023592594887039088.png │ ├── 13-102598221790460311.png │ ├── 13-1037528491266790692.png │ ├── 13-1278064344411680398.png │ ├── 13-1767576396938451259.png │ ├── 13-2160315400703055653.png │ ├── 13-27440736798507524.png │ ├── 13-2951848453403160234.png │ ├── 13-3371394493544641033.png │ ├── 13-3511084842032277539.png │ ├── 13-3570932775112242561.png │ ├── 13-3688944527199105108.png │ ├── 13-3713184338581812656.png │ ├── 13-3735483042630984156.png │ ├── 13-4513164947294324238.png │ ├── 13-4764193930231960186.png │ ├── 13-4776971268818325606.png │ ├── 13-4856433709491691837.png │ ├── 13-4963816391501253228.png │ ├── 13-5031790952252282029.png │ ├── 13-5183532094724107249.png │ ├── 13-5260013713964025253.png │ ├── 13-5456555609594511692.png │ ├── 13-5464850248744285665.png │ ├── 13-5646297479297114505.png │ ├── 13-5848364162849435254.png │ ├── 13-5859374809465439520.png │ ├── 13-6681674425728526979.png │ ├── 13-6896806014464856131.png │ ├── 13-7031334226066909995.png │ ├── 13-7135908203198493178.png │ ├── 13-7279477836414445162.png │ ├── 13-7593402898594521775.png │ ├── 13-8022704842149014745.png │ ├── 13-8072267191633938527.png │ ├── 13-864668289591505269.png │ ├── 13-8826648132354525971.png │ ├── 13-8855904715395174455.png │ ├── 13-969833352094348869.png │ ├── 13-995204871575620383.png │ ├── 132symbolicalgebra-1278064344411680398.png │ ├── 132symbolicalgebra-4856433709491691837.png │ ├── 132symbolicalgebra-4963816391501253228.png │ ├── 133calculus-2798343428087035764.png │ ├── 133calculus-5848364162849435254.png │ ├── 133calculus-5859374809465439520.png │ ├── 133calculus-6246138609363623203.png │ ├── 134builtindataandunits-1623103641045896793.png │ ├── 134builtindataandunits-3735483042630984156.png │ ├── 134builtindataandunits-5464850248744285665.png │ ├── 134builtindataandunits-7593402898594521775.png │ ├── 134builtindataandunits-864668289591505269.png │ ├── 21-1709303150763371217.png │ ├── 21-1722784371355657163.png │ ├── 21-1760282929081317088.png │ ├── 21-2242955263637576379.png │ ├── 21-2582507560232164189.png │ ├── 21-3675499559684164904.png │ ├── 21-3692143705990288316.png │ ├── 21-3746347517276191002.png │ ├── 21-4320265213233087576.png │ ├── 21-4454967654715330391.png │ ├── 21-4910082451528274266.png │ ├── 21-5351566995130891547.png │ ├── 21-5408027383975409113.png │ ├── 21-613264738046767344.png │ ├── 21-649432503142289867.png │ ├── 21-6663125985827735989.png │ ├── 21-6795375748047348788.png │ ├── 21-7026757674080903183.png │ ├── 21-7468015508976701203.png │ ├── 21-7706351181004478065.png │ ├── 21-8170670331652490370.png │ ├── 21-8172745357234148820.png │ ├── 2112errorhandling-6070949172998910373.png │ ├── 2112errorhandling-6809837667784981244.png │ ├── 211symbolsandexpressions-7059428318388094490.png │ ├── 212expressionsstructure-3292976767487415699.png │ ├── 212expressionsstructure-8617515708092443925.png │ ├── 215functions-1722784371355657163.png │ ├── 215functions-1760282929081317088.png │ ├── 215functions-649432503142289867.png │ ├── 215functions-6795375748047348788.png │ ├── 215functions-7026757674080903183.png │ ├── 215functions-7706351181004478065.png │ ├── 216contexts-7468015508976701203.png │ ├── 22-1114857042421127565.png │ ├── 22-1131873469982841262.png │ ├── 22-1348963780000788127.png │ ├── 22-1383702410993826304.png │ ├── 22-2270667353347243618.png │ ├── 22-2463392914657171378.png │ ├── 22-2781982858912025980.png │ ├── 22-2797206139365313108.png │ ├── 22-3037897936210855976.png │ ├── 22-3086354690352550579.png │ ├── 22-3154713215007475231.png │ ├── 22-333367112565904913.png │ ├── 22-3841721997576765643.png │ ├── 22-3911689400241820706.png │ ├── 22-3950594597190533933.png │ ├── 22-395271241287311702.png │ ├── 22-3974473653961945538.png │ ├── 22-4331124232957805111.png │ ├── 22-4737251508472738868.png │ ├── 22-4783366720916156075.png │ ├── 22-4823551658722428068.png │ ├── 22-4855681135816685350.png │ ├── 22-4939794383627769131.png │ ├── 22-4991518592214860267.png │ ├── 22-5092333917311493067.png │ ├── 22-524780254544371368.png │ ├── 22-5388265198911020986.png │ ├── 22-5451681266245674562.png │ ├── 22-5509702874528235278.png │ ├── 22-5574092216230116245.png │ ├── 22-5678734961258451771.png │ ├── 22-5986014195479156880.png │ ├── 22-6000845343406865510.png │ ├── 22-612737366913310971.png │ ├── 22-6197124947707195918.png │ ├── 22-671211221228907509.png │ ├── 22-6848720549811875181.png │ ├── 22-7244818211856538291.png │ ├── 22-7326022483212805039.png │ ├── 22-7457865169315486083.png │ ├── 22-7554777481255894278.png │ ├── 22-7671711646045324051.png │ ├── 22-7860618826219449006.png │ ├── 22-7899734745879872875.png │ ├── 22-8255594840969041608.png │ ├── 22-8507675721582783082.png │ ├── 22-873404383870698890.png │ ├── 22-8871422904547814990.png │ ├── 22-9001538133314045945.png │ ├── 22-901697867635371312.png │ ├── 22-9124020099798135891.png │ ├── 22-9203543330558690139.png │ ├── 22-96816251163000789.png │ ├── 222dynamic-2381226532866321571.png │ ├── 222dynamic-3600955783346224363.png │ ├── 222dynamic-3801747813210570362.png │ ├── 222dynamic-8291210888907479400.png │ ├── 222dynamic-8464373383437301006.png │ ├── 225thefrontend-1131873469982841262.png │ ├── 225thefrontend-3219513531743503804.png │ ├── 225thefrontend-4918419529169561977.png │ ├── 225thefrontend-5146191520937075414.png │ ├── 226compile-7345567143506603576.png │ ├── 226compile-931223256879963949.png │ ├── 23-1237034483645259624.png │ ├── 23-1468420283344945119.png │ ├── 23-1539613407351655567.png │ ├── 23-1822040011122505851.png │ ├── 23-2031280556622007435.png │ ├── 23-2584241647775519822.png │ ├── 23-2741827820454628413.png │ ├── 23-3030685361976493762.png │ ├── 23-3747043155035056144.png │ ├── 23-4434809189540581916.png │ ├── 23-463471582337378389.png │ ├── 23-4882192801311268958.png │ ├── 23-4892882470254506065.png │ ├── 23-4943031955755802123.png │ ├── 23-539493156854353424.png │ ├── 23-5468118257856689382.png │ ├── 23-5736906100322766460.png │ ├── 23-5814771385969442190.png │ ├── 23-6253259551905170089.png │ ├── 23-6577318282343855371.png │ ├── 23-6586763805728018642.png │ ├── 23-7466255935374283148.png │ ├── 23-7518515718458752709.png │ ├── 23-7762893621120136491.png │ ├── 23-7974878992120245803.png │ ├── 23-8116941541411865245.png │ ├── 23-8797637419045844720.png │ ├── 23-9106721915401155694.png │ ├── 233importandreadlist-2584241647775519822.png │ ├── 24-2101793461828607164.png │ ├── 24-3287449732829733262.png │ ├── 24-3772276586742963859.png │ ├── 24-3790712868165053827.png │ ├── 24-4711230888145092901.png │ ├── 24-4967182193891839896.png │ ├── 24-5031638771548097970.png │ ├── 24-5410312031510072809.png │ ├── 24-5467324402590948253.png │ ├── 24-588547064546270495.png │ ├── 24-6253915837061469610.png │ ├── 24-6486010287479323106.png │ ├── 24-6592286703145291220.png │ ├── 24-6708879871255587013.png │ ├── 24-7188863773697757790.png │ ├── 24-7298600359178422764.png │ ├── 24-8599681838666113304.png │ ├── 24-902733499638966594.png │ ├── 251compile-1541471245257336081.png │ ├── 251compile-5113809365852715934.png │ ├── 251compile-6656821290333338907.png │ ├── 251compile-7345567143506603576.png │ ├── 251compile-931223256879963949.png │ ├── 252specialarrays-7323871970862718619.png │ ├── 252specialarrays-7668129619617107787.png │ ├── 312installationbasics-3001995490788476466.png │ ├── 312installationbasics-7671577574912776238.png │ ├── 321installation-3001995490788476466.png │ ├── 321installation-7671577574912776238.png │ ├── 322pacletservers-5296222007074979075.png │ ├── 322pacletservers-7251570539084711450.png │ ├── 342functionpreparation-8579650201645694798.png │ ├── 36-1560325371174196536.png │ ├── 36-5137065355729740508.png │ ├── 36-5560197663506762293.png │ ├── 412internal-635264222018588987.png │ ├── 413frontend-4330817502451337122.png │ ├── 413frontend-6408243860282986610.png │ ├── 413frontend-6899044001331197557.png │ └── 413frontend-732377038742225435.png ├── old │ └── chemical-modeling │ │ ├── atoms │ │ ├── 3.3.1-making-an-atom.md │ │ ├── 3.3.1-making-an-atom.nb │ │ ├── 3.3.2-working-with-atoms.md │ │ └── 3.3.2-working-with-atoms.nb │ │ ├── bonds │ │ ├── 3.4.1-making-a-bond.md │ │ ├── 3.4.1-making-a-bond.nb │ │ ├── 3.4.2-working-with-bonds.md │ │ └── 3.4.2-working-with-bonds.nb │ │ ├── modeling │ │ ├── 3.6.1-molecular-modeling.md │ │ └── 3.6.1-molecular-modeling.nb │ │ ├── molecules │ │ ├── 3.5.1-making-a-molecule.md │ │ ├── 3.5.1-making-a-molecule.nb │ │ ├── 3.5.2-working-with-molecules.md │ │ └── 3.5.2-working-with-molecules.nb │ │ ├── overview │ │ ├── 3.1.1-overview.md │ │ └── 3.1.1-overview.nb │ │ └── systems │ │ ├── 3.2.1-creating-a-system.md │ │ ├── 3.2.1-creating-a-system.nb │ │ ├── 3.2.2-adding-and-removing.md │ │ ├── 3.2.2-adding-and-removing.nb │ │ ├── 3.2.3-editing-a-system.md │ │ └── 3.2.3-editing-a-system.nb ├── pages │ ├── About.md │ ├── About.nb │ ├── Contact.md │ ├── Contact.nb │ ├── toc.md │ └── toc.nb ├── posts │ ├── mathematica-programming │ │ ├── assorted-tricks │ │ │ ├── 2.3.1-trott-strzebonski.md │ │ │ ├── 2.3.1-trott-strzebonski.nb │ │ │ ├── 2.3.2-villegas-gayley.md │ │ │ ├── 2.3.2-villegas-gayley.nb │ │ │ ├── 2.3.3-import-and-readlist.md │ │ │ ├── 2.3.3-import-and-readlist.nb │ │ │ ├── 2.3.4-currentvalue-and-frontendtokens.md │ │ │ ├── 2.3.4-currentvalue-and-frontendtokens.nb │ │ │ ├── 2.3.5-scraping.md │ │ │ ├── 2.3.5-scraping.nb │ │ │ ├── 2.3.6-object-oriented-programming.md │ │ │ └── 2.3.6-object-oriented-programming.nb │ │ ├── code-structure │ │ │ ├── 2.1.1-symbols-and-expressions.md │ │ │ ├── 2.1.1-symbols-and-expressions.nb │ │ │ ├── 2.1.10-scoping-revisited.md │ │ │ ├── 2.1.10-scoping-revisited.nb │ │ │ ├── 2.1.11-flow-control.md │ │ │ ├── 2.1.11-flow-control.nb │ │ │ ├── 2.1.12-error-handling.md │ │ │ ├── 2.1.12-error-handling.nb │ │ │ ├── 2.1.2-expressions-structure.md │ │ │ ├── 2.1.2-expressions-structure.nb │ │ │ ├── 2.1.3-patterns.md │ │ │ ├── 2.1.3-patterns.nb │ │ │ ├── 2.1.4-replacement-patterns.md │ │ │ ├── 2.1.4-replacement-patterns.nb │ │ │ ├── 2.1.5-functions.md │ │ │ ├── 2.1.5-functions.nb │ │ │ ├── 2.1.6-contexts.md │ │ │ ├── 2.1.6-contexts.nb │ │ │ ├── 2.1.7-ownvalues-set-and-setdelayed.md │ │ │ ├── 2.1.7-ownvalues-set-and-setdelayed.nb │ │ │ ├── 2.1.8-function-values.md │ │ │ ├── 2.1.8-function-values.nb │ │ │ ├── 2.1.9-hold-and-evaluation-order.md │ │ │ └── 2.1.9-hold-and-evaluation-order.nb │ │ ├── functional-programming │ │ │ ├── 2.4.1-procedural-programming.md │ │ │ ├── 2.4.1-procedural-programming.nb │ │ │ ├── 2.4.2-table-and-do.md │ │ │ ├── 2.4.2-table-and-do.nb │ │ │ ├── 2.4.3-map-and-scan.md │ │ │ ├── 2.4.3-map-and-scan.nb │ │ │ ├── 2.4.4-nest-and-nestlist.md │ │ │ ├── 2.4.4-nest-and-nestlist.nb │ │ │ ├── 2.4.5-fold-and-foldlist.md │ │ │ ├── 2.4.5-fold-and-foldlist.nb │ │ │ ├── 2.4.6-fixedpoint-and-gradients.md │ │ │ └── 2.4.6-fixedpoint-and-gradients.nb │ │ ├── higher-level-functionality │ │ │ ├── 2.2.1-packages.md │ │ │ ├── 2.2.1-packages.nb │ │ │ ├── 2.2.2-dynamic.md │ │ │ ├── 2.2.2-dynamic.nb │ │ │ ├── 2.2.3-formatting.md │ │ │ ├── 2.2.3-formatting.nb │ │ │ ├── 2.2.4-interfaces.md │ │ │ ├── 2.2.4-interfaces.nb │ │ │ ├── 2.2.5-the-front-end.md │ │ │ ├── 2.2.5-the-front-end.nb │ │ │ ├── 2.2.6-remote-kernels.md │ │ │ └── 2.2.6-remote-kernels.nb │ │ └── performance-tuning │ │ │ ├── 2.5.1-compile.md │ │ │ ├── 2.5.1-compile.nb │ │ │ ├── 2.5.2-special-arrays.md │ │ │ └── 2.5.2-special-arrays.nb │ ├── package-usage-and-development │ │ ├── basics │ │ │ ├── 3.1.1-packages-in-mathematica.md │ │ │ ├── 3.1.1-packages-in-mathematica.nb │ │ │ ├── 3.1.2-paclets.md │ │ │ └── 3.1.2-paclets.nb │ │ ├── higher-level-features │ │ │ ├── 3.4.1-multi-package-paclets.md │ │ │ ├── 3.4.1-multi-package-paclets.nb │ │ │ ├── 3.4.2-function-preparation.md │ │ │ ├── 3.4.2-function-preparation.nb │ │ │ ├── 3.4.3-new-style-packages.md │ │ │ ├── 3.4.3-new-style-packages.nb │ │ │ ├── 3.4.4-special-paclets.md │ │ │ └── 3.4.4-special-paclets.nb │ │ ├── paclet-development │ │ │ ├── 3.3.1-paclet-structure.md │ │ │ ├── 3.3.1-paclet-structure.nb │ │ │ ├── 3.3.2-paclet-development.md │ │ │ ├── 3.3.2-paclet-development.nb │ │ │ ├── 3.3.3-paclet-distribution.md │ │ │ ├── 3.3.3-paclet-distribution.nb │ │ │ ├── 3.3.4-tips-and-tricks copy.md │ │ │ ├── 3.3.4-tips-and-tricks copy.nb │ │ │ ├── 3.3.5-sample-paclets-structures.md │ │ │ └── 3.3.5-sample-paclets-structures.nb │ │ └── paclet-usage │ │ │ ├── 3.2.1-installation.md │ │ │ ├── 3.2.1-installation.nb │ │ │ ├── 3.2.2-paclet-servers.md │ │ │ └── 3.2.2-paclet-servers.nb │ ├── reference-guides │ │ └── undocumented-contexts │ │ │ ├── 4.1.1-overview.md │ │ │ ├── 4.1.1-overview.nb │ │ │ ├── 4.1.2-internal.md │ │ │ ├── 4.1.2-internal.nb │ │ │ ├── 4.1.3-front-end.md │ │ │ ├── 4.1.3-front-end.nb │ │ │ ├── 4.1.4-system-private.md │ │ │ ├── 4.1.4-system-private.nb │ │ │ ├── 4.1.5-language.md │ │ │ ├── 4.1.5-language.nb │ │ │ ├── 4.1.6-general-utilities.md │ │ │ ├── 4.1.6-general-utilities.nb │ │ │ ├── 4.1.7-package.md │ │ │ └── 4.1.7-package.nb │ └── using-mathematica │ │ ├── basics │ │ ├── 1.1.1-types.md │ │ ├── 1.1.1-types.nb │ │ ├── 1.1.2-variables.md │ │ ├── 1.1.2-variables.nb │ │ ├── 1.1.3-functions.md │ │ ├── 1.1.3-functions.nb │ │ ├── 1.1.4-loops-and-scoping.md │ │ ├── 1.1.4-loops-and-scoping.nb │ │ ├── 1.1.5-errors.md │ │ ├── 1.1.5-errors.nb │ │ ├── 1.1.6-clear.md │ │ └── 1.1.6-clear.nb │ │ ├── interface │ │ ├── 1.2.1-function-aliases.md │ │ ├── 1.2.1-function-aliases.nb │ │ ├── 1.2.2-documentation.md │ │ ├── 1.2.2-documentation.nb │ │ ├── 1.2.3-keyboard-aliases-and-special-characters.md │ │ ├── 1.2.3-keyboard-aliases-and-special-characters.nb │ │ ├── 1.2.4-palettes-and-toolbars.md │ │ ├── 1.2.4-palettes-and-toolbars.nb │ │ ├── 1.2.5-styles.md │ │ └── 1.2.5-styles.nb │ │ └── useful-features │ │ ├── 1.3.1-plotting.md │ │ ├── 1.3.1-plotting.nb │ │ ├── 1.3.2-symbolic-algebra.md │ │ ├── 1.3.2-symbolic-algebra.nb │ │ ├── 1.3.3-calculus.md │ │ ├── 1.3.3-calculus.nb │ │ ├── 1.3.4-built-in-data-and-units.md │ │ └── 1.3.4-built-in-data-and-units.nb └── site-icon.png ├── docs ├── authors.html ├── categories.html ├── categories │ ├── assorted-tricks.html │ ├── atoms.html │ ├── basics.html │ ├── bonds.html │ ├── chemical-modeling.html │ ├── code-structure.html │ ├── functional-programming.html │ ├── higher-level-functionality.html │ ├── interface.html │ ├── mathematica-programming.html │ ├── modeling.html │ ├── molecules.html │ ├── overview.html │ ├── package-usage-and-development.html │ ├── performance-tuning.html │ ├── reference-guides.html │ ├── systems.html │ ├── undocumented-contexts.html │ ├── useful-features.html │ └── using-mathematica.html ├── chemical-modeling │ ├── atoms │ │ ├── making-an-atom.html │ │ └── working-with-atoms.html │ ├── bonds │ │ ├── making-a-bond.html │ │ └── working-with-bonds.html │ ├── modeling │ │ ├── modeling.html │ │ └── molecular-modeling.html │ ├── molecules │ │ ├── making-a-molecule.html │ │ └── working-with-molecules.html │ ├── overview │ │ └── intro.html │ └── systems │ │ ├── adding-to-and-removing-from-a-system.html │ │ ├── creating-a-system.html │ │ └── editing-a-system.html ├── favicon-16x16.png ├── favicon-32x32.png ├── img │ ├── 11-3313247468270440649.png │ ├── 115errors-611550152511888119.png │ ├── 12-1688074291526202115.png │ ├── 12-5159485901130549445.png │ ├── 12-5405623299749968708.png │ ├── 12-6383125132510836538.png │ ├── 122documentation-5159485901130549445.png │ ├── 123keyboardaliasesandspecialcharacters-5405623299749968708.png │ ├── 123keyboardaliasesandspecialcharacters-6383125132510836538.png │ ├── 13-1023592594887039088.png │ ├── 13-102598221790460311.png │ ├── 13-1037528491266790692.png │ ├── 13-1278064344411680398.png │ ├── 13-1767576396938451259.png │ ├── 13-2160315400703055653.png │ ├── 13-27440736798507524.png │ ├── 13-2951848453403160234.png │ ├── 13-3371394493544641033.png │ ├── 13-3511084842032277539.png │ ├── 13-3570932775112242561.png │ ├── 13-3688944527199105108.png │ ├── 13-3713184338581812656.png │ ├── 13-3735483042630984156.png │ ├── 13-4513164947294324238.png │ ├── 13-4764193930231960186.png │ ├── 13-4776971268818325606.png │ ├── 13-4856433709491691837.png │ ├── 13-4963816391501253228.png │ ├── 13-5031790952252282029.png │ ├── 13-5183532094724107249.png │ ├── 13-5260013713964025253.png │ ├── 13-5456555609594511692.png │ ├── 13-5464850248744285665.png │ ├── 13-5646297479297114505.png │ ├── 13-5848364162849435254.png │ ├── 13-5859374809465439520.png │ ├── 13-6681674425728526979.png │ ├── 13-6896806014464856131.png │ ├── 13-7031334226066909995.png │ ├── 13-7135908203198493178.png │ ├── 13-7279477836414445162.png │ ├── 13-7593402898594521775.png │ ├── 13-8022704842149014745.png │ ├── 13-8072267191633938527.png │ ├── 13-864668289591505269.png │ ├── 13-8826648132354525971.png │ ├── 13-8855904715395174455.png │ ├── 13-969833352094348869.png │ ├── 13-995204871575620383.png │ ├── 132symbolicalgebra-1278064344411680398.png │ ├── 132symbolicalgebra-4856433709491691837.png │ ├── 132symbolicalgebra-4963816391501253228.png │ ├── 133calculus-2798343428087035764.png │ ├── 133calculus-5848364162849435254.png │ ├── 133calculus-5859374809465439520.png │ ├── 133calculus-6246138609363623203.png │ ├── 134builtindataandunits-1623103641045896793.png │ ├── 134builtindataandunits-3735483042630984156.png │ ├── 134builtindataandunits-5464850248744285665.png │ ├── 134builtindataandunits-7593402898594521775.png │ ├── 134builtindataandunits-864668289591505269.png │ ├── 21-1709303150763371217.png │ ├── 21-1722784371355657163.png │ ├── 21-1760282929081317088.png │ ├── 21-2242955263637576379.png │ ├── 21-2582507560232164189.png │ ├── 21-3675499559684164904.png │ ├── 21-3692143705990288316.png │ ├── 21-3746347517276191002.png │ ├── 21-4320265213233087576.png │ ├── 21-4454967654715330391.png │ ├── 21-4910082451528274266.png │ ├── 21-5351566995130891547.png │ ├── 21-5408027383975409113.png │ ├── 21-613264738046767344.png │ ├── 21-649432503142289867.png │ ├── 21-6663125985827735989.png │ ├── 21-6795375748047348788.png │ ├── 21-7026757674080903183.png │ ├── 21-7468015508976701203.png │ ├── 21-7706351181004478065.png │ ├── 21-8170670331652490370.png │ ├── 21-8172745357234148820.png │ ├── 2112errorhandling-6070949172998910373.png │ ├── 2112errorhandling-6809837667784981244.png │ ├── 211symbolsandexpressions-7059428318388094490.png │ ├── 212expressionsstructure-3292976767487415699.png │ ├── 212expressionsstructure-8617515708092443925.png │ ├── 215functions-1722784371355657163.png │ ├── 215functions-1760282929081317088.png │ ├── 215functions-649432503142289867.png │ ├── 215functions-6795375748047348788.png │ ├── 215functions-7026757674080903183.png │ ├── 215functions-7706351181004478065.png │ ├── 216contexts-7468015508976701203.png │ ├── 22-1114857042421127565.png │ ├── 22-1131873469982841262.png │ ├── 22-1348963780000788127.png │ ├── 22-1383702410993826304.png │ ├── 22-2270667353347243618.png │ ├── 22-2463392914657171378.png │ ├── 22-2781982858912025980.png │ ├── 22-2797206139365313108.png │ ├── 22-3037897936210855976.png │ ├── 22-3086354690352550579.png │ ├── 22-3154713215007475231.png │ ├── 22-333367112565904913.png │ ├── 22-3841721997576765643.png │ ├── 22-3911689400241820706.png │ ├── 22-3950594597190533933.png │ ├── 22-395271241287311702.png │ ├── 22-3974473653961945538.png │ ├── 22-4331124232957805111.png │ ├── 22-4737251508472738868.png │ ├── 22-4783366720916156075.png │ ├── 22-4823551658722428068.png │ ├── 22-4855681135816685350.png │ ├── 22-4939794383627769131.png │ ├── 22-4991518592214860267.png │ ├── 22-5092333917311493067.png │ ├── 22-524780254544371368.png │ ├── 22-5388265198911020986.png │ ├── 22-5451681266245674562.png │ ├── 22-5509702874528235278.png │ ├── 22-5574092216230116245.png │ ├── 22-5678734961258451771.png │ ├── 22-5986014195479156880.png │ ├── 22-6000845343406865510.png │ ├── 22-612737366913310971.png │ ├── 22-6197124947707195918.png │ ├── 22-671211221228907509.png │ ├── 22-6848720549811875181.png │ ├── 22-7244818211856538291.png │ ├── 22-7326022483212805039.png │ ├── 22-7457865169315486083.png │ ├── 22-7554777481255894278.png │ ├── 22-7671711646045324051.png │ ├── 22-7860618826219449006.png │ ├── 22-7899734745879872875.png │ ├── 22-8255594840969041608.png │ ├── 22-8507675721582783082.png │ ├── 22-873404383870698890.png │ ├── 22-8871422904547814990.png │ ├── 22-9001538133314045945.png │ ├── 22-901697867635371312.png │ ├── 22-9124020099798135891.png │ ├── 22-9203543330558690139.png │ ├── 22-96816251163000789.png │ ├── 222dynamic-2381226532866321571.png │ ├── 222dynamic-3600955783346224363.png │ ├── 222dynamic-3801747813210570362.png │ ├── 222dynamic-8291210888907479400.png │ ├── 222dynamic-8464373383437301006.png │ ├── 225thefrontend-1131873469982841262.png │ ├── 225thefrontend-3219513531743503804.png │ ├── 225thefrontend-4918419529169561977.png │ ├── 225thefrontend-5146191520937075414.png │ ├── 226compile-7345567143506603576.png │ ├── 226compile-931223256879963949.png │ ├── 23-1237034483645259624.png │ ├── 23-1468420283344945119.png │ ├── 23-1539613407351655567.png │ ├── 23-1822040011122505851.png │ ├── 23-2031280556622007435.png │ ├── 23-2584241647775519822.png │ ├── 23-2741827820454628413.png │ ├── 23-3030685361976493762.png │ ├── 23-3747043155035056144.png │ ├── 23-4434809189540581916.png │ ├── 23-463471582337378389.png │ ├── 23-4882192801311268958.png │ ├── 23-4892882470254506065.png │ ├── 23-4943031955755802123.png │ ├── 23-539493156854353424.png │ ├── 23-5468118257856689382.png │ ├── 23-5736906100322766460.png │ ├── 23-5814771385969442190.png │ ├── 23-6253259551905170089.png │ ├── 23-6577318282343855371.png │ ├── 23-6586763805728018642.png │ ├── 23-7466255935374283148.png │ ├── 23-7518515718458752709.png │ ├── 23-7762893621120136491.png │ ├── 23-7974878992120245803.png │ ├── 23-8116941541411865245.png │ ├── 23-8797637419045844720.png │ ├── 23-9106721915401155694.png │ ├── 233importandreadlist-2584241647775519822.png │ ├── 24-2101793461828607164.png │ ├── 24-3287449732829733262.png │ ├── 24-3772276586742963859.png │ ├── 24-3790712868165053827.png │ ├── 24-4711230888145092901.png │ ├── 24-4967182193891839896.png │ ├── 24-5031638771548097970.png │ ├── 24-5410312031510072809.png │ ├── 24-5467324402590948253.png │ ├── 24-588547064546270495.png │ ├── 24-6253915837061469610.png │ ├── 24-6486010287479323106.png │ ├── 24-6592286703145291220.png │ ├── 24-6708879871255587013.png │ ├── 24-7188863773697757790.png │ ├── 24-7298600359178422764.png │ ├── 24-8599681838666113304.png │ ├── 24-902733499638966594.png │ ├── 251compile-1541471245257336081.png │ ├── 251compile-5113809365852715934.png │ ├── 251compile-6656821290333338907.png │ ├── 251compile-7345567143506603576.png │ ├── 251compile-931223256879963949.png │ ├── 252specialarrays-7323871970862718619.png │ ├── 252specialarrays-7668129619617107787.png │ ├── 312installationbasics-3001995490788476466.png │ ├── 312installationbasics-7671577574912776238.png │ ├── 321installation-3001995490788476466.png │ ├── 321installation-7671577574912776238.png │ ├── 322pacletservers-5296222007074979075.png │ ├── 322pacletservers-7251570539084711450.png │ ├── 342functionpreparation-8579650201645694798.png │ ├── 36-1560325371174196536.png │ ├── 36-5137065355729740508.png │ ├── 36-5560197663506762293.png │ ├── 412internal-635264222018588987.png │ ├── 413frontend-4330817502451337122.png │ ├── 413frontend-6408243860282986610.png │ ├── 413frontend-6899044001331197557.png │ └── 413frontend-732377038742225435.png ├── index.html ├── index │ └── rss_feed.xml ├── mathematica-programming │ ├── assorted-tricks │ │ ├── currentvalue-and-frontendtokens.html │ │ ├── import-and-readlist.html │ │ ├── info-scraping.html │ │ ├── object-oriented-programming.html │ │ ├── trottstrzebonski.html │ │ └── villegasgayley.html │ ├── code-structure │ │ ├── contexts.html │ │ ├── error-handling.html │ │ ├── expressions-structure.html │ │ ├── flow-control.html │ │ ├── function-values-and-definition-clearing-.html │ │ ├── functions.html │ │ ├── hold-and-evaluation-order.html │ │ ├── ownvalues-set-and-setdelayed.html │ │ ├── patterns.html │ │ ├── replacement-patterns.html │ │ ├── scoping-revisited.html │ │ └── symbols-and-expressions.html │ ├── functional-programming │ │ ├── fixedpoint-and-gradients.html │ │ ├── fold--foldlist.html │ │ ├── map--scan.html │ │ ├── nest--nestlist.html │ │ ├── procedural-programming.html │ │ └── table--do.html │ ├── higher-level-functionality │ │ ├── dynamic.html │ │ ├── formatting.html │ │ ├── interfaces.html │ │ ├── packages.html │ │ ├── remote-kernels.html │ │ └── the-front-end.html │ └── performance-tuning │ │ ├── compile.html │ │ └── special-array-types.html ├── old │ └── chemical-modeling │ │ ├── atoms │ │ ├── 3.3.1-making-an-atom.md │ │ ├── 3.3.1-making-an-atom.nb │ │ ├── 3.3.2-working-with-atoms.md │ │ └── 3.3.2-working-with-atoms.nb │ │ ├── bonds │ │ ├── 3.4.1-making-a-bond.md │ │ ├── 3.4.1-making-a-bond.nb │ │ ├── 3.4.2-working-with-bonds.md │ │ └── 3.4.2-working-with-bonds.nb │ │ ├── modeling │ │ ├── 3.6.1-molecular-modeling.md │ │ └── 3.6.1-molecular-modeling.nb │ │ ├── molecules │ │ ├── 3.5.1-making-a-molecule.md │ │ ├── 3.5.1-making-a-molecule.nb │ │ ├── 3.5.2-working-with-molecules.md │ │ └── 3.5.2-working-with-molecules.nb │ │ ├── overview │ │ ├── 3.1.1-overview.md │ │ └── 3.1.1-overview.nb │ │ └── systems │ │ ├── 3.2.1-creating-a-system.md │ │ ├── 3.2.1-creating-a-system.nb │ │ ├── 3.2.2-adding-and-removing.md │ │ ├── 3.2.2-adding-and-removing.nb │ │ ├── 3.2.3-editing-a-system.md │ │ └── 3.2.3-editing-a-system.nb ├── package-usage-and-development │ ├── basics │ │ ├── packages-in-mathematica.html │ │ └── paclets.html │ ├── higher-level-features │ │ ├── function-preparation.html │ │ ├── multipackage-paclets.html │ │ ├── newstyle-packages.html │ │ └── special-paclets.html │ ├── paclet-development │ │ ├── paclet-development.html │ │ ├── paclet-distribution.html │ │ ├── pacletinfo-and-paclet-structure.html │ │ ├── sample-paclet-structures.html │ │ └── tips-and-tricks.html │ └── paclet-usage │ │ ├── installation.html │ │ └── paclet-servers.html ├── pages │ ├── about.html │ ├── contact.html │ └── toc.html ├── reference-guides │ └── undocumented-contexts │ │ ├── frontend.html │ │ ├── generalutilities.html │ │ ├── internal.html │ │ ├── language.html │ │ ├── overview.html │ │ ├── package.html │ │ └── system-*.html ├── search.html ├── site-icon.png ├── tags.html ├── tags │ ├── aliases.html │ ├── assignment.html │ ├── calculus.html │ ├── chemical-atom.html │ ├── chemical-bond.html │ ├── chemical-modeling.html │ ├── chemical-molecule.html │ ├── chemical-system.html │ ├── clear.html │ ├── compile.html │ ├── contexts.html │ ├── curated-data.html │ ├── current-value.html │ ├── development.html │ ├── distribution.html │ ├── do.html │ ├── documentation.html │ ├── dynamic.html │ ├── errors.html │ ├── evaluation-order.html │ ├── expressions.html │ ├── fixedpoint.html │ ├── flow-control.html │ ├── fold.html │ ├── foldlist.html │ ├── formatting.html │ ├── front-end-tokens.html │ ├── front-end.html │ ├── functional-programming.html │ ├── functions.html │ ├── hold.html │ ├── import.html │ ├── interfaces.html │ ├── kernels.html │ ├── keyboard-aliases.html │ ├── loops.html │ ├── map.html │ ├── nest.html │ ├── nestlist.html │ ├── object-oriented-programming.html │ ├── packages.html │ ├── packed-array.html │ ├── paclet-servers.html │ ├── paclets.html │ ├── palettes.html │ ├── patterns.html │ ├── plotting.html │ ├── procedural-programming.html │ ├── readlist.html │ ├── scan.html │ ├── scoping.html │ ├── scraping.html │ ├── special-characters.html │ ├── styles.html │ ├── symbolic-algebra.html │ ├── symbols.html │ ├── systems.html │ ├── table.html │ ├── toolbars.html │ ├── tricks.html │ ├── trott-strzebonski.html │ ├── types.html │ ├── undocumented.html │ ├── units.html │ ├── values.html │ ├── variables.html │ └── villegas-gayley.html ├── theme │ ├── css │ │ ├── bootstrap.css │ │ ├── bootstrap.min.css │ │ ├── common.css │ │ ├── font-awesome.css │ │ ├── font-awesome.min.css │ │ └── style.css │ ├── fonts │ │ ├── FontAwesome.otf │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ ├── glyphicons-halflings-regular.eot │ │ ├── glyphicons-halflings-regular.svg │ │ ├── glyphicons-halflings-regular.ttf │ │ ├── glyphicons-halflings-regular.woff │ │ ├── glyphicons-halflings-regular.woff2 │ │ └── mathematica │ │ │ ├── Mathematica-Bold.woff │ │ │ ├── Mathematica.woff │ │ │ ├── MathematicaMono-Bold.woff │ │ │ └── MathematicaMono.woff │ ├── img │ │ ├── bar.png │ │ ├── cloud-notebook-close.png │ │ ├── cloud-notebook-open.png │ │ ├── cloud-notebook-open.svg │ │ └── redbar.png │ ├── js │ │ ├── bootstrap.min.js │ │ └── jquery.min.js │ ├── prettify │ │ ├── .gitignore │ │ ├── src │ │ │ ├── lang-mma.min.js │ │ │ ├── prettify.css │ │ │ ├── prettify.js │ │ │ └── run_prettify.js │ │ └── styles │ │ │ └── prettify-mma.min.css │ ├── search │ │ ├── search_index.json │ │ ├── search_options.json │ │ ├── search_related.json │ │ ├── search_replacements.json │ │ ├── search_stems.json │ │ ├── search_stopwords.json │ │ └── search_weights.json │ └── tipuesearch │ │ ├── tipuesearch.css │ │ ├── tipuesearch.js │ │ ├── tipuesearch.min.js │ │ ├── tipuesearch_content.js │ │ └── tipuesearch_set.js ├── toc.html └── using-mathematica │ ├── basics │ ├── clear.html │ ├── errors.html │ ├── functions.html │ ├── loops-and-scoping.html │ ├── types.html │ └── variables.html │ ├── interface │ ├── documentation.html │ ├── function-aliases.html │ ├── keyboard-aliases-and-special-characters.html │ ├── palettes-and-toolbars.html │ └── styles.html │ └── useful-features │ ├── builtin-data-and-units.html │ ├── calculus.html │ ├── plotting.html │ ├── styles.html │ └── symbolic-algebra.html ├── theme ├── README.md ├── static │ ├── css │ │ ├── bootstrap.css │ │ ├── common.css │ │ ├── font-awesome.css │ │ └── style.css │ ├── fonts │ │ ├── fontawesome-webfont.eot │ │ ├── fontawesome-webfont.svg │ │ ├── fontawesome-webfont.ttf │ │ ├── fontawesome-webfont.woff │ │ ├── fontawesome-webfont.woff2 │ │ └── mathematica │ │ │ ├── Mathematica-Bold.woff │ │ │ ├── Mathematica.woff │ │ │ ├── MathematicaMono-Bold.woff │ │ │ └── MathematicaMono.woff │ ├── img │ │ ├── cloud-notebook-close.png │ │ └── cloud-notebook-open.png │ └── prettify │ │ ├── .gitignore │ │ ├── src │ │ ├── lang-mma.min.js │ │ ├── prettify.css │ │ ├── prettify.js │ │ └── run_prettify.js │ │ └── styles │ │ └── prettify-mma.min.css └── templates │ ├── _index.html │ ├── article.html │ ├── author.html │ ├── authors.html │ ├── base.html │ ├── categories.html │ ├── category.html │ ├── include │ └── config │ │ ├── icons.m │ │ ├── links.m │ │ ├── page_links.m │ │ ├── social_links.m │ │ └── stylesheets.m │ ├── index.html │ ├── indexes │ └── rss_feed.xml │ ├── page.html │ ├── subindex.html │ ├── tag.html │ └── tags.html └── tutorialHelper.nb /.gitignore: -------------------------------------------------------------------------------- 1 | *.DS_Store 2 | -------------------------------------------------------------------------------- /BuildInfo.wl: -------------------------------------------------------------------------------- 1 | (* Created with the Wolfram Language : www.wolfram.com *) 2 | {"LastBuild" -> DateObject[{2019, 4, 12, 19, 52, 3 | 34.376727`8.288839505131367}, "Instant", "Gregorian", -7.]} 4 | -------------------------------------------------------------------------------- /ContentCache.mx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/ContentCache.mx -------------------------------------------------------------------------------- /DeploymentInfo.m: -------------------------------------------------------------------------------- 1 | (* Created with the Wolfram Language : www.wolfram.com *) 2 | <|Monitor -> False, "LastDeployment" -> 3 | DateObject[{2018, 7, 20, 23, 14, 52.203718`8.470276409959554}, "Instant", 4 | "Gregorian", -7.]|> 5 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # Mathematica Tutorial 2 | 3 | This is the back matter driving the tutorial at https://www.wolframcloud.com/objects/b3m2a1/tutorial/ 4 | 5 | --- 6 | 7 | ## A (Somewhat) Quick Intro to Mathematica 8 | 9 | This is a little Mathematica tutorial written for a group of chemists I knew. Its purpose is to quickly get one used to programming in Mathematica with an eye for its various strengths, weakness, pitfalls, and idiosyncrasies. 10 | 11 | ### Navigation 12 | 13 | The tutorial is broken into sections which may be browsed in the Table of Contents. There is also navigation bar to take one between sections. 14 | 15 | ### Running Code 16 | 17 | To facilitate the ease of use, this tutorial provides a sandbox Wolfram Cloud notebook accessible via the thumb at the bottom of each tutorial page. 18 | 19 | ### Contributing 20 | 21 | If you'd like to contribute, a copy of this lives at [github.com/mresources/tutorial](https://github.com/mresources/tutorial) and any changes you make can be merged in. 22 | 23 | The website is built from a collection of Mathematica notebooks using the ```SiteBuilder``` package in [BTools](https://github.com/b3m2a1/mathematica-BTools) and so any contributions will have to be in the form of either Markdown or Markdown notebooks. 24 | 25 | ### Errors 26 | 27 | This tutorial was written very quickly. There are undoubtedly errors in it. Please feel free to report any to me on the tutorial GitHub repository and I'll try to correct them at my soonest convenience. 28 | -------------------------------------------------------------------------------- /SiteConfig.wl: -------------------------------------------------------------------------------- 1 | (* ::Package:: *) 2 | 3 | (* Created with the Wolfram Language : www.wolfram.com *) 4 | { 5 | "SiteName" -> "Mathematica Tutorial", 6 | "SiteURL"-> "https://mresources.github.io/tutorial", 7 | "PrettyPrint"->True, 8 | "CodeLanguage"->"mma", 9 | "PatchFonts"->True, 10 | "SplitInOut"->True, 11 | "AttachIDs"->True, 12 | "DeployOptions"-> 13 | { 14 | CloudConnect->"DeploymentsAccount" 15 | }, 16 | "EnableSearch"->True, 17 | "GoogleAnalytics"->"UA-103560228-2", 18 | "BuildOptions"-> 19 | { 20 | "SearchPageOptions"-> 21 | { 22 | "Options"->{"WholeWords"->False} 23 | } 24 | }, 25 | "DisqusSiteName"->"tutorial-6" 26 | } 27 | 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and wrapping the ```Head``` ```Atom``` around it: 16 | 17 | SetChemicalSystemUpValues@Atom; 18 | 19 | elementDict[el_]:=<| 20 | "Position"->{0,0,0}, 21 | "Mass"->ElementData[el,"AtomicMass"], 22 | "Radius"->ElementData[el,"VanDerWaalsRadius"], 23 | "Bonds"->{}, 24 | "Valence"->ElementData[el,"Valence"], 25 | "Color"->ColorData["Atoms"][el] 26 | |>; 27 | Atom[attrs:(_Rule|_RuleDelayed)..]:=ChemicalSystemAdd[ 28 | Atom@With[{ad=<|attrs|>}, 29 | Replace[ad["Element"],{ 30 | e_String:>Merge[{ad,elementDict[e]},First], 31 | _->$Failed}] 32 | ]]; 33 | Atom[element_String, 34 | position:{x_?NumericQ,y_?NumericQ,z_?NumericQ}:Automatic, 35 | mass:_?NumericQ:Automatic 36 | ]:=Atom@@DeleteCases[{"Element"->element,"Position"->position,"Mass"->mass},_->Automatic] -------------------------------------------------------------------------------- /content/old/chemical-modeling/atoms/3.3.2-working-with-atoms.md: -------------------------------------------------------------------------------- 1 | Title: Working with Atoms 2 | Authors: 3 | Categories: chemical-modeling,atoms 4 | Date: 2017-12-29 17:22:40 5 | ID: 3.3.2 6 | Modified: 2017-12-29 17:22:40 7 | Path: Chemical Modeling/Atoms 8 | Slug: working-with-atoms 9 | Tags: systems,object-oriented-programming,chemical-atom 10 | 11 | ‌ 12 | 13 | ## Working with Atoms 14 | 15 | Next define some general methods for working with atoms: 16 | 17 | Options[MoveAtom]={"x"->0,"y"->0,"z"->0}; 18 | MoveAtom[a_Atom, 19 | x:_?NumericQ:Automatic, 20 | y:_?NumericQ:Automatic, 21 | z:_?NumericQ:Automatic, 22 | OptionsPattern[]]:=(a["Position"]=(a["Position"]+{ 23 | Replace[x,Automatic:>OptionValue["x"]], 24 | Replace[y,Automatic:>OptionValue["y"]], 25 | Replace[z,Automatic:>OptionValue["z"]] 26 | })); 27 | Options[DisplayAtom]=Flatten@{ 28 | FilterRules[Options@Graphics3D, 29 | Except[Boxed|Lighting|ImageSize] 30 | ], 31 | Boxed->False, 32 | Lighting->"Neutral", 33 | ImageSize->Small, 34 | Scaled->.25 35 | }; 36 | DisplayAtom[a_Atom,ops:OptionsPattern[]]:=Graphics3D[{ 37 | a["Color"], 38 | Sphere[a["Position"],Replace[OptionValue[Scaled],Except[_?NumericQ]:>1]QuantityMagnitude@UnitConvert[a["Radius"],"Angstroms"]] 39 | }, 40 | FilterRules[{ops,Options@DisplayAtom},Options@Graphics3D] 41 | ]; 42 | 43 | Note that these are just a few of the functions we can define. Later, once our whole framework is set up we can define reams more. -------------------------------------------------------------------------------- /content/old/chemical-modeling/bonds/3.4.1-making-a-bond.md: -------------------------------------------------------------------------------- 1 | Title: Making a Bond 2 | Authors: 3 | Categories: chemical-modeling,bonds 4 | Date: 2017-12-29 17:24:49 5 | ID: 3.4.1 6 | Modified: 2017-12-29 17:24:49 7 | Path: Chemical Modeling/Bonds 8 | Slug: making-a-bond 9 | Tags: systems,object-oriented-programming,chemical-bond 10 | 11 | ‌ 12 | 13 | ## Making a Bond 14 | 15 | Our strategy instead will be to have the bond hold the IDs of the atoms. 16 | 17 | With that in mind, we can define our constructor: 18 | 19 | SetChemicalSystemUpValues@Bond; 20 | 21 | CanBond[a1_Atom,a2_Atom,type_:1]:=(a1=!=a2&&a1["System"]===a2["System"]&&( 22 | MatchQ[type,Except[_?NumericQ]]|| 23 | a1["Valence"]>=type&&a2["Valence"]>=type) 24 | ); 25 | Bond[a1_Atom,a2_Atom,type_:1]:=If[CanBond[a1,a2,type], 26 | If[MatchQ[type,_?NumericQ], 27 | Do[ 28 | ChemicalSystemApply[ 29 | #["Valence"]-=type&, 30 | a 31 | ], 32 | {a,{a1,a2}} 33 | ]; 34 | With[{b=ChemicalSystemAdd[ 35 | With[{s=a1["System"]},ChemicalSystem@s], 36 | Bond@<| 37 | "Atom1"->Atom[a1["ID"],a1["System"]], 38 | "Atom2"->Atom[a2["ID"],a1["System"]], 39 | "Type"->type 40 | |> 41 | ]}, 42 | AppendTo[a1["Bonds"],b]; 43 | AppendTo[a2["Bonds"],b]; 44 | b 45 | ], 46 | $Failed 47 | ] 48 | ]; -------------------------------------------------------------------------------- /content/old/chemical-modeling/bonds/3.4.2-working-with-bonds.md: -------------------------------------------------------------------------------- 1 | Title: Working with Bonds 2 | Authors: 3 | Categories: chemical-modeling,bonds 4 | Date: 2017-12-29 17:24:30 5 | ID: 3.4.1 6 | Modified: 2017-12-29 17:24:30 7 | Path: Chemical Modeling/Bonds 8 | Slug: working-with-bonds 9 | Tags: systems,object-oriented-programming,chemical-bond 10 | 11 | ‌ 12 | 13 | ## Working with Bonds 14 | 15 | Once again we can define many functions on our ```Bond``` , but for now we can just define the following: 16 | 17 | Options[DisplayBond]=Flatten@{ 18 | Options@DisplayAtom, 19 | BondWidth->Automatic 20 | }; 21 | DisplayBond[b_Bond,ops:OptionsPattern[]]:=Graphics3D[ 22 | With[{p1=b["Atom1"]["Position"], 23 | p2=b["Atom2"]["Position"], 24 | v=b["Atom2"]["Position"]-b["Atom1"]["Position"], 25 | bw=Replace[OptionValue@BondWidth,Except[_?NumericQ]:>.1]}, 26 | {EdgeForm[None], 27 | {b["Atom1"]["Color"],Cylinder[{p1,p1+1/2Norm@v*Normalize@v},bw]}, 28 | {b["Atom2"]["Color"],Cylinder[{p2,p2-1/2Norm@v*Normalize@v},bw]} 29 | }],FilterRules[{ops, 30 | Options@DisplayBond 31 | }, 32 | Options@Graphics3D] 33 | ] -------------------------------------------------------------------------------- /content/old/chemical-modeling/molecules/3.5.2-working-with-molecules.md: -------------------------------------------------------------------------------- 1 | Title: Working with Molecules 2 | Authors: 3 | Categories: chemical-modeling,molecules 4 | Date: 2017-12-29 17:25:31 5 | ID: 3.5.2 6 | Modified: 2017-12-29 17:25:31 7 | Path: Chemical Modeling/Molecules 8 | Slug: working-with-molecules 9 | Tags: systems,object-oriented-programming,chemical-molecule 10 | 11 | ‌ 12 | 13 | ## Working with Molecules 14 | 15 | Just like with the bond, let’s only write a single method for now, to display our molecule. 16 | 17 | Options[DisplayMolecule]=Options@DisplayBond; 18 | DisplayMolecule[m_Molecule,ops:OptionsPattern[]]:= 19 | With[{atoms=m["Atoms"],bonds=DeleteDuplicates@Flatten@(#["Bonds"]&/@m["Atoms"])}, 20 | Graphics3D[{ 21 | First@DisplayAtom[#]&/@atoms, 22 | First@DisplayBond[#]&/@bonds}, 23 | FilterRules[{ops, 24 | Options@DisplayMolecule 25 | }, 26 | Options@Graphics3D] 27 | ] 28 | ] -------------------------------------------------------------------------------- /content/old/chemical-modeling/overview/3.1.1-overview.md: -------------------------------------------------------------------------------- 1 | Title: Intro 2 | Authors: 3 | Categories: chemical-modeling,overview 4 | Date: 2017-12-29 17:20:36 5 | ID: 3.1.1 6 | Modified: 2017-12-29 17:20:36 7 | Path: Chemical Modeling/Overview 8 | Slug: intro 9 | Tags: 10 | 11 | ‌ 12 | 13 | ## Intro 14 | 15 | The following is a way to work atoms and molecules in Mathematica. We’ll use a combination of all the methods described in the section ```Useful Tricks ▸ Object Oriented Programming``` . 16 | 17 | This degree of complexity is unnecessary, but informative. 18 | 19 | We’ll use a symbol interface type for our systems, and a mixture of managed types and association interfaces for the rest of our objects. -------------------------------------------------------------------------------- /content/old/chemical-modeling/systems/3.2.1-creating-a-system.md: -------------------------------------------------------------------------------- 1 | Title: Creating a System 2 | Authors: 3 | Categories: chemical-modeling,systems 4 | Date: 2017-12-29 17:21:12 5 | ID: 3.2.1 6 | Modified: 2017-12-29 17:21:12 7 | Path: Chemical Modeling/Systems 8 | Slug: creating-a-system 9 | Tags: systems,object-oriented-programming,chemical-system 10 | 11 | ‌ 12 | 13 | ## Creating a system 14 | 15 | Our object manager will in turn be an object called ```ChemicalSystem``` , this time built according to the symbol interface method 16 | 17 | $ChemicalSystems=1; 18 | ChemicalSystem~SetAttributes~HoldFirst; 19 | $DefaultChemicalSystem:=ChemicalSystem[]; 20 | 21 | ChemicalSystem[]:=( 22 | $DefaultChemicalSystem= 23 | With[{ID=$ChemicalSystems++}, 24 | With[{system=Symbol["ChemicalSystem$"<>ToString@ID]}, 25 | system=<| 26 | "ID"->ID, 27 | "Index"->1|>; 28 | ChemicalSystem[system] 29 | ] 30 | ]); 31 | ChemicalSystem[ID_Integer]:=With[{c=Names@Evaluate["ChemicalSystem$"<>ToString@ID]}, 32 | If[Length@c>0, 33 | ToExpression[First@c,StandardForm,ChemicalSystem] 34 | ] 35 | ] 36 | 37 | We’ll reset a default system every time a new system is made so that this system can be used by functions by default. -------------------------------------------------------------------------------- /content/old/chemical-modeling/systems/3.2.2-adding-and-removing.md: -------------------------------------------------------------------------------- 1 | Title: Adding to and removing from a system 2 | Authors: 3 | Categories: chemical-modeling,systems 4 | Date: 2017-12-29 17:21:39 5 | ID: 3.2.2 6 | Modified: 2017-12-29 17:21:39 7 | Path: Chemical Modeling/Systems 8 | Slug: adding-to-and-removing-from-a-system 9 | Tags: systems,object-oriented-programming,chemical-system 10 | 11 | ‌ 12 | 13 | ## Adding to and removing from a system 14 | 15 | Once we’ve made a system, we can use it just like a normal object manager. 16 | 17 | Every object will get an ID to track, which will be the an incrementing index. 18 | 19 | ChemicalSystemAdd[ChemicalSystem[system_Symbol], 20 | h_[a_Association] 21 | ]:=With[{ID=system["Index"]}, 22 | system[ID]=h[Merge[{a,<|"ID"ID,"System"system["ID"]|>},Last]]; 23 | system["Index"]=ID+1; 24 | h[ID,system["ID"]] 25 | ]; 26 | 27 | ChemicalSystemDelete[ChemicalSystem[system_Symbol],ID_Integer]:=KeyDropFrom[system,ID]; 28 | 29 | ChemicalSystemAdd[e:Except[_ChemicalSystem]]:=ChemicalSystemAdd[$DefaultChemicalSystem,e] 30 | 31 | ChemicalSystemDelete[e:Except[_ChemicalSystem]]:=ChemicalSystemDelete[$DefaultChemicalSystem,e] 32 | 33 | Finally the following will be useful for accessing these objects: 34 | 35 | ChemicalSystem[system_Symbol][objectID_Integer]:=system[objectID]; -------------------------------------------------------------------------------- /content/pages/About.md: -------------------------------------------------------------------------------- 1 | Title: About 2 | Date: 2017-12-24 09:21:43 3 | Modified: 2018-07-17 12:42:44 4 | Slug: about 5 | 6 | ‌ 7 | 8 | ## A (Somewhat) Quick Intro to Mathematica 9 | 10 | This is a little Mathematica tutorial written for a group of chemists I knew. Its purpose is to quickly get one used to programming in Mathematica with an eye for its various strengths, weakness, pitfalls, and idiosyncrasies. 11 | 12 | ### Navigation 13 | 14 | The tutorial is broken into sections which may be browsed in the Table of Contents. There is also navigation bar to take one between sections. 15 | 16 | ### Running Code 17 | 18 | To facilitate the ease of use, this tutorial provides a sandbox Wolfram Cloud notebook accessible via the thumb at the bottom of each tutorial page. 19 | 20 | ### Contributing 21 | 22 | If you'd like to contribute, a copy of this lives at [github.com/mresources/tutorial](https://github.com/mresources/tutorial) and any changes you make can be merged in. 23 | 24 | The website is built from a collection of Mathematica notebooks using the ```SiteBuilder``` package in [BTools](https://github.com/b3m2a1/mathematica-BTools) and so any contributions will have to be in the form of either Markdown or Markdown notebooks. 25 | 26 | ### Errors 27 | 28 | This tutorial was written very quickly. There are undoubtedly errors in it. Please feel free to report any to me on the tutorial GitHub repository and I'll try to correct them at my soonest convenience. 29 | 30 | ‌ 31 | 32 | ## See Also: 33 | 34 | * [Other References](https://mathematica.stackexchange.com/questions/18/where-can-i-find-examples-of-good-mathematica-programming-practice) 35 | 36 | * [Common Pitfalls](https://mathematica.stackexchange.com/questions/18393/what-are-the-most-common-pitfalls-awaiting-new-users) -------------------------------------------------------------------------------- /content/pages/Contact.md: -------------------------------------------------------------------------------- 1 | Title: Contact 2 | Date: 2018-07-17 10:59:26 3 | EnableComments: True 4 | Modified: 2018-07-17 12:25:30 5 | Slug: contact 6 | 7 | ‌ 8 | 9 | ## Contact 10 | 11 | If you need to contact me, there are a few ways to do it. For many inquiries, email will work. My email is [b3m2a1@gmail.com](mailto:b3m2a1%40gmail.com) . 12 | 13 | If you want help from a more public form (recommended) you can ping me on the [Mathematica StackExchange chat](https://chat.stackexchange.com/rooms/2234/wolfram-mathematica) . 14 | 15 | Finally, I'm trying out including comments on pages, so there is a comment area at the bottom of this page. I'll see all the posted comments (and helpfully so will everyone else). If this works well I might expand this to some other pages and posts. -------------------------------------------------------------------------------- /content/posts/mathematica-programming/assorted-tricks/2.3.1-trott-strzebonski.md: -------------------------------------------------------------------------------- 1 | Title: Trott-Strzebonski 2 | Authors: 3 | Categories: mathematica-programming,assorted-tricks 4 | Date: 2017-12-29 17:17:27 5 | ID: 2.3.1 6 | Modified: 2018-07-17 14:19:18 7 | Path: Mathematica Programming/Assorted Tricks 8 | Slug: trottstrzebonski 9 | Tags: tricks,trott-strzebonski 10 | 11 | ‌ 12 | 13 | ## Trott-Strzebonski (replace with evaluation) 14 | 15 | This is the pattern we saw earlier for replacing a part of an expression with an evaluated expression: 16 | 17 | Hold[holdReplace]/.{holdReplace:>With[{eval=Integrate[Sin[θ], {θ, 2, π}]}, eval/;True]} 18 | 19 | (*Out:*) 20 | 21 | Hold[1+Cos[2]] 22 | 23 | It is a nice trick to keep in mind for those cases when you need to insert something into a held context and it would be too much of a pain to wrap everything in a ```With``` . 24 | 25 | This pattern is really a side-effect of the way scoping constructs work in Mathematica. By placing a ```Condition (/;)``` at the end of a scoping construct the whole construct evaluates or not depending on that condition. 26 | 27 | We take advantage of the fact that the scoping construct will always scan to the end if there is a condition there, plus the fact that ```With``` inserts values, not symbols, to force the evaluated chunk of code to be inserted in our otherwise unevaluated structure. 28 | 29 | ‌ 30 | 31 | ## See Also: 32 | 33 | * [https://mathematica.stackexchange.com/questions/29317/replacement-inside-held-expression](https://mathematica.stackexchange.com/questions/29317/replacement-inside-held-expression) -------------------------------------------------------------------------------- /content/posts/mathematica-programming/code-structure/2.1.1-symbols-and-expressions.md: -------------------------------------------------------------------------------- 1 | Title: Symbols and Expressions 2 | Authors: 3 | Categories: mathematica-programming,code-structure 4 | Date: 2017-12-28 17:38:57 5 | ID: 2.1.1 6 | Modified: 2018-07-18 23:47:42 7 | Path: Mathematica Programming/Code Structure/Symbols and Expressions 8 | Slug: symbols-and-expressions 9 | Tags: symbols,expressions 10 | 11 | ‌ 12 | 13 | ## Symbols and Expressions 14 | 15 | ### Symbols 16 | 17 | Mathematica has one more basic type than those mentioned before: ```Symbol``` 18 | 19 | In reality, every variable we've used and function we've defined (excluding pure functions) has been a symbol. 20 | 21 | One thing to keep in mind is that the only things that can have properties or values in Mathematica are symbols, although a symbol need not have any. 22 | 23 | All of the following are symbols: 24 | 25 | Automatic 26 | AxesLabel 27 | $ModuleNumber 28 | Rule 29 | SetDelayed 30 | 31 | (*Out:*) 32 | 33 | Automatic 34 | 35 | (*Out:*) 36 | 37 | AxesLabel 38 | 39 | (*Out:*) 40 | 41 | 1205 42 | 43 | (*Out:*) 44 | 45 | Rule 46 | 47 | (*Out:*) 48 | 49 | SetDelayed 50 | 51 | ### Expressions 52 | 53 | In Mathematica, they say everything is an expression. What this means, really, is that outside of the primitive types everything has one common form: 54 | 55 | (head)[arg1,arg2,arg2,...,argn] 56 | 57 | Furthermore, there are tools to parse these structures: 58 | 59 | {1,2,3}//FullForm 60 | 61 | (*Out:*) 62 | 63 | List[1,2,3] 64 | 65 | This even applies to things like graphics. Consider the following graphic: 66 | 67 | Graphics3D[Sphere[],Boxed->False,Lighting->"Neutral",ImageSize->Small] 68 | 69 | (*Out:*) 70 | 71 | ![211symbolsandexpressions-7059428318388094490]({filename}/img/211symbolsandexpressions-7059428318388094490.png) 72 | 73 | It is, however, still just an expression: 74 | 75 | Graphics3D[Sphere[], Boxed->False, Lighting->"Neutral", ImageSize->Small ]//FullForm 76 | 77 | (*Out:*) 78 | 79 | Graphics3D[Sphere[List[0,0,0]],Rule[Boxed,False],Rule[Lighting,"Neutral"],Rule[ImageSize,Small]] -------------------------------------------------------------------------------- /content/posts/mathematica-programming/code-structure/2.1.11-flow-control.md: -------------------------------------------------------------------------------- 1 | Title: Flow Control 2 | Authors: 3 | Categories: mathematica-programming,code-structure 4 | Date: 2018-07-16 22:25:47 5 | ID: 2.1.11 6 | Modified: 2018-07-16 23:27:15 7 | Path: Mathematica Programming/Code Structure 8 | Slug: flow-control 9 | Tags: flow-control 10 | 11 | Mathematica, being primarily a functional programming language, doesn't use standard flow-control techniques such as [```While```](https://reference.wolfram.com/language/ref/While.html) , [```Break```](https://reference.wolfram.com/language/ref/Break.html) , [```Continue```](https://reference.wolfram.com/language/ref/Continue.html) , [```etc```](https://reference.wolfram.com/language/guide/FlowControl.html) . to the same degree that a primarily procedural language like python does. 12 | 13 | Despite that, these are still useful things to know how to work with. We'll go through them pretty quickly, one-by-one. 14 | 15 | ### While 16 | 17 | Of all of these, ```While``` is likely the most common to be used, although as mentioned previously it can be emulated perhaps more cleanly by [```Do```](https://reference.wolfram.com/language/ref/Do.html) with ```Infinity``` as the iterator spec. 18 | 19 | On the other hand, particularly in the context of ```Compile``` or other cases where a predominantly procedural paradigm is use, ```While``` can be useful. 20 | 21 | ### For 22 | 23 | ```For``` is never useful. Any time it could be used ```Table``` or ```Do``` would be a better choice. 24 | 25 | ### Break / Continue / Return 26 | 27 | As noted, ```For``` isn't useful, which renders moot the primary use case of ```Break``` and ```Continue``` . They can potentially still be useful in ```Do``` and ```Table``` , though. 28 | 29 | All Mathematica functions have an implicit ```Return``` in them, which makes use of ```Return``` infrequent, but it has its place. Especially when there are multiple possible points of exit from a function ```Return``` can be highly useful. 30 | 31 | It also helpfully has a second argument specifying the scope from which the value should be returned, which can allow for somewhat more targeted usage in, say ```Do``` . 32 | 33 | Similarly, ```FixedPoint``` and other nested functional programming constructs provide support for ```Return``` , ```Break``` , and potentially ```Continue``` . -------------------------------------------------------------------------------- /content/posts/mathematica-programming/functional-programming/2.4.2-table-and-do.md: -------------------------------------------------------------------------------- 1 | Title: Table / Do 2 | Authors: 3 | Categories: mathematica-programming,functional-programming 4 | Date: 2017-12-29 17:18:59 5 | ID: 2.4.2 6 | Modified: 2017-12-29 17:18:59 7 | Path: Mathematica Programming/Functional Programming 8 | Slug: table--do 9 | Tags: functional-programming,table,do 10 | 11 | ‌ 12 | 13 | ## Table / Do 14 | 15 | Both ```Table``` and ```Do``` are only barely functional programming, still generally used procedurally, but they are simple, much more efficient alternatives to ```For``` and ```While``` loops. All they do is loop over a list or range, with optional localized loop variables: 16 | 17 | Compare: 18 | 19 | For[ i = 1, i< 10^6, i++, PrimeQ@i]// 20 | AbsoluteTiming//First 21 | 22 | (*Out:*) 23 | 24 | 0.830501` 25 | 26 | and 27 | 28 | Do[ PrimeQ@i,{i,10^6}]// 29 | AbsoluteTiming//First 30 | 31 | (*Out:*) 32 | 33 | 0.31723` 34 | 35 | It’s over 2x faster to use ```Do``` here and the result is exactly the same. Moreover, as shown before, ```Table``` will automatically accumulate the results of each step, with huge efficiency gains over the equivalent procedural construct: 36 | 37 | results={}; 38 | For[ i = 1, i< 2.5*10^4, i++,AppendTo[results, PrimeQ@i]]// 39 | AbsoluteTiming//First 40 | 41 | (*Out:*) 42 | 43 | 3.008666` 44 | 45 | Table[PrimeQ@i,{i,2.5*10^4}]// 46 | AbsoluteTiming//First 47 | 48 | (*Out:*) 49 | 50 | 0.008375` -------------------------------------------------------------------------------- /content/posts/mathematica-programming/functional-programming/2.4.3-map-and-scan.md: -------------------------------------------------------------------------------- 1 | Title: Map / Scan 2 | Authors: 3 | Categories: mathematica-programming,functional-programming 4 | Date: 2017-12-29 17:19:07 5 | ID: 2.4.3 6 | Modified: 2017-12-29 17:19:07 7 | Path: Mathematica Programming/Functional Programming 8 | Slug: map--scan 9 | Tags: functional-programming,map,scan 10 | 11 | ‌ 12 | 13 | ## Map / Scan 14 | 15 | Note that often we can even one-up ```Table``` and ```Do``` in terms of simplicity, while losing no performance. ```Map``` and ```Scan``` pass an argument from a list to a function, much as ```Table``` and ```Do``` iterate over a range or list: 16 | 17 | Table[PrimeQ@i,{i,10^6}]// 18 | AbsoluteTiming//First 19 | 20 | (*Out:*) 21 | 22 | 0.369371` 23 | 24 | compared to 25 | 26 | Map[PrimeQ,Range[10^6]]// 27 | AbsoluteTiming//First 28 | 29 | (*Out:*) 30 | 31 | 0.3625` 32 | 33 | Even better, though, ```Map``` has a more compact in-line syntax: 34 | 35 | PrimeQ/@Range[10^6]// 36 | AbsoluteTiming//First 37 | 38 | (*Out:*) 39 | 40 | 0.374421` 41 | 42 | Over time you will start thinking in this new syntax. Rather than “map prime-q over range of 10^6” you will start to think “prime-q slash at range of 10^6”. 43 | 44 | Note that both ```Map``` and ```Table``` generate output, while their equivalents ```Scan``` and ```Do``` don’t. Even though ```Scan``` does not have in-line syntax it is worth getting to know, as it can sometimes be more efficient than ```Do``` and is, of course, vastly more efficient than ```For``` -------------------------------------------------------------------------------- /content/posts/mathematica-programming/functional-programming/2.4.5-fold-and-foldlist.md: -------------------------------------------------------------------------------- 1 | Title: Fold / FoldList 2 | Authors: 3 | Categories: mathematica-programming,functional-programming 4 | Date: 2017-12-29 17:19:22 5 | ID: 2.4.5 6 | Modified: 2017-12-29 17:19:22 7 | Path: Mathematica Programming/Functional Programming 8 | Slug: fold--foldlist 9 | Tags: functional-programming,fold,foldlist 10 | 11 | ‌ 12 | 13 | ## Fold / FoldList 14 | 15 | Where ```Nest``` applies a function in to the result of the previous function call in a nested fashion, ```Fold``` and its related functions apply a function to the previous function call and simultaneously map over a list. 16 | 17 | As a very simple example we can turn an expression like this: 18 | 19 | c[a1,a2,a3,...,an] 20 | 21 | into one like 22 | 23 | c[a1][a2][a3][...][an] 24 | 25 | in one line of code. This process is closely related to the concept “currying” in standard functional programming so we can call this pseudocurrying (in fact this example comes directly from a question I asked on the Mathematica stack exchange): 26 | 27 | curry= 28 | Function[expr, 29 | Replace[expr,h_[a__]:>Fold[#1[#2]&,{h,a}]], 30 | HoldFirst]; 31 | 32 | where we take advantage of Mathematica’s ability to set attributes on pure functions. We can use this to, for example, drill into nested associations, where we will also build our association using ```Fold``` : 33 | 34 | data=Association@Fold[#2Replace[#,_Rule->Association@#]&,Range[1,10]] 35 | 36 | (*Out:*) 37 | 38 | 10987654321 39 | 40 | curry@data[10,9,8] 41 | 42 | (*Out:*) 43 | 44 | 7654321 45 | 46 | Note that Mathematica already implements this type currying for associations: 47 | 48 | data[10,9,8] 49 | 50 | (*Out:*) 51 | 52 | 7654321 53 | 54 | But for other user-defined types this can be incredibly useful -------------------------------------------------------------------------------- /content/posts/package-usage-and-development/paclet-development/3.3.4-tips-and-tricks copy.md: -------------------------------------------------------------------------------- 1 | Title: Tips and Tricks 2 | Authors: 3 | Categories: package-usage-and-development 4 | Date: 2018-07-16 16:45:30 5 | ID: 3.3.4 6 | Modified: 2018-07-16 17:58:10 7 | Path: Package Usage and Development/Paclet Development/ 8 | Slug: tips-and-tricks 9 | Tags: packages,paclets,development 10 | 11 | ‌ 12 | 13 | ## Paclet Directories 14 | 15 | When developing a paclet it can be useful to be able to test code without having to uninstall and reinstall the paclet. That's why there's a ```PacletDirectory*``` mechanism that makes this easier. We can use the function ```PacletDirectoryAdd``` to add another directory in which paclets will be looked for. When we're done with this we can use ```PacletDirectoryRemove``` to clear the directory and test what development looks like without the code being directly accessible. -------------------------------------------------------------------------------- /content/posts/reference-guides/undocumented-contexts/4.1.1-overview.md: -------------------------------------------------------------------------------- 1 | Title: Overview 2 | Authors: 3 | Categories: reference-guides,undocumented-contexts 4 | Date: 2018-07-17 01:16:59 5 | ID: 4.1.1 6 | Modified: 2018-07-17 13:10:09 7 | Path: Reference Guides/Undocumented Contexts/ 8 | Slug: overview 9 | Tags: undocumented 10 | 11 | ‌ 12 | 13 | ## Undocumented Functions 14 | 15 | Mathematica is a sprawling system and WRI loves to brag about the number of functions in it. Unfortunately it also often under-performs due to this sprawl. Targeted, highly-specialized functions get buried deep in the system, while the most general form of the function exists at the ```"System`"``` level. 16 | 17 | Therefore, a lot of using Mathematica well comes from taking advantage of the nominally undocumented, unsupported parts of the system. 18 | 19 | To make this easier, I've attempted to compile lists of useful undocumented functionality, separated by context. 20 | 21 | ‌ 22 | 23 | ## See Also: 24 | 25 | * [https://mathematica.stackexchange.com/questions/805/what-are-some-useful-undocumented-mathematica-functions](https://mathematica.stackexchange.com/questions/805/what-are-some-useful-undocumented-mathematica-functions) -------------------------------------------------------------------------------- /content/posts/reference-guides/undocumented-contexts/4.1.5-language.md: -------------------------------------------------------------------------------- 1 | Title: Language 2 | Authors: 3 | Categories: reference-guides,undocumented-contexts 4 | Date: 2018-07-17 01:16:59 5 | ID: 4.1.5 6 | Modified: 2018-07-17 15:14:58 7 | Path: Reference Guides/Undocumented Contexts/ 8 | Slug: language 9 | Tags: undocumented 10 | 11 | ‌ 12 | 13 | ## Language 14 | 15 | The ```"Language`"``` context is a relatively new addition. We won't get into it too much since it's already well handled [here](https://mathematica.stackexchange.com/questions/165843/language-documentation-project) 16 | 17 | ‌ 18 | 19 | ## See Also: 20 | 21 | * [https://mathematica.stackexchange.com/questions/165843/language-documentation-project](https://mathematica.stackexchange.com/questions/165843/language-documentation-project) 22 | 23 | * [https://mathematica.stackexchange.com/questions/152823/what-can-the-mutationhandler-functions-do](https://mathematica.stackexchange.com/questions/152823/what-can-the-mutationhandler-functions-do) 24 | 25 | * [https://mathematica.stackexchange.com/questions/52414/error-changing-dataset-using-part](https://mathematica.stackexchange.com/questions/52414/error-changing-dataset-using-part) -------------------------------------------------------------------------------- /content/posts/reference-guides/undocumented-contexts/4.1.6-general-utilities.md: -------------------------------------------------------------------------------- 1 | Title: GeneralUtilities 2 | Authors: 3 | Categories: reference-guides,undocumented-contexts 4 | Date: 2018-07-17 15:18:20 5 | ID: 4.1.6 6 | Modified: 2018-07-17 15:18:28 7 | Path: Reference Guides/Undocumented Contexts/ 8 | Slug: generalutilities 9 | Tags: undocumented 10 | 11 | ‌ 12 | 13 | ## GeneralUtilities 14 | 15 | The ```"GeneralUtilities`"``` context is new as of version 10. It provides a wide arrary of useful functionality, of which I only know a small part. 16 | 17 | ### PrintDefinitions 18 | 19 | ### PrintDefinitionsLocal 20 | 21 | ### WithMessageHandler 22 | 23 | ### ThrowFailure 24 | 25 | ### ToMessage -------------------------------------------------------------------------------- /content/posts/using-mathematica/interface/1.2.4-palettes-and-toolbars.md: -------------------------------------------------------------------------------- 1 | Title: Palettes and Toolbars 2 | Authors: 3 | Categories: using-mathematica,interface 4 | Date: 2017-12-29 01:49:00 5 | ID: 1.2.4 6 | Modified: 2017-12-29 01:49:00 7 | Path: Using Mathematica/Interface 8 | Slug: palettes-and-toolbars 9 | Tags: palettes,toolbars 10 | 11 | ‌ 12 | 13 | ## Palettes and Toolbars 14 | 15 | Mathematica provides a series of toolbars and palettes. 16 | 17 | Toolbars are found under Window ▸ Toolbar 18 | 19 | Palettes are found under the Palettes menu 20 | 21 | Most useful of the toolbars for every day use is the Formatting toolbar. 22 | 23 | All of the palettes are useful, but perhaps the Writing Assistant more so than the others. -------------------------------------------------------------------------------- /content/posts/using-mathematica/interface/1.2.5-styles.md: -------------------------------------------------------------------------------- 1 | Title: Styles 2 | Authors: 3 | Categories: using-mathematica,interface 4 | Date: 2017-12-30 02:23:05 5 | ID: 1.2.5 6 | Modified: 2018-07-18 14:36:12 7 | Path: Using Mathematica/Interface 8 | Slug: styles 9 | Tags: styles 10 | 11 | ‌ 12 | 13 | ## Styles 14 | 15 | Different cells have different styles, which you can access via the style menu ( Format ▸ Style ) or keyboard shortcuts. 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-------------------------------------------------------------------------------- 1 | Title: Making an Atom 2 | Authors: 3 | Categories: chemical-modeling,atoms 4 | Date: 2017-12-29 17:22:25 5 | ID: 3.3.1 6 | Modified: 2017-12-29 17:22:25 7 | Path: Chemical Modeling/Atoms 8 | Slug: making-an-atom 9 | Tags: systems,object-oriented-programming,chemical-atom 10 | 11 | ‌ 12 | 13 | ## Making an Atom 14 | 15 | To make an atom we start out by simply making an association to hold the properties of the atom and wrapping the ```Head``` ```Atom``` around it: 16 | 17 | SetChemicalSystemUpValues@Atom; 18 | 19 | elementDict[el_]:=<| 20 | "Position"->{0,0,0}, 21 | "Mass"->ElementData[el,"AtomicMass"], 22 | "Radius"->ElementData[el,"VanDerWaalsRadius"], 23 | "Bonds"->{}, 24 | "Valence"->ElementData[el,"Valence"], 25 | "Color"->ColorData["Atoms"][el] 26 | |>; 27 | Atom[attrs:(_Rule|_RuleDelayed)..]:=ChemicalSystemAdd[ 28 | Atom@With[{ad=<|attrs|>}, 29 | Replace[ad["Element"],{ 30 | e_String:>Merge[{ad,elementDict[e]},First], 31 | _->$Failed}] 32 | ]]; 33 | Atom[element_String, 34 | position:{x_?NumericQ,y_?NumericQ,z_?NumericQ}:Automatic, 35 | mass:_?NumericQ:Automatic 36 | ]:=Atom@@DeleteCases[{"Element"->element,"Position"->position,"Mass"->mass},_->Automatic] -------------------------------------------------------------------------------- /docs/old/chemical-modeling/atoms/3.3.2-working-with-atoms.md: -------------------------------------------------------------------------------- 1 | Title: Working with Atoms 2 | Authors: 3 | Categories: chemical-modeling,atoms 4 | Date: 2017-12-29 17:22:40 5 | ID: 3.3.2 6 | Modified: 2017-12-29 17:22:40 7 | Path: Chemical Modeling/Atoms 8 | Slug: working-with-atoms 9 | Tags: systems,object-oriented-programming,chemical-atom 10 | 11 | ‌ 12 | 13 | ## Working with Atoms 14 | 15 | Next define some general methods for working with atoms: 16 | 17 | Options[MoveAtom]={"x"->0,"y"->0,"z"->0}; 18 | MoveAtom[a_Atom, 19 | x:_?NumericQ:Automatic, 20 | y:_?NumericQ:Automatic, 21 | z:_?NumericQ:Automatic, 22 | OptionsPattern[]]:=(a["Position"]=(a["Position"]+{ 23 | Replace[x,Automatic:>OptionValue["x"]], 24 | Replace[y,Automatic:>OptionValue["y"]], 25 | Replace[z,Automatic:>OptionValue["z"]] 26 | })); 27 | Options[DisplayAtom]=Flatten@{ 28 | FilterRules[Options@Graphics3D, 29 | Except[Boxed|Lighting|ImageSize] 30 | ], 31 | Boxed->False, 32 | Lighting->"Neutral", 33 | ImageSize->Small, 34 | Scaled->.25 35 | }; 36 | DisplayAtom[a_Atom,ops:OptionsPattern[]]:=Graphics3D[{ 37 | a["Color"], 38 | Sphere[a["Position"],Replace[OptionValue[Scaled],Except[_?NumericQ]:>1]QuantityMagnitude@UnitConvert[a["Radius"],"Angstroms"]] 39 | }, 40 | FilterRules[{ops,Options@DisplayAtom},Options@Graphics3D] 41 | ]; 42 | 43 | Note that these are just a few of the functions we can define. Later, once our whole framework is set up we can define reams more. -------------------------------------------------------------------------------- /docs/old/chemical-modeling/bonds/3.4.1-making-a-bond.md: -------------------------------------------------------------------------------- 1 | Title: Making a Bond 2 | Authors: 3 | Categories: chemical-modeling,bonds 4 | Date: 2017-12-29 17:24:49 5 | ID: 3.4.1 6 | Modified: 2017-12-29 17:24:49 7 | Path: Chemical Modeling/Bonds 8 | Slug: making-a-bond 9 | Tags: systems,object-oriented-programming,chemical-bond 10 | 11 | ‌ 12 | 13 | ## Making a Bond 14 | 15 | Our strategy instead will be to have the bond hold the IDs of the atoms. 16 | 17 | With that in mind, we can define our constructor: 18 | 19 | SetChemicalSystemUpValues@Bond; 20 | 21 | CanBond[a1_Atom,a2_Atom,type_:1]:=(a1=!=a2&&a1["System"]===a2["System"]&&( 22 | MatchQ[type,Except[_?NumericQ]]|| 23 | a1["Valence"]>=type&&a2["Valence"]>=type) 24 | ); 25 | Bond[a1_Atom,a2_Atom,type_:1]:=If[CanBond[a1,a2,type], 26 | If[MatchQ[type,_?NumericQ], 27 | Do[ 28 | ChemicalSystemApply[ 29 | #["Valence"]-=type&, 30 | a 31 | ], 32 | {a,{a1,a2}} 33 | ]; 34 | With[{b=ChemicalSystemAdd[ 35 | With[{s=a1["System"]},ChemicalSystem@s], 36 | Bond@<| 37 | "Atom1"->Atom[a1["ID"],a1["System"]], 38 | "Atom2"->Atom[a2["ID"],a1["System"]], 39 | "Type"->type 40 | |> 41 | ]}, 42 | AppendTo[a1["Bonds"],b]; 43 | AppendTo[a2["Bonds"],b]; 44 | b 45 | ], 46 | $Failed 47 | ] 48 | ]; -------------------------------------------------------------------------------- /docs/old/chemical-modeling/bonds/3.4.2-working-with-bonds.md: -------------------------------------------------------------------------------- 1 | Title: Working with Bonds 2 | Authors: 3 | Categories: chemical-modeling,bonds 4 | Date: 2017-12-29 17:24:30 5 | ID: 3.4.1 6 | Modified: 2017-12-29 17:24:30 7 | Path: Chemical Modeling/Bonds 8 | Slug: working-with-bonds 9 | Tags: systems,object-oriented-programming,chemical-bond 10 | 11 | ‌ 12 | 13 | ## Working with Bonds 14 | 15 | Once again we can define many functions on our ```Bond``` , but for now we can just define the following: 16 | 17 | Options[DisplayBond]=Flatten@{ 18 | Options@DisplayAtom, 19 | BondWidth->Automatic 20 | }; 21 | DisplayBond[b_Bond,ops:OptionsPattern[]]:=Graphics3D[ 22 | With[{p1=b["Atom1"]["Position"], 23 | p2=b["Atom2"]["Position"], 24 | v=b["Atom2"]["Position"]-b["Atom1"]["Position"], 25 | bw=Replace[OptionValue@BondWidth,Except[_?NumericQ]:>.1]}, 26 | {EdgeForm[None], 27 | {b["Atom1"]["Color"],Cylinder[{p1,p1+1/2Norm@v*Normalize@v},bw]}, 28 | {b["Atom2"]["Color"],Cylinder[{p2,p2-1/2Norm@v*Normalize@v},bw]} 29 | }],FilterRules[{ops, 30 | Options@DisplayBond 31 | }, 32 | Options@Graphics3D] 33 | ] -------------------------------------------------------------------------------- /docs/old/chemical-modeling/molecules/3.5.2-working-with-molecules.md: -------------------------------------------------------------------------------- 1 | Title: Working with Molecules 2 | Authors: 3 | Categories: chemical-modeling,molecules 4 | Date: 2017-12-29 17:25:31 5 | ID: 3.5.2 6 | Modified: 2017-12-29 17:25:31 7 | Path: Chemical Modeling/Molecules 8 | Slug: working-with-molecules 9 | Tags: systems,object-oriented-programming,chemical-molecule 10 | 11 | ‌ 12 | 13 | ## Working with Molecules 14 | 15 | Just like with the bond, let’s only write a single method for now, to display our molecule. 16 | 17 | Options[DisplayMolecule]=Options@DisplayBond; 18 | DisplayMolecule[m_Molecule,ops:OptionsPattern[]]:= 19 | With[{atoms=m["Atoms"],bonds=DeleteDuplicates@Flatten@(#["Bonds"]&/@m["Atoms"])}, 20 | Graphics3D[{ 21 | First@DisplayAtom[#]&/@atoms, 22 | First@DisplayBond[#]&/@bonds}, 23 | FilterRules[{ops, 24 | Options@DisplayMolecule 25 | }, 26 | Options@Graphics3D] 27 | ] 28 | ] -------------------------------------------------------------------------------- /docs/old/chemical-modeling/overview/3.1.1-overview.md: -------------------------------------------------------------------------------- 1 | Title: Intro 2 | Authors: 3 | Categories: chemical-modeling,overview 4 | Date: 2017-12-29 17:20:36 5 | ID: 3.1.1 6 | Modified: 2017-12-29 17:20:36 7 | Path: Chemical Modeling/Overview 8 | Slug: intro 9 | Tags: 10 | 11 | ‌ 12 | 13 | ## Intro 14 | 15 | The following is a way to work atoms and molecules in Mathematica. We’ll use a combination of all the methods described in the section ```Useful Tricks ▸ Object Oriented Programming``` . 16 | 17 | This degree of complexity is unnecessary, but informative. 18 | 19 | We’ll use a symbol interface type for our systems, and a mixture of managed types and association interfaces for the rest of our objects. -------------------------------------------------------------------------------- /docs/old/chemical-modeling/systems/3.2.1-creating-a-system.md: -------------------------------------------------------------------------------- 1 | Title: Creating a System 2 | Authors: 3 | Categories: chemical-modeling,systems 4 | Date: 2017-12-29 17:21:12 5 | ID: 3.2.1 6 | Modified: 2017-12-29 17:21:12 7 | Path: Chemical Modeling/Systems 8 | Slug: creating-a-system 9 | Tags: systems,object-oriented-programming,chemical-system 10 | 11 | ‌ 12 | 13 | ## Creating a system 14 | 15 | Our object manager will in turn be an object called ```ChemicalSystem``` , this time built according to the symbol interface method 16 | 17 | $ChemicalSystems=1; 18 | ChemicalSystem~SetAttributes~HoldFirst; 19 | $DefaultChemicalSystem:=ChemicalSystem[]; 20 | 21 | ChemicalSystem[]:=( 22 | $DefaultChemicalSystem= 23 | With[{ID=$ChemicalSystems++}, 24 | With[{system=Symbol["ChemicalSystem$"<>ToString@ID]}, 25 | system=<| 26 | "ID"->ID, 27 | "Index"->1|>; 28 | ChemicalSystem[system] 29 | ] 30 | ]); 31 | ChemicalSystem[ID_Integer]:=With[{c=Names@Evaluate["ChemicalSystem$"<>ToString@ID]}, 32 | If[Length@c>0, 33 | ToExpression[First@c,StandardForm,ChemicalSystem] 34 | ] 35 | ] 36 | 37 | We’ll reset a default system every time a new system is made so that this system can be used by functions by default. -------------------------------------------------------------------------------- /docs/old/chemical-modeling/systems/3.2.2-adding-and-removing.md: -------------------------------------------------------------------------------- 1 | Title: Adding to and removing from a system 2 | Authors: 3 | Categories: chemical-modeling,systems 4 | Date: 2017-12-29 17:21:39 5 | ID: 3.2.2 6 | Modified: 2017-12-29 17:21:39 7 | Path: Chemical Modeling/Systems 8 | Slug: adding-to-and-removing-from-a-system 9 | Tags: systems,object-oriented-programming,chemical-system 10 | 11 | ‌ 12 | 13 | ## Adding to and removing from a system 14 | 15 | Once we’ve made a system, we can use it just like a normal object manager. 16 | 17 | Every object will get an ID to track, which will be the an incrementing index. 18 | 19 | ChemicalSystemAdd[ChemicalSystem[system_Symbol], 20 | h_[a_Association] 21 | ]:=With[{ID=system["Index"]}, 22 | system[ID]=h[Merge[{a,<|"ID"ID,"System"system["ID"]|>},Last]]; 23 | system["Index"]=ID+1; 24 | h[ID,system["ID"]] 25 | ]; 26 | 27 | ChemicalSystemDelete[ChemicalSystem[system_Symbol],ID_Integer]:=KeyDropFrom[system,ID]; 28 | 29 | ChemicalSystemAdd[e:Except[_ChemicalSystem]]:=ChemicalSystemAdd[$DefaultChemicalSystem,e] 30 | 31 | ChemicalSystemDelete[e:Except[_ChemicalSystem]]:=ChemicalSystemDelete[$DefaultChemicalSystem,e] 32 | 33 | Finally the following will be useful for accessing these objects: 34 | 35 | ChemicalSystem[system_Symbol][objectID_Integer]:=system[objectID]; -------------------------------------------------------------------------------- /docs/site-icon.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/docs/site-icon.png -------------------------------------------------------------------------------- /docs/theme/css/common.css: -------------------------------------------------------------------------------- 1 | @font-face { 2 | font-family: 'Mathematica'; 3 | src: url('../fonts/mathematica/Mathematica.eot'); 4 | src: url('../fonts/mathematica/Mathematica.eot?#iefix') format('embedded-opentype'), 5 | url('../fonts/mathematica/Mathematica.woff') format('woff'), 6 | 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-------------------------------------------------------------------------------- 1 | { 2 | "wholeWords":false 3 | } -------------------------------------------------------------------------------- /docs/theme/search/search_related.json: -------------------------------------------------------------------------------- 1 | { 2 | "Related":[] 3 | } -------------------------------------------------------------------------------- /docs/theme/search/search_replacements.json: -------------------------------------------------------------------------------- 1 | { 2 | "words":[] 3 | } -------------------------------------------------------------------------------- /docs/theme/search/search_stems.json: -------------------------------------------------------------------------------- 1 | { 2 | "words":[] 3 | } -------------------------------------------------------------------------------- /docs/theme/search/search_stopwords.json: -------------------------------------------------------------------------------- 1 | [] -------------------------------------------------------------------------------- /docs/theme/search/search_weights.json: -------------------------------------------------------------------------------- 1 | { 2 | "weight":[] 3 | } -------------------------------------------------------------------------------- /docs/theme/tipuesearch/tipuesearch_content.js: -------------------------------------------------------------------------------- 1 | 2 | var tipuesearch; 3 | $.getJSON(search_SiteURL+"/theme/search/search_index.json", 4 | function(data) { tipuesearch = data } 5 | ); 6 | 7 | var tipuesearch_options; 8 | $.getJSON(search_SiteURL+"/theme/search/search_options.json", 9 | function(data) { tipuesearch_options = data } 10 | ); 11 | -------------------------------------------------------------------------------- /docs/theme/tipuesearch/tipuesearch_set.js: -------------------------------------------------------------------------------- 1 | 2 | /* 3 | Tipue Search 7.0 4 | Copyright (c) 2018 Tipue 5 | Tipue Search is released under the MIT License 6 | http://www.tipue.com/search 7 | */ 8 | 9 | // Stop words 10 | 11 | var tipuesearch_stop_words; 12 | $.getJSON(search_SiteURL+"/theme/search/search_stopwords.json", 13 | function(data) { tipuesearch_stop_words = data } 14 | ); 15 | 16 | 17 | // Word replace 18 | 19 | var tipuesearch_replace; 20 | $.getJSON(search_SiteURL+"/theme/search/search_replacements.json", 21 | function(data) { tipuesearch_replace = data } 22 | ); 23 | 24 | // Weighting 25 | 26 | var tipuesearch_weight; 27 | $.getJSON(search_SiteURL+"/theme/search/search_weights.json", 28 | function(data) { tipuesearch_weight = data } 29 | ); 30 | 31 | // Illogical stemming 32 | 33 | var tipuesearch_stem; 34 | $.getJSON(search_SiteURL+"/theme/search/search_stems.json", 35 | function(data) { tipuesearch_stem = data } 36 | ); 37 | 38 | 39 | // Related 40 | 41 | var tipuesearch_related; 42 | $.getJSON(search_SiteURL+"/theme/search/search_related.json", 43 | function(data) { tipuesearch_related = data } 44 | ); 45 | 46 | // Internal strings 47 | 48 | var tipuesearch_string_1 = 'No title'; 49 | var tipuesearch_string_2 = 'Showing results for'; 50 | var tipuesearch_string_3 = 'Search instead for'; 51 | var tipuesearch_string_4 = '1 result'; 52 | var tipuesearch_string_5 = 'results'; 53 | var tipuesearch_string_6 = '<'; 54 | var tipuesearch_string_7 = '>'; 55 | var tipuesearch_string_8 = 'Nothing found.'; 56 | var tipuesearch_string_9 = 'Common words are largely ignored.'; 57 | var tipuesearch_string_10 = 'Related'; 58 | var tipuesearch_string_11 = 'Search too short. Should be one character or more.'; 59 | var tipuesearch_string_12 = 'Search too short. Should be'; 60 | var tipuesearch_string_13 = 'characters or more.'; 61 | var tipuesearch_string_14 = 'seconds'; 62 | var tipuesearch_string_15 = 'Open Image'; 63 | var tipuesearch_string_16 = 'Goto Page'; 64 | 65 | 66 | // Internals 67 | 68 | 69 | // Timer for showTime 70 | 71 | var startTimer = new Date().getTime(); 72 | -------------------------------------------------------------------------------- /theme/README.md: -------------------------------------------------------------------------------- 1 | # SiteBuilder Themes 2 | 3 | The site builder package uses different themes to make its sites look a specific way 4 | 5 | The core of these themes are static content (e.g. css, js, etc.) and templates 6 | 7 | The templates are Wolfram XML templates that get processed into raw HTML. 8 | In general there will be a base.html template and others will inherit from that. 9 | There are a few things made available to the templates as they build: 10 | 11 | * Content stack 12 | * Template function library 13 | 14 | ## The stack 15 | 16 | The stack is generally accessed via the # parameter. 17 | 18 | Looking at the minimal theme you'll see that the #Articles accessor is passed. 19 | This gives all the bits in the stack with the article.html template in its 20 | #Templates parameter 21 | 22 | Every entry in the content stack has the following parameters: 23 | * #Summary 24 | * #Date 25 | * #Content 26 | * #URL 27 | * #Slug 28 | * #Templates 29 | * #FilePath 30 | * #SourceFile 31 | * #SiteName 32 | * #SiteURL 33 | 34 | Then the agg stack provides aggregated content. It has the following: 35 | * #Pages -- Entries with the page template 36 | * #Articles -- Entries with the article template 37 | * #Archives -- All entries sorted by date 38 | * #ContentStack -- Accessor function to entries in the stack 39 | * #ContentData -- Accessor function to attributes of pages in the stack 40 | * #SelectObjects -- Picks objects whose templates contain a passed template 41 | * #NextObjectBy -- Returns the next entry for a given sort and type 42 | * #PreviousObjectBy -- Returns the previous entry for a given sort and type 43 | 44 | ## Template function library 45 | 46 | This is a set of functions accessed via the $$templateLib symbol 47 | These functions provide cleaner access to higher-level WL features than templates 48 | -------------------------------------------------------------------------------- /theme/static/css/common.css: -------------------------------------------------------------------------------- 1 | @font-face { 2 | font-family: 'Mathematica'; 3 | src: url('../fonts/mathematica/Mathematica.eot'); 4 | src: url('../fonts/mathematica/Mathematica.eot?#iefix') format('embedded-opentype'), 5 | url('../fonts/mathematica/Mathematica.woff') format('woff'), 6 | url('../fonts/mathematica/Mathematica.ttf') format('truetype'); 7 | font-weight: normal; 8 | } 9 | 10 | @font-face { 11 | font-family: 'Mathematica'; 12 | src: url('../fonts/mathematica/Mathematica-Bold.eot'); 13 | src: url('../fonts/mathematica/Mathematica-Bold.eot?#iefix') format('embedded-opentype'), 14 | url('../fonts/mathematica/Mathematica-Bold.woff') format('woff'), 15 | url('../fonts/mathematica/Mathematica-Bold.ttf') format('truetype'); 16 | font-weight: bold; 17 | } 18 | 19 | @font-face { 20 | font-family: 'MathematicaMono'; 21 | src: url('../fonts/mathematica/MathematicaMono.eot'); 22 | src: url('../fonts/mathematica/MathematicaMono.eot?#iefix') format('embedded-opentype'), 23 | url('../fonts/mathematica/MathematicaMono.woff') format('woff'), 24 | url('../fonts/mathematica/MathematicaMono.ttf') format('truetype'); 25 | font-weight: normal; 26 | } 27 | 28 | @font-face { 29 | font-family: 'MathematicaMono'; 30 | src: url('../fonts/mathematica/MathematicaMono-Bold.eot'); 31 | src: url('../fonts/mathematica/MathematicaMono-Bold.eot?#iefix') format('embedded-opentype'), 32 | url('../fonts/mathematica/MathematicaMono-Bold.woff') format('woff'), 33 | url('../fonts/mathematica/MathematicaMono-Bold.ttf') format('truetype'); 34 | font-weight: bold; 35 | } 36 | -------------------------------------------------------------------------------- /theme/static/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/theme/static/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /theme/static/fonts/fontawesome-webfont.ttf: 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/theme/static/fonts/mathematica/Mathematica-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/theme/static/fonts/mathematica/Mathematica-Bold.woff -------------------------------------------------------------------------------- /theme/static/fonts/mathematica/Mathematica.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/theme/static/fonts/mathematica/Mathematica.woff -------------------------------------------------------------------------------- /theme/static/fonts/mathematica/MathematicaMono-Bold.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/theme/static/fonts/mathematica/MathematicaMono-Bold.woff -------------------------------------------------------------------------------- /theme/static/fonts/mathematica/MathematicaMono.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/theme/static/fonts/mathematica/MathematicaMono.woff -------------------------------------------------------------------------------- /theme/static/img/cloud-notebook-close.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/theme/static/img/cloud-notebook-close.png -------------------------------------------------------------------------------- /theme/static/img/cloud-notebook-open.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/mresources/tutorial/39c5860da74b0d0a6cc47899b37606030e9f6579/theme/static/img/cloud-notebook-open.png -------------------------------------------------------------------------------- /theme/static/prettify/.gitignore: -------------------------------------------------------------------------------- 1 | # temporary files 2 | *~ 3 | *.swp 4 | .DS_Store 5 | 6 | # package managers 7 | /node_modules/ 8 | /bower_components/ 9 | npm-debug.log 10 | .bower.json 11 | 12 | # generated files 13 | #/src/prettify.js 14 | #/src/run_prettify.js 15 | #/loader/*.js 16 | #/loader/*.css 17 | #/loader/skins/*.css 18 | #/distrib/*.zip 19 | -------------------------------------------------------------------------------- /theme/static/prettify/styles/prettify-mma.min.css: -------------------------------------------------------------------------------- 1 | .pln{color:#326ab3}@media screen{.str{color:#833}.mma_msg{color:#833;font-style:italic}.mma_use{color:#833;font-weight:bold}.mma_iot{color:#555;font-weight:bold}.atn{color:#326ab3;font-weight:bold}.com{color:#555}.kwd{color:#000}.atv{color:#060;font-style:italic}.atn{color:#326ab3;font-weight:bold}.tag{color:#000;font-weight:bold}.lit{color:#833}.pln{color:#326ab3}.pun{color:#000}}@media print,projection{.str,.use,.msg{color:#833}.com{color:#555}.kwd{color:#000;font-weight:bold}.atv{color:#060;font-style:italic}.tag{color:#000;font-weight:bold}.lit{color:#833}.mma_use{color:#833;font-weight:bold}.mma_msg{color:#833;font-style:italic}.mma_iot{color:#555;font-weight:bold}.atn{color:#326ab3;font-weight:bold}.pun{color:#000}}pre.prettyprint{background:#EEE;padding:20px}ol.linenums{margin-top:0;margin-bottom:0}li.L0,li.L1,li.L2,li.L3,li.L5,li.L6,li.L7,li.L8{list-style-type:none}li.L1,li.L3,li.L5,li.L7,li.L9{background:#eee} -------------------------------------------------------------------------------- /theme/templates/author.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | | $$templateLib["getSiteName"][#] 5 | 6 | 7 | 8 | Author: 9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /theme/templates/authors.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Authors 5 | 6 | 7 | 8 | Authors 9 | 10 | 11 | 12 | 13 | 14 | 15 | 19 | 20 | 21 | 22 |
16 | 17 | #["Author"] 18 | Length@#["Articles"]
23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /theme/templates/categories.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Categories 5 | 6 | 7 | 8 | Categories 9 | 10 | 11 | 12 | 13 | 14 | 15 | 19 | 20 | 21 | 22 |
16 | 17 | #["Category"] 18 | Length@#["Articles"]
23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /theme/templates/category.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | | $$templateLib["getSiteName"][#] 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /theme/templates/include/config/icons.m: -------------------------------------------------------------------------------- 1 | { 2 | <| 3 | "type"->"link", 4 | "rel"->"apple-touch-icon", 5 | "href"->"apple-touch-icon.png", 6 | "sizes"->"180x180" 7 | |>, 8 | <| 9 | "type"->"link", 10 | "rel"->"icon", 11 | "href"->"favicon-32x32.png", 12 | "sizes"->"32x32" 13 | |>, 14 | <| 15 | "type"->"link", 16 | "rel"->"icon", 17 | "href"->"favicon-16x16.png", 18 | "sizes"->"16x16" 19 | |>, 20 | <| 21 | "type"->"link", 22 | "rel"->"manifest", 23 | "href"->"manifest.json" 24 | |> 25 | } 26 | -------------------------------------------------------------------------------- /theme/templates/include/config/links.m: -------------------------------------------------------------------------------- 1 | { 2 | <| 3 | "href"->"https://www.wolfram.com", 4 | "body"->"Wolfram" 5 | |> 6 | } 7 | -------------------------------------------------------------------------------- /theme/templates/include/config/page_links.m: -------------------------------------------------------------------------------- 1 | { 2 | <| 3 | "href"->"pages/about.html", 4 | "body"->"About" 5 | |>, 6 | <| 7 | "href"->"pages/toc.html", 8 | "body"->"Table Of Contents" 9 | |>, 10 | <| 11 | "href"->"categories.html", 12 | "body"->"Categories" 13 | |>, 14 | <| 15 | "href"->"tags.html", 16 | "body"->"Tags" 17 | |>, 18 | <| 19 | "href"->"pages/contact.html", 20 | "body"->"Contact" 21 | |> 22 | } 23 | -------------------------------------------------------------------------------- /theme/templates/include/config/social_links.m: -------------------------------------------------------------------------------- 1 | { 2 | <| 3 | "href"->"https://mathematica.stackexchange.com", 4 | "body"->"StackExchange" 5 | |> 6 | } 7 | -------------------------------------------------------------------------------- /theme/templates/include/config/stylesheets.m: -------------------------------------------------------------------------------- 1 | { 2 | "bootstrap.css", 3 | "font-awesome.css", 4 | "https://www.w3schools.com/w3css/4/w3.css", 5 | "https://fonts.googleapis.com/css?family=Robot", 6 | "https://fonts.googleapis.com/css?family=Montserrat", 7 | "https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css", 8 | "https://fonts.googleapis.com/css?family=Source+Code+Pro", 9 | "https://reference.wolfram.com/language-assets/css/special-styles.css", 10 | "common.css", 11 | "style.css" 12 | } 13 | -------------------------------------------------------------------------------- /theme/templates/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This generates the index.html page 4 | 5 | 6 | 7 | 8 | 9 | 10 | (*This is debug code*) 11 | Echo@#Articles 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | "Description" 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | "SiteSubtitle" 34 | 35 | 36 | 37 | 38 | $$templateLib["getSiteName"][#] 39 | | 40 | 41 | 42 | 43 | $$templateLib["getSiteName"][#] 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | pages/about.html 54 | 55 |
56 |
57 | 58 | $$templateLib["extractBody"]@ 59 | #ContentData["pages/about.html"]["RawXML"] 60 | 61 |
62 |
63 | 64 | 65 | 66 | 67 | 68 | 69 | -------------------------------------------------------------------------------- /theme/templates/indexes/rss_feed.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | This generates the rss_feed for the page 4 | 5 | 6 | 7 | 8 | 9 | Mathematica Tutorial 10 | 11 | 12 | 13 | /favicon-32x32.png 14 | Mathematica Tutorial 15 | 16 | 17 | Mathematica Tutorial 18 | 19 | 20 | 21 | 22 | -------------------------------------------------------------------------------- /theme/templates/page.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | Summary 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 18 | 19 | 20 | 21 | 22 | 23 | $$templateLib["getPageTitle"][#] 24 | | 25 | $$templateLib["getSiteName"][#] 26 | 27 | 28 | 29 | 30 |
31 |
32 | 33 |
34 |
35 | 36 | 37 | 38 | 39 | 40 | 41 | -------------------------------------------------------------------------------- /theme/templates/subindex.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | This generates a subindex page 4 | 5 | 6 | 7 | 8 | 9 | 10 | (*This is debug code*) 11 | Echo@#Articles 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | "SiteSubtitle" 22 | 23 | 24 | 25 | 26 | $$templateLib["getSiteName"][#] 27 | | 28 | 29 | 30 | 31 | $$templateLib["getSiteName"][#] 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 |
41 | 42 |
43 | 66 |
67 | 68 |
69 | 70 | 71 | 72 | 73 | -------------------------------------------------------------------------------- /theme/templates/tag.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Articles | $$templateLib["getSiteName"][#] 5 | 6 | 7 | 8 | Tagged: 9 | 10 | 11 | 12 | -------------------------------------------------------------------------------- /theme/templates/tags.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | Tags 5 | 6 | 7 | 8 | Tags 9 | 10 | 11 | 12 | 13 | 14 | 15 | 19 | 24 | 25 | 26 |
16 | 17 | #["Tag"] 18 | 20 | 21 | Length@#["Articles"] 22 | 23 |
27 | 28 | 29 | 30 | --------------------------------------------------------------------------------