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< body >
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< div id = "org-div-home-and-up" >
< a accesskey = "h" href = "" > UP < / a >
|
< a accesskey = "H" href = "index.html" > HOME < / a >
< / div > < div id = "content" >
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< h1 class = "title" > Common< / h1 >
< div id = "table-of-contents" >
< h2 > Table of Contents< / h2 >
< div id = "text-table-of-contents" >
< ul >
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< li > < a href = "#org6df3964" > 1. Summary< / a > < / li >
< li > < a href = "#org5753373" > 2. Electrons< / a >
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< ul >
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< li > < a href = "#org25fbdd2" > 2.1. Type< / a > < / li >
< li > < a href = "#org5d0f6c5" > 2.2. Creation< / a > < / li >
< li > < a href = "#org6c90a8b" > 2.3. Access< / a > < / li >
< li > < a href = "#orgd40dbf2" > 2.4. Printers< / a > < / li >
< li > < a href = "#org20072b6" > 2.5. Tests< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#orgb411aa8" > 3. Element< / a >
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< ul >
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< li > < a href = "#org7b29939" > 3.1. Type< / a > < / li >
< li > < a href = "#org46b8b47" > 3.2. Conversion< / a > < / li >
< li > < a href = "#org1d70546" > 3.3. Database information< / a > < / li >
< li > < a href = "#orgd5738cc" > 3.4. Printers< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#org61359db" > 4. Atomic mass< / a > < / li >
< li > < a href = "#org3653358" > 5. Nuclei< / a >
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< ul >
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< li > < a href = "#orgdc5c638" > 5.1. Type< / a > < / li >
< li > < a href = "#org795558e" > 5.2. xyz file lexer/parser< / a >
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< ul >
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< li > < a href = "#orgfa3e0b9" > 5.2.1. Lexer< / a > < / li >
< li > < a href = "#orge4240df" > 5.2.2. Parser< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#orgfe57c35" > 5.3. Conversion< / a > < / li >
< li > < a href = "#org14de381" > 5.4. Query< / a > < / li >
< li > < a href = "#org9224cc6" > 5.5. TREXIO< / a >
< ul >
< li > < a href = "#org7046b2a" > 5.5.1. Read< / a > < / li >
< li > < a href = "#orgd1b3675" > 5.5.2. Write< / a > < / li >
< / ul >
< / li >
< li > < a href = "#org3ece660" > 5.6. Printers< / a > < / li >
< li > < a href = "#org6a90479" > 5.7. Tests< / a > < / li >
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< / ul >
< / li >
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< li > < a href = "#org46003da" > 6. Z-matrix< / a >
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< ul >
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< li > < a href = "#org5fcb7ed" > 6.1. Type< / a > < / li >
< li > < a href = "#orga6c6d0e" > 6.2. Conversion< / a > < / li >
< li > < a href = "#org37a7c2e" > 6.3. Printers< / a > < / li >
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< / ul >
< / li >
< / ul >
< / div >
< / div >
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< div id = "outline-container-org6df3964" class = "outline-2" >
< h2 id = "org6df3964" > < span class = "section-number-2" > 1< / span > Summary< / h2 >
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< / div >
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< h2 id = "org5753373" > < span class = "section-number-2" > 2< / span > Electrons< / h2 >
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< div class = "outline-text-2" id = "text-2" >
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< p >
Data structure which contains the number of α and β electrons.
< / p >
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< div id = "outline-container-org25fbdd2" class = "outline-3" >
< h3 id = "org25fbdd2" > < span class = "section-number-3" > 2.1< / span > Type< / h3 >
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< pre class = "src src-ocaml" id = "org59c86ec" > < span class = "org-tuareg-font-lock-governing" > type< / span > < span class = "org-type" > t< / span >
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< div id = "outline-container-org5d0f6c5" class = "outline-3" >
< h3 id = "org5d0f6c5" > < span class = "section-number-3" > 2.2< / span > Creation< / h3 >
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< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > open < / span > < span class = "org-tuareg-font-lock-module" > Common< / span >
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > make< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > int < span class = "org-tuareg-font-lock-operator" > -> < / span > int < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_atoms< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-label" > ?multiplicity< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > int < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-label" > ?charge< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > int < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-module" > Nuclei.< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-comment-delimiter" > (* < / span > < span class = "org-comment" > @param multiplicity default is 1< / span >
< span class = "org-comment" > @param charge default is 0< / span >
< span class = "org-comment" > @raise Invalid_argument if the spin multiplicity is not compatible with< / span >
< span class = "org-comment" > the molecule and the total charge.< / span >
< span class = "org-comment-delimiter" > *)< / span >
< / pre >
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< td class = "org-left" > < code > make< / code > < / td >
< td class = "org-left" > < code > make n_alfa n_beta< / code > < / td >
< / tr >
< tr >
< td class = "org-left" > < code > of_atoms< / code > < / td >
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< td class = "org-left" > Creates the data relative to electrons for a molecular system described by < a href = "#org1056889" > < code > Nuclei.t< / code > < / a > for a given total charge and spin multiplicity.< / td >
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< h3 id = "org6c90a8b" > < span class = "section-number-3" > 2.3< / span > Access< / h3 >
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< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > charge< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-module" > Charge.< / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > n_elec< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > n_alfa< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > n_beta< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > multiplicity< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
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< td class = "org-left" > < code > charge< / code > < / td >
< td class = "org-left" > Sum of the charges of the electrons< / td >
< / tr >
< tr >
< td class = "org-left" > < code > n_elec< / code > < / td >
< td class = "org-left" > Number of electrons< / td >
< / tr >
< tr >
< td class = "org-left" > < code > n_alfa< / code > < / td >
< td class = "org-left" > Number of alpha electrons< / td >
< / tr >
< tr >
< td class = "org-left" > < code > n_beta< / code > < / td >
< td class = "org-left" > Number of beta electrons< / td >
< / tr >
< tr >
< td class = "org-left" > < code > multiplicity< / code > < / td >
< td class = "org-left" > Spin multiplicity: \(2S+1\)< / td >
< / tr >
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< h3 id = "orgd40dbf2" > < span class = "section-number-3" > 2.4< / span > Printers< / h3 >
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< div class = "outline-text-3" id = "text-2-4" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > pp< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Format.< / span > formatter < span class = "org-tuareg-font-lock-operator" > -> < / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > unit
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org20072b6" class = "outline-3" >
< h3 id = "org20072b6" > < span class = "section-number-3" > 2.5< / span > Tests< / h3 >
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< / div >
< / div >
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< div id = "outline-container-orgb411aa8" class = "outline-2" >
< h2 id = "orgb411aa8" > < span class = "section-number-2" > 3< / span > Element< / h2 >
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< div class = "outline-text-2" id = "text-3" >
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< p >
Chemical elements.
< / p >
< / div >
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< div id = "outline-container-org7b29939" class = "outline-3" >
< h3 id = "org7b29939" > < span class = "section-number-3" > 3.1< / span > Type< / h3 >
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< div class = "outline-text-3" id = "text-3-1" >
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< div class = "org-src-container" >
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< pre class = "src src-ocaml" id = "org088d0e5" > < span class = "org-tuareg-font-lock-governing" > type< / span > < span class = "org-type" > t< / span > < span class = "org-tuareg-font-lock-operator" > =< / span >
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< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > X< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > H< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > He< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Li< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Be< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > B< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > C< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > N< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > O< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > F< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ne< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Na< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Mg< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Al< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Si< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > P< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > S< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Cl< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ar< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > K< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ca< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Sc< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ti< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > V< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Cr< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Mn< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Fe< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Co< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ni< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Cu< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Zn< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ga< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ge< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > As< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Se< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Br< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Kr< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Rb< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Sr< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Y< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Zr< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Nb< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Mo< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Tc< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ru< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Rh< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Pd< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Ag< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Cd< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > In< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Sn< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Sb< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Te< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > I< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Xe< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > Pt< / span >
< span class = "org-keyword" > exception< / span > < span class = "org-tuareg-font-lock-constructor" > ElementError< / span > < span class = "org-keyword" > of< / span > string
< span class = "org-tuareg-font-lock-governing" > open < / span > < span class = "org-tuareg-font-lock-module" > Common< / span >
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org46b8b47" class = "outline-3" >
< h3 id = "org46b8b47" > < span class = "section-number-3" > 3.2< / span > Conversion< / h3 >
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< div class = "outline-text-3" id = "text-3-2" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > string
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_long_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > string
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_int< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_int< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > int < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_charge< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-module" > Charge.< / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_charge< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Charge.< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< / pre >
< / div >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< tbody >
< tr >
< td class = "org-left" > < code > of_string< / code > < / td >
< td class = "org-left" > Creates an < code > Element.t< / code > from a chemical symbol or from the full name of the element (case insensitive)< / td >
< / tr >
< tr >
< td class = "org-left" > < code > to_string< / code > < / td >
< td class = "org-left" > Gets the chemical symbol of the < code > Element.t< / code > in a string< / td >
< / tr >
< tr >
< td class = "org-left" > < code > to_long_string< / code > < / td >
< td class = "org-left" > Gets the full name of the < code > Element.t< / code > in a string< / td >
< / tr >
< tr >
< td class = "org-left" > < code > to_int< / code > < / td >
< td class = "org-left" > Convert to the atomic charge, with < code > int< / code > type< / td >
< / tr >
< tr >
< td class = "org-left" > < code > of_int< / code > < / td >
< td class = "org-left" > Create from the atomic charge, with < code > int< / code > type< / td >
< / tr >
< tr >
< td class = "org-left" > < code > to_charge< / code > < / td >
< td class = "org-left" > Convert to the atomic charge, with < code > Charge.t< / code > type< / td >
< / tr >
< tr >
< td class = "org-left" > < code > of_charge< / code > < / td >
< td class = "org-left" > Create from the atomic charge, with < code > Charge.t< / code > type< / td >
< / tr >
< / tbody >
< / table >
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< pre class = "example" id = "org3545bb2" >
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Element.of_string "Fe" ;;
- : Element.t = Particles.Element.Fe
Element.of_string "hydrogen" ;;
- : Element.t = Particles.Element.H
Element.of_string "Kryptonite" ;;
Exception: Particles.Element.ElementError "Element Kryptonite unknown".
Element.(to_long_string Fe) ;;
- : string = "Iron"
Element.(to_string Fe);;
- : string = "Fe"
< / pre >
< / div >
< / div >
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< div id = "outline-container-org1d70546" class = "outline-3" >
< h3 id = "org1d70546" > < span class = "section-number-3" > 3.3< / span > Database information< / h3 >
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< div class = "outline-text-3" id = "text-3-3" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > covalent_radius< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-module" > Non_negative_float.< / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > vdw_radius< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-module" > Non_negative_float.< / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > mass< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-module" > Mass.< / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > small_core< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > large_core< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< / pre >
< / div >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< tbody >
< tr >
< td class = "org-left" > < code > covalent_radius< / code > < / td >
< td class = "org-left" > Covalent radii of the elements, in atomic units< / td >
< / tr >
< tr >
< td class = "org-left" > < code > vdw_radius< / code > < / td >
< td class = "org-left" > Van der Waals radii of the elements, in atomic units< / td >
< / tr >
< tr >
< td class = "org-left" > < code > mass< / code > < / td >
< td class = "org-left" > Atomic mass of the elements, in atomic units)< / td >
< / tr >
< tr >
< td class = "org-left" > < code > small_core< / code > < / td >
< td class = "org-left" > Number of electrons in the small core model (all except the outermost two shells)< / td >
< / tr >
< tr >
< td class = "org-left" > < code > large_core< / code > < / td >
< td class = "org-left" > Number of electrons in the large core model (all except the outermost shell)< / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
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< div id = "outline-container-orgd5738cc" class = "outline-3" >
< h3 id = "orgd5738cc" > < span class = "section-number-3" > 3.4< / span > Printers< / h3 >
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< div class = "outline-text-3" id = "text-3-4" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > pp< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Format.< / span > formatter < span class = "org-tuareg-font-lock-operator" > -> < / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > unit
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > pp_long< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Format.< / span > formatter < span class = "org-tuareg-font-lock-operator" > -> < / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > unit
< / pre >
< / div >
< / div >
< / div >
< / div >
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< div id = "outline-container-org61359db" class = "outline-2" >
< h2 id = "org61359db" > < span class = "section-number-2" > 4< / span > Atomic mass< / h2 >
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< div class = "outline-text-2" id = "text-4" >
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< p >
Atomic mass, a non-negative float.
< / p >
< div class = "org-src-container" >
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< pre class = "src src-ocaml" id = "orgff86835" > < span class = "org-tuareg-font-lock-governing" > include< / span > < span class = "org-tuareg-font-lock-governing" > module type of< / span > < span class = "org-tuareg-font-lock-module" > Common.Non_negative_float< / span >
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< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org3653358" class = "outline-2" >
< h2 id = "org3653358" > < span class = "section-number-2" > 5< / span > Nuclei< / h2 >
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< div class = "outline-text-2" id = "text-5" >
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< / div >
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< div id = "outline-container-orgdc5c638" class = "outline-3" >
< h3 id = "orgdc5c638" > < span class = "section-number-3" > 5.1< / span > Type< / h3 >
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< div class = "outline-text-3" id = "text-5-1" >
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< p >
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< a id = "org1056889" > < code > Nuclei.t< / code > < / a >
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< / p >
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< div class = "org-src-container" >
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< pre class = "src src-ocaml" id = "org5d75f82" > < span class = "org-tuareg-font-lock-governing" > open < / span > < span class = "org-tuareg-font-lock-module" > Common< / span >
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< span class = "org-tuareg-font-lock-governing" > type< / span > < span class = "org-type" > t< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > < span class = "org-tuareg-font-lock-module" > Element.< / span > t < span class = "org-tuareg-font-lock-operator" > *< / span > < span class = "org-tuareg-font-lock-module" > Coordinate.< / span > t< span class = "org-tuareg-font-lock-operator" > )< / span > array
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org795558e" class = "outline-3" >
< h3 id = "org795558e" > < span class = "section-number-3" > 5.2< / span > xyz file lexer/parser< / h3 >
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< div class = "outline-text-3" id = "text-5-2" >
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< / div >
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< div id = "outline-container-orgfa3e0b9" class = "outline-4" >
< h4 id = "orgfa3e0b9" > < span class = "section-number-4" > 5.2.1< / span > Lexer< / h4 >
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< div class = "outline-text-4" id = "text-5-2-1" >
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< p >
< code > nuclei_lexer.mll< / code > contains the description of the lexemes used in
an xyz file.
< / p >
< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-operator" > {< / span >
< span class = "org-tuareg-font-lock-governing" > open < / span > < span class = "org-tuareg-font-lock-module" > Xyz_parser< / span >
< span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > eol< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > < span class = "org-tuareg-font-lock-operator" > [< / span > < span class = "org-string" > '\n'< / span > < span class = "org-tuareg-font-lock-operator" > ]< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > white< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > < span class = "org-tuareg-font-lock-operator" > [< / span > < span class = "org-string" > ' '< / span > < span class = "org-string" > '\t'< / span > < span class = "org-tuareg-font-lock-operator" > ]+< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > word< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > < span class = "org-tuareg-font-lock-operator" > [^< / span > < span class = "org-string" > ' '< / span > < span class = "org-string" > '\t'< / span > < span class = "org-string" > '\n'< / span > < span class = "org-tuareg-font-lock-operator" > ]+< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > letter< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > < span class = "org-tuareg-font-lock-operator" > [< / span > < span class = "org-string" > 'A'< / span > < span class = "org-tuareg-font-lock-operator" > -< / span > < span class = "org-string" > 'Z'< / span > < span class = "org-string" > 'a'< / span > < span class = "org-tuareg-font-lock-operator" > -< / span > < span class = "org-string" > 'z'< / span > < span class = "org-tuareg-font-lock-operator" > ]< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > integer< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > < span class = "org-tuareg-font-lock-operator" > [< / span > < span class = "org-string" > '0'< / span > < span class = "org-tuareg-font-lock-operator" > -< / span > < span class = "org-string" > '9'< / span > < span class = "org-tuareg-font-lock-operator" > ]+< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > real< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > < span class = "org-string" > '-'< / span > < span class = "org-tuareg-font-lock-operator" > ?< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > integer < span class = "org-string" > '.'< / span > integer < span class = "org-tuareg-font-lock-operator" > |< / span > integer < span class = "org-string" > '.'< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-string" > '.'< / span > integer< span class = "org-tuareg-font-lock-operator" > )< / span > < span class = "org-tuareg-font-lock-operator" > ([< / span > < span class = "org-string" > 'e'< / span > < span class = "org-string" > 'E'< / span > < span class = "org-tuareg-font-lock-operator" > ]< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > < span class = "org-string" > '+'< / span > < span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-string" > '-'< / span > < span class = "org-tuareg-font-lock-operator" > )?< / span > integer< span class = "org-tuareg-font-lock-operator" > )?< / span >
rule read_all < span class = "org-tuareg-font-lock-operator" > =< / span > parse
< span class = "org-tuareg-font-lock-operator" > |< / span > eof < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-constructor" > EOF< / span > < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > eol < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > white < span class = "org-keyword" > as< / span > w < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > w < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > integer < span class = "org-keyword" > as< / span > i < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > int_of_string i< span class = "org-tuareg-font-lock-operator" > )< / span > < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > real < span class = "org-keyword" > as< / span > f < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > float_of_string f< span class = "org-tuareg-font-lock-operator" > )< / span > < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > word < span class = "org-keyword" > as< / span > w < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-constructor" > WORD< / span > w < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > {< / span >
< span class = "org-comment-delimiter" > (* < / span > < span class = "org-comment" > DEBUG< / span >
< span class = "org-comment" > let () =< / span >
< span class = "org-comment" > let ic = open_in "h2o.xyz" in< / span >
< span class = "org-comment" > let lexbuf = Lexing.from_channel ic in< / span >
< span class = "org-comment" > while true do< / span >
< span class = "org-comment" > let s =< / span >
< span class = "org-comment" > match read_all lexbuf with< / span >
< span class = "org-comment" > | EOL -> "EOL"< / span >
< span class = "org-comment" > | SPACE w -> "SPACE("^w^")"< / span >
< span class = "org-comment" > | INTEGER i -> "INTEGER("^(string_of_int i)^")"< / span >
< span class = "org-comment" > | FLOAT f -> "FLOAT("^(string_of_float f)^")"< / span >
< span class = "org-comment" > | WORD w -> "WORD("^w^")"< / span >
< span class = "org-comment" > | EOF -> "EOF"< / span >
< span class = "org-comment" > in< / span >
< span class = "org-comment" > print_endline s< / span >
< span class = "org-comment" > done;< / span >
< span class = "org-comment-delimiter" > *)< / span >
< span class = "org-tuareg-font-lock-operator" > }< / span >
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-orge4240df" class = "outline-4" >
< h4 id = "orge4240df" > < span class = "section-number-4" > 5.2.2< / span > Parser< / h4 >
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< div class = "outline-text-4" id = "text-5-2-2" >
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< p >
2023-04-24 19:01:42 +02:00
< code > xyz_parser.mly< / code > parses nuclear coordinates in xyz format.
2021-01-01 16:39:33 +01:00
< / p >
< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-operator" > %{< / span >
< span class = "org-tuareg-font-lock-governing" > open < / span > < span class = "org-tuareg-font-lock-module" > Common< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-function-name" > make_angstrom< / span > < span class = "org-variable-name" > x y z< / span > < span class = "org-tuareg-font-lock-operator" > =< / span >
< span class = "org-tuareg-font-lock-module" > Coordinate.< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > make_angstrom < span class = "org-tuareg-font-lock-operator" > {< / span >
x < span class = "org-tuareg-font-lock-operator" > ;< / span > y < span class = "org-tuareg-font-lock-operator" > ;< / span > z
< span class = "org-tuareg-font-lock-operator" > })< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-function-name" > output_of< / span > < span class = "org-variable-name" > f x y z< / span > < span class = "org-tuareg-font-lock-operator" > =< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > a< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > make_angstrom x y z < span class = "org-tuareg-font-lock-governing" > in< / span >
< span class = "org-keyword" > fun< / span > < span class = "org-variable-name" > e< / span > < span class = "org-tuareg-font-lock-operator" > -> < / span >
< span class = "org-tuareg-font-lock-operator" > {< / span >
< span class = "org-tuareg-font-lock-module" > Xyz_ast.< / span >
element < span class = "org-tuareg-font-lock-operator" > =< / span > f e< span class = "org-tuareg-font-lock-operator" > ;< / span >
coord < span class = "org-tuareg-font-lock-operator" > =< / span > a < span class = "org-tuareg-font-lock-operator" > ;< / span >
< span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > output_of_string< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > output_of < span class = "org-tuareg-font-lock-module" > Element.< / span > of_string
< span class = "org-tuareg-font-lock-governing" > let< / span > < span class = "org-variable-name" > output_of_int< / span > < span class = "org-tuareg-font-lock-operator" > =< / span > output_of < span class = "org-tuareg-font-lock-module" > Element.< / span > of_int
< span class = "org-tuareg-font-lock-operator" > %}< / span >
< span class = "org-tuareg-font-lock-operator" > %< / span > token < span class = "org-tuareg-font-lock-constructor" > EOL< / span >
< span class = "org-tuareg-font-lock-operator" > %< / span > token < span class = "org-tuareg-font-lock-operator" > < < / span > string< span class = "org-tuareg-font-lock-operator" > > < / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span >
< span class = "org-tuareg-font-lock-operator" > %< / span > token < span class = "org-tuareg-font-lock-operator" > < < / span > string< span class = "org-tuareg-font-lock-operator" > > < / span > < span class = "org-tuareg-font-lock-constructor" > WORD< / span >
< span class = "org-tuareg-font-lock-operator" > %< / span > token < span class = "org-tuareg-font-lock-operator" > < < / span > int< span class = "org-tuareg-font-lock-operator" > > < / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span >
< span class = "org-tuareg-font-lock-operator" > %< / span > token < span class = "org-tuareg-font-lock-operator" > < < / span > float< span class = "org-tuareg-font-lock-operator" > > < / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span >
< span class = "org-tuareg-font-lock-operator" > %< / span > token < span class = "org-tuareg-font-lock-constructor" > EOF< / span >
< span class = "org-tuareg-font-lock-operator" > %< / span > start input
< span class = "org-tuareg-font-lock-operator" > %< / span > < span class = "org-tuareg-font-lock-governing" > type< / span > < span class = "org-tuareg-font-lock-operator" > < < / span > < span class = "org-tuareg-font-lock-module" > Xyz_ast.< / span > xyz_file< span class = "org-tuareg-font-lock-operator" > > < / span > input
< span class = "org-tuareg-font-lock-operator" > %%< / span > < span class = "org-tuareg-font-lock-operator" > /*< / span > < span class = "org-tuareg-font-lock-constructor" > Grammar< / span > rules < span class = "org-tuareg-font-lock-governing" > and< / span > < span class = "org-function-name" > actions< / span > < span class = "org-variable-name" > follow< / span > < span class = "org-tuareg-font-lock-operator" > */< / span >
input< span class = "org-tuareg-font-lock-operator" > :< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > integer title atoms_xyz < span class = "org-tuareg-font-lock-operator" > {< / span >
< span class = "org-tuareg-font-lock-operator" > {< / span >
number_of_atoms < span class = "org-tuareg-font-lock-operator" > =< / span > $1< span class = "org-tuareg-font-lock-operator" > ;< / span >
file_title < span class = "org-tuareg-font-lock-operator" > =< / span > $2< span class = "org-tuareg-font-lock-operator" > ;< / span >
nuclei < span class = "org-tuareg-font-lock-operator" > =< / span > $3< span class = "org-tuareg-font-lock-operator" > ;< / span >
< span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > ;< / span >
integer< span class = "org-tuareg-font-lock-operator" > :< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > $2 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > $2 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > ;< / span >
title< span class = "org-tuareg-font-lock-operator" > :< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > title_list < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > ;< / span >
text< span class = "org-tuareg-font-lock-operator" > :< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > WORD< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > string_of_float $1< span class = "org-tuareg-font-lock-operator" > )}< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > string_of_int $1< span class = "org-tuareg-font-lock-operator" > )}< / span >
< span class = "org-tuareg-font-lock-operator" > ;< / span >
title_list< span class = "org-tuareg-font-lock-operator" > :< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-string" > ""< / span > < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > title_list text < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-operator" > (< / span > $1 < span class = "org-tuareg-font-lock-operator" > ^< / span > $2< span class = "org-tuareg-font-lock-operator" > )< / span > < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > ;< / span >
atoms_xyz< span class = "org-tuareg-font-lock-operator" > :< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-module" > List.< / span > rev $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > EOF< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-module" > List.< / span > rev $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > ;< / span >
atoms_list< span class = "org-tuareg-font-lock-operator" > :< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > < span class = "org-tuareg-font-lock-operator" > []< / span > < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > WORD< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_string $4 $6 $8 $2 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > WORD< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_string $4 $6 $8 $2 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_int $4 $6 $8 $2 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_int $4 $6 $8 $2 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > WORD< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_string $5 $7 $9 $3 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > WORD< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_string $5 $7 $9 $3 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_int $5 $7 $9 $3 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > |< / span > atoms_list < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > INTEGER< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > FLOAT< / span > < span class = "org-tuareg-font-lock-constructor" > SPACE< / span > < span class = "org-tuareg-font-lock-constructor" > EOL< / span > < span class = "org-tuareg-font-lock-operator" > {< / span > output_of_int $5 $7 $9 $3 < span class = "org-tuareg-font-lock-operator" > ::< / span > $1 < span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-operator" > ;< / span >
< / pre >
< / div >
< p >
When an xyz file is read by < code > xyz_parser.mly< / code > , it is converted into
an < code > xyz_file< / code > data structure.
< / p >
< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > open < / span > < span class = "org-tuareg-font-lock-module" > Common< / span >
< span class = "org-tuareg-font-lock-governing" > type< / span > < span class = "org-type" > nucleus< / span > < span class = "org-tuareg-font-lock-operator" > =< / span >
< span class = "org-tuareg-font-lock-operator" > {< / span >
element< span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Element.< / span > t < span class = "org-tuareg-font-lock-operator" > ;< / span >
coord < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Coordinate.< / span > angstrom < span class = "org-tuareg-font-lock-module" > Coordinate.< / span > point< span class = "org-tuareg-font-lock-operator" > ;< / span >
< span class = "org-tuareg-font-lock-operator" > }< / span >
< span class = "org-tuareg-font-lock-governing" > type< / span > < span class = "org-type" > xyz_file< / span > < span class = "org-tuareg-font-lock-operator" > =< / span >
< span class = "org-tuareg-font-lock-operator" > {< / span >
number_of_atoms < span class = "org-tuareg-font-lock-operator" > :< / span > int < span class = "org-tuareg-font-lock-operator" > ;< / span >
file_title < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > ;< / span >
nuclei < span class = "org-tuareg-font-lock-operator" > :< / span > nucleus list < span class = "org-tuareg-font-lock-operator" > ;< / span >
< span class = "org-tuareg-font-lock-operator" > }< / span >
< / pre >
< / div >
< / div >
< / div >
< / div >
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< div id = "outline-container-orgfe57c35" class = "outline-3" >
< h3 id = "orgfe57c35" > < span class = "section-number-3" > 5.3< / span > Conversion< / h3 >
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< div class = "outline-text-3" id = "text-5-3" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_xyz_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_xyz_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > string
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_xyz_file< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_zmt_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_zmt_file< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > string
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_filename< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< / pre >
< / div >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< tbody >
< tr >
< td class = "org-left" > < code > of_xyz_string< / code > < / td >
< td class = "org-left" > Create from a string, in xyz format< / td >
< / tr >
< tr >
< td class = "org-left" > < code > of_xyz_file< / code > < / td >
< td class = "org-left" > Create from a file, in xyz format< / td >
< / tr >
< tr >
< td class = "org-left" > < code > of_zmt_string< / code > < / td >
< td class = "org-left" > Create from a string, in z-matrix format< / td >
< / tr >
< tr >
< td class = "org-left" > < code > of_zmt_file< / code > < / td >
< td class = "org-left" > Create from a file, in z-matrix format< / td >
< / tr >
< tr >
< td class = "org-left" > < code > to_string< / code > < / td >
< td class = "org-left" > Transform to a string, for printing< / td >
< / tr >
< tr >
< td class = "org-left" > < code > of_filename< / code > < / td >
< td class = "org-left" > Detects the type of file (xyz, z-matrix) and reads the file< / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
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< div id = "outline-container-org14de381" class = "outline-3" >
< h3 id = "org14de381" > < span class = "section-number-3" > 5.4< / span > Query< / h3 >
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< div class = "outline-text-3" id = "text-5-4" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > formula< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > string
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > repulsion< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > float
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > charge< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-module" > Charge.< / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > small_core< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > large_core< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > int
< / pre >
< / div >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< tbody >
< tr >
< td class = "org-left" > < code > formula< / code > < / td >
< td class = "org-left" > Returns the chemical formula< / td >
< / tr >
< tr >
< td class = "org-left" > < code > repulsion< / code > < / td >
< td class = "org-left" > Nuclear repulsion energy, in atomic units< / td >
< / tr >
< tr >
< td class = "org-left" > < code > charge< / code > < / td >
< td class = "org-left" > Sum of the charges of the nuclei< / td >
< / tr >
< tr >
< td class = "org-left" > < code > small_core< / code > < / td >
< td class = "org-left" > Number of core electrons in the small core model< / td >
< / tr >
< tr >
< td class = "org-left" > < code > large_core< / code > < / td >
< td class = "org-left" > Number of core electrons in the large core model< / td >
< / tr >
< / tbody >
< / table >
< / div >
< / div >
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< div id = "outline-container-org9224cc6" class = "outline-3" >
< h3 id = "org9224cc6" > < span class = "section-number-3" > 5.5< / span > TREXIO< / h3 >
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< div class = "outline-text-3" id = "text-5-5" >
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< / div >
< div id = "outline-container-org7046b2a" class = "outline-4" >
< h4 id = "org7046b2a" > < span class = "section-number-4" > 5.5.1< / span > Read< / h4 >
< div class = "outline-text-4" id = "text-5-5-1" >
< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_trexio< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Trexio.< / span > trexio_file < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< / pre >
< / div >
< / div >
< / div >
< div id = "outline-container-orgd1b3675" class = "outline-4" >
< h4 id = "orgd1b3675" > < span class = "section-number-4" > 5.5.2< / span > Write< / h4 >
< div class = "outline-text-4" id = "text-5-5-2" >
< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_trexio< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Trexio.< / span > trexio_file < span class = "org-tuareg-font-lock-operator" > -> < / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > unit
< / pre >
< / div >
< / div >
< / div >
< / div >
< div id = "outline-container-org3ece660" class = "outline-3" >
< h3 id = "org3ece660" > < span class = "section-number-3" > 5.6< / span > Printers< / h3 >
< div class = "outline-text-3" id = "text-5-6" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > pp< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Format.< / span > formatter < span class = "org-tuareg-font-lock-operator" > -> < / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > unit
< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-org6a90479" class = "outline-3" >
< h3 id = "org6a90479" > < span class = "section-number-3" > 5.7< / span > Tests< / h3 >
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< / div >
< / div >
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< div id = "outline-container-org46003da" class = "outline-2" >
< h2 id = "org46003da" > < span class = "section-number-2" > 6< / span > Z-matrix< / h2 >
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< div class = "outline-text-2" id = "text-6" >
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< p >
Z-matrix representation of nuclear coordinates.
< / p >
< / div >
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< div id = "outline-container-org5fcb7ed" class = "outline-3" >
< h3 id = "org5fcb7ed" > < span class = "section-number-3" > 6.1< / span > Type< / h3 >
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< div class = "outline-text-3" id = "text-6-1" >
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< div class = "org-src-container" >
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< pre class = "src src-ocaml" id = "orgf9db5fa" > < span class = "org-tuareg-font-lock-governing" > type< / span > < span class = "org-type" > t< / span >
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< / pre >
< / div >
< / div >
< / div >
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< div id = "outline-container-orga6c6d0e" class = "outline-3" >
< h3 id = "orga6c6d0e" > < span class = "section-number-3" > 6.2< / span > Conversion< / h3 >
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< div class = "outline-text-3" id = "text-6-2" >
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< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > of_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > string < span class = "org-tuareg-font-lock-operator" > -> < / span > t
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_xyz< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > < span class = "org-tuareg-font-lock-operator" > (< / span > < span class = "org-tuareg-font-lock-module" > Element.< / span > t < span class = "org-tuareg-font-lock-operator" > *< / span > float < span class = "org-tuareg-font-lock-operator" > *< / span > float < span class = "org-tuareg-font-lock-operator" > *< / span > float< span class = "org-tuareg-font-lock-operator" > )< / span > array
< span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > to_xyz_string< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > string
< / pre >
< / div >
< table border = "2" cellspacing = "0" cellpadding = "6" rules = "groups" frame = "hsides" >
< colgroup >
< col class = "org-left" / >
< col class = "org-left" / >
< / colgroup >
< tbody >
< tr >
< td class = "org-left" > < code > of_string< / code > < / td >
< td class = "org-left" > Reads a z-matrix from a string< / td >
< / tr >
< tr >
< td class = "org-left" > < code > to_xyz< / code > < / td >
< td class = "org-left" > Converts to xyz format, as in the < code > Nuclei< / code > module< / td >
< / tr >
< tr >
< td class = "org-left" > < code > to_xyz_string< / code > < / td >
< td class = "org-left" > Converts to xyz format, as a string< / td >
< / tr >
< / tbody >
< / table >
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< pre class = "example" id = "org7e18520" >
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let zmt = Zmatrix.of_string "
n
n 1 nn
h 1 hn 2 hnn
h 2 hn 1 hnn 3 dih4
h 1 hn 2 hnn 4 dih5
h 2 hn 1 hnn 3 dih5
nn 1.446
hn 1.016
hnn 106.0
dih4 -54.38
dih5 54.38
" ;;
- : Zmatrix.t = N
N 1 1.446000
H 1 1.016000 2 106.000000
H 2 1.016000 1 106.000000 3 -54.380000
H 1 1.016000 2 106.000000 4 54.380000
H 2 1.016000 1 106.000000 3 54.380000
Zmatrix.to_xyz zmt ;;
- : (Element.t * float * float * float) array =
[|(N, 0., 0., 0.); (N, 0., 0., 1.446);
(H, -0.976641883073332107, 0., -0.280047553510071046);
(H, -0.568802835186988709, 0.793909757123734683, 1.726047553510071);
(H, 0.314092649983635563, 0.924756819385119, -0.280047553510071101);
(H, -0.568802835186988709, -0.793909757123734683, 1.726047553510071)|]
Zmatrix.to_xyz_string zmt ;;
- : string =
"N 0.000000 0.000000 0.000000
N 0.000000 0.000000 1.446000
H -0.976642 0.000000 -0.280048
H -0.568803 0.793910 1.726048
H 0.314093 0.924757 -0.280048
H -0.568803 -0.793910 1.726048"
< / pre >
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2023-04-24 19:01:42 +02:00
< div id = "outline-container-org37a7c2e" class = "outline-3" >
< h3 id = "org37a7c2e" > < span class = "section-number-3" > 6.3< / span > Printers< / h3 >
2021-01-28 00:34:26 +01:00
< div class = "outline-text-3" id = "text-6-3" >
2021-01-01 16:39:33 +01:00
< div class = "org-src-container" >
< pre class = "src src-ocaml" > < span class = "org-tuareg-font-lock-governing" > val< / span > < span class = "org-function-name" > pp< / span > < span class = "org-tuareg-font-lock-operator" > :< / span > < span class = "org-tuareg-font-lock-module" > Format.< / span > formatter < span class = "org-tuareg-font-lock-operator" > -> < / span > t < span class = "org-tuareg-font-lock-operator" > -> < / span > unit
< / pre >
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< / div >
< div id = "postamble" class = "status" >
< p class = "author" > Author: Anthony Scemama< / p >
2023-04-24 19:01:42 +02:00
< p class = "date" > Created: 2023-04-24 Mon 18:07< / p >
2021-01-01 16:39:33 +01:00
< p class = "validation" > < a href = "https://validator.w3.org/check?uri=referer" > Validate< / a > < / p >
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