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--- post-processing_of_output_and_databases [2020/06/11 18:17] – external edit 127.0.0.1
+++ post-processing_of_output_and_databases [2025/03/12 09:38] (current) – Revamp molpro-output and database peterk
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+====== Post-processing of output and databases ======
+===== Output =====
+Molpro produces an output file that is in XML format with appropriate mark-up for all important results. This file, which has a ''.xml'' suffix, conforms strictly to a [[https://www.molpro.net/schema/molpro-output.xsd|well-defined schema]], and the the schema definition file can be found in the main Molpro source or installation tree in the directory ''%%lib/schema%%''. The principal elements of marked-up output are
+  * **jobstep** The results from one job step.
+  * **molecule** A container for data on a single molecule.
+  * **cml:molecule** Molecular geometry in the Chemical Markup Language (CML) format.
+  * **property** A computed property, for example an energy or dipole moment.
+  * **table** The output of Molpro’s ''TABLE'' command in XHTML format.
+  * **basisSet** A self-contained description of the orbital basis set.
+  * **orbitals** A set of orbitals.
+  * **vibrations** Harmonic normal vibrational modes.
+  * **variables** Molpro’s internal variables.
+  * **platform** Information about the computing system on which a job was run.
+Not all of these elements are produced by default in the regular job transcript ''.xml'' file; some of them can result from using the ''%%PUT,XML%%'' to make a separate dump file.
+''molpro-output'' is understood by several post-processing programs, including [[https://jmol.org|Jmol]], [[https://github.com/molpro/sjef|sjef]], [[https://github.com/molpro/iMolpro|iMolpro]], and gmolpro. There is extensive support for it in the [[https://github.com/molpro/pymolpro|pymolpro]] library, which should be the normal route for accessing data. Pymolpro is available on [[https://conda-forge.org/|conda forge]], and some examples of its use can be found [[https://molpro.github.io/pymolpro/examples.html|here]].
+===== Databases =====
+Pymolpro also provides a facility  to store and interrogate sets of molecules, together with information about how they are to be combined in balanced chemical equations. This collection of information is referred to as a //database//, and can be generated completely manually, or partially by running appropriate Molpro calculations; the library contains also a number of the standard quantum chemistry benchmark sets. Analysis of the database can give a summary of the energy changes associated with each described reaction, and two or more similar databases can be compared reaction by reaction, to give a statistical analysis of the differences between them. See pymolpro documentation for [[https://molpro.github.io/pymolpro/pymolpro.html#module-pymolpro.database|details]] and [[https://molpro.github.io/pymolpro/examples/thermochemical_benchmark_Bak2000_atomisations.html|examples]].