DFT，密度泛函理论+第一性原理计算+过渡态+活化能计算+吸附能+MS运行脚本

This folder contains example scripts and their input documents. AtomicClock.pl ============== Displays a clock using silicon atoms for the numbers, hydrogen for the minute hand and an oxygen for the hour hand. A Best Fit Line is used through a hidden atom to display seconds. Hit Escape to terminate the script! BoltzmannInversion.pl [Input.xtd] ================================= Generates a coarse-grained force field that reproduces the statistics of an atomistic trajectory. Uses an iterative procedure that runs repeated dynamics simulations BuildMethane.pl =============== This script builds a 'correct' methane molecule completely from scratch. First the atoms and bonds are created in a planar cross formation. Then Forcite is run to produce a minimal energy structure. BuildStudyTable.pl [MORCh3Cl.xsd] ================================= Completed version of the above that adds structures and Forcite calculated results to a new StudyTable. BuildZeolite.pl [TON.xsd] ========================= Replaces 10% of the silicon atoms in a zeolite with aluminium. A sodium atom is then bonded to any aluminium atoms introduced into the structure. Lowenstein's rule (which forbids Al-O-Al) is checked before any new Aluminium atoms are added. CalcUniqueBondLengthAngles.pl [urea.xsd] ======================================== This script generates a list of all the bond lengths and angles in a crystal structure. Any symmetry replicates are ignored. ConvertEAMtoOFF.pl [CuNi_Example.eam.alloy.txt, CuNi_Example.eam.fs.txt] ======================================================================== This script converts tabulated EAM potentials in the ".eam.fs" or ".eam.alloy" to the ".off" format usable by Forcite. Example text files of both formats are provided. DFTBEval.pl [ethane.xsd, methane.xsd] ===================================== Runs geometry optimizations with DMol3 and DFTB+ and compares the distance and angle monitors. Used in the tutorial "Creating parameters for DFTB+" in the Materials Studio online help. ForeachDocument.pl ================== This script demonstrates performing an analysis or calculation on each 3D Atomistic Document (.xsd) document in a project. HBondStats.pl [urea.xsd] ======================== This script calculates the average length of all Hydrogen Bonds in a specified structure. It generates a Study Table with a list of all the HBonds, the average length, plus the minimum and maximum bond lengths found. MandleBrot.pl ============= Demonstrates pure Perl running inside Materials Studio. MoleculeStructure.pl [Phenol.xsd] ================================= This script navigates the objects contained in a simple phenol molecule and prints to stdout information on Atom position and how it is bonded to other Atoms in the molecule. MoveChloroMethane.pl [MORCh3Cl.xsd] ==================================== Users want to place a molecule at a series of points (e.g. in a zeolite) and do a single point energy calculation or a short optimisation. This script currently only contains the code to move the molecule. The remaining components will be introduced shortly. MoveChloroMethaneMG.pl is a variant of the base script that uses a MotionGroup defined in the input document [MORCh3ClMotionGroup.xsd] instead of a set. PES.pl [water.xsd] ================== This script demonstrates how to create potential energy surface (PES) using DMol3 geometry optimization with internal constraints. PolymorphPrediction.pl [ohd.xsd] ================================ This script executes a polymorph predictions sequence for 3-oxabicyclo(3.2.0)hepta-1,4-diene (ohd.xsd) searching in two space groups (P212121 and PBCA). Results are inserted into an output study table. The example is based on the Polymorph tutorial "Predicting the crystal structure of 3-oxabicyclo(3.2.0)hepta-1,4-diene" accessible via the Materials Studio on-line help. PowderQPA.pl [all files Acetohexamide*, corundum.xsd, SMXReflex_Extension_QPA.xms] =================================================================================== This script demonstrates a qualitative phase analysis of a mixture powder pattern containing three different phases. StressStrain.pl [Fe.xsd] ======================== This script uses the Souza-Martins barostat and an applied stress in one direction (zero stresses in the others) and measures the strain. The output is a study table containing the stress-strain curve. SubstitutionalDisorder.pl [TON.xsd] =================================== This script is an extension of the BuildZeolite script, making it a more generic example for randomly substituting one element with another element in a periodic system. It is used in the Scripting tutorial "Executing scripts from the user menu" to demonstrate adapting an existing script. TrajectoryCoarseGrainer.pl [Polydimeth_siloxane.xtd, Polydimeth_siloxane.trj] ============================== This script converts an input trajectory containing atoms and bonds to an output trajectory containing beads and connectors. VelocityInitialization.pl [urea-P1.xsd] ======================================= This script sets the velocities on the atoms of a P-1 crystal structure to random values that give a specified overall temperature for the structure. These velocities can then be used as initial values for a Forcite dynamics calculation using the "Current" setting for Initial velocities.