Introduction to CPMD 1
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1 Introduction to CPMD 1
2 CPMD program ab initio electronic structure (DFT) and molecular dynamics program plane wave basis set (PBC), pseudopotentials massively parallelized, linear scaling up to thousands of CPU s WF, GEO, CPMD, BOMD, KS-orbitals, response functions, TDDFT, properties solids, liquids, gas-phase, materials, chemistry, biology download, manual, mailing list, PP s 2
3 Installation and Running more details in the manual or in the source 3
4 Installation Distribution of source via for free for non-commercial users. # mkconfig.sh to see for which platforms a Makefile can be generated. # mkconfig.sh platform > Makefile to obtain Makefile for your platform. # make to get executable cpmd.x. frequent problem: libraries and paths are incorrect in Makefile, Makefile needs to be edited manually. if you change preprocessor flags type # make clean. 4
5 Running # cpmd.x input pseudopotentialdirectory > output required files: executable, input, pseudopotentials pseudopotentialdirectory is either 1 omitted and instead given by an environment variable called PP LIBRARY PATH, 2 or explicitly given, 3 or omitted and the pseudopotentials are in the running directory. other files: detailed/more condensed output is written to various files depending on the keyword. RESTART-files are written upon a proper ending of a run. runs can be properly ended by creating a file EXIT in the running directory. 5
6 Input more details in the manual or in the source 6
7 &CPMD... &END Control (mandatory) Sections &DFT... &END Functional (mandatory) &SYSTEM... &END Cell (mandatory) &ATOMS... &END Pseudopotentials, Coordinates, Constraints (mandatory) &TDDFT... &END TDDFT &PIMD... &END Path Integral Molecular Dynamics &RESP... &END Response &VDW... &END Empirical van der Waals correction 7
8 Keywords Manual is incomplete by construction only source is complete. Keywords relate to variables which trigger desired calculations, relations are often found in control.f, sysin.f, pi cnt1.f, ratom.f, recpnew.f, dftin.f, proppt.f, respin.f, lr in.f Order of keywords is arbitrary unless stated otherwise Only capital letters Choose one item from lists enclosed in {...} Choose any number of items from lists enclosed in [...] Arguments (for instance numbers) for keywords are given on following lines 8
9 Keywords are read using FORTRAN INDEX(); order of keywords on a line is USUALLY irrelevant Abbreviations are allowed, NOT recommended
10 Most important parametres: Physical task (OPTIMISE GEOMETRY / WAVEFUNCTION / MOLECULAR DY- NAMICS /...) TIMESTEP (&CPMD) EMASS (&CPMD) CONVERGENCE (&CPMD) SYMMETRY (&SYSTEM) CELL (&SYSTEM) CUTOFF (&SYSTEM) atoms (&ATOM) 9
11 ISOTOPE (&ATOM) FUNCTIONAL (&DFT) LSD (&CPMD) MULTIPLICITY (&SYSTEM)
12 &CPMD Most important parametres: Practical FILEPATH (CPMD_FILEPATH as environmental variable) MAXCPUTIME MAXSTEP STORE RESTFILE REAL SPACE WFN KEEP MIRROR 10
13 Most important parametres: Analysis TRAJECTORY SAMPLE XYZ (&CPMD) STRUCTURE BONDS ANGLES... (&CPMD) STRESS TENSOR (&CPMD) DIPOLE DYNAMICS WANNIER SAMPLE (&CPMD) CUBEFILE (RHOOUT [BANDS], ELECTROSTATIC POTENTIAL) (&PROP/&CPMD) 11
14 Examples 12
15 Optimise electron structure of H 2 O Optimise geometry of H 2 O Visualise geometry [gopenmol] Tasks: Tuesday Vibrational modes using displacements Isotope effect? (RESTART VIBANALYSIS!) Perform BO and CP dynamics for H 2 O Visualise ENERGIES; what are constants of motion? Is there a drift? What is the average temperature? Etc [xmgrace] Visualise TRAJEC.xyz [gopenmol] Vary time step, emass (in CP); when does the adiabatic approximation fail? When is the time step too large in BOMD? If you have time, optimise the geometry of (H 2 O) 2. Calculate the binding energy, vibrational frequencies. How does the vibrational frequency of OH along the hydrogen bond change wrt monomer? 13
16 Tasks: Wednesday Perform CP dynamics for H 2 O constraining the bending mode to the equilibrium value Perform simulated annealing for H 2 O from the end of the previous trajectory; do you recover the geometry of Tuesday? Calculate the Kohn-Sham energies of H 2 O; are the positive energies reliable? Visualise orbitals (CUBEFILE) [gopenmol] Mean square displacement of Tuesday s trajectory Vibrational spectrum of H 2 O using Tuesday s trajectory Calculate charges on oxygen and hydrogen using Bader s method [charge] Calculate dipole moment of H 2 O (DIPOLE MOMENT / &PROP) Calculate Wannier functions for H 2 O; what is the hybridisation of H 2 O? Calculate adsorption and emission spectrum of formaldehyde in the second excited state; how does the geometry look like? What is the fluoresence shift? 14
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