====== Nanostructures and adsorption on metallic surfaces ====== Problem: compute activation barrier for the last step (6 to 7) of the cyclodehydrogenation reaction CHP@Cu(111) -> TBC {{ :exercises:2015_cecam_tutorial:exercise.jpg?direct&500 |}} * Original author: Carlo Pignedoli * Complete source and output files: [[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB.tar.xz|NEB.tar.xz]] ===== Introduction ===== The system is composed by a molecule (56 atoms) adsorbed on a Cu(111) slab (~2900 atoms). The molecule is treated within DFT (PM6[(Stewart2007>J.J.P. Stewart, J. Mol. Model. 13, 1173 (2007))] in the exercise) and the substrate with EAM[(Daw1983>M.S. Daw, M.I. Baskes, Phys. Rev. Lett. 50, 1285 (1983))] potentials. The substrate and the molecule are coupled through a par potential mimicking the van der Waals interaction and Pauli repulsion.[(Levi2007>A.C. Levi, P.Calvini, Surf. Sci. 601, 1494 (2007))] ===== Exercise 1: NEB ===== We need ''MULTIPLE_FORCE_EVALS'': * In a first section we define how to partition the whole system in a DFT+EMPIRICAL part * in a second section we define the force fields for the EMPIRICAL part * and in the third section we define the parameters for the DFT part. * The fourth and final section defines the target of the calculation(GEO_OPT, NEB, Molecular dynamics..) The files for this part of the exercise are found in the **''EX2''** folder. ==== First Section ==== Here we specify that our system consists of two fragments: atoms 1 to 56 and atoms 57 to 2936, the whole system is contained in the cell specified in ''[[inp>FORCE_EVAL/SUBSYS]]'' section. We declare that the first ''[[inp>FORCE_EVAL]]'' section following the present one will be dedicated to FRAGMENTS 1 and 2 (it will contain the empirical potentials) and the second ''[[inp>FORCE_EVAL]]'' section will be devoted to FRAGMENT 1 only (the DFT treatment of the molecule). &MULTIPLE_FORCE_EVALS FORCE_EVAL_ORDER 2 3 MULTIPLE_SUBSYS T &END &FORCE_EVAL METHOD MIXED &MIXED MIXING_TYPE GENMIX GROUP_PARTITION 1 1 &GENERIC ERROR_LIMIT 1.0E-10 MIXING_FUNCTION E1+E2 VARIABLES E1 E2 &END &MAPPING &FORCE_EVAL_MIXED &FRAGMENT 1 1 56 &END &FRAGMENT 2 57 2936 &END &END &FORCE_EVAL 1 DEFINE_FRAGMENTS 1 2 &END &FORCE_EVAL 2 DEFINE_FRAGMENTS 1 &END &END &END &SUBSYS &COLVAR &DISTANCE ATOMS 49 50 &END &END &CELL ABC 40.764229 39.715716 70. &END CELL &TOPOLOGY COORD_FILE_NAME ./s.xyz COORDINATE XYZ CONNECTIVITY OFF &END TOPOLOGY &END SUBSYS &END ==== Second Section ==== In this section we define the empirical potentials for the whole system: EAM will be used for the Cu-Cu interactions (parametrized in the file ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/Files/CU.pot|Files/CU.pot]]''), a //C6/R^6 + pauli repulsion// will be defined for C-Cu and H-Cu and, finally, NULL interactions will be defined for C-C, C-H and H-H since these will be obtained from DFT in the next section. The charge of every specie (zero in our example) as well as the interaction within each possible type-pair has to be defined. &FORCE_EVAL METHOD FIST &MM &FORCEFIELD &SPLINE EPS_SPLINE 1.0E-6 EMAX_SPLINE 0.9 &END &CHARGE ATOM Cu CHARGE 0.0 &END CHARGE &CHARGE ATOM H CHARGE 0.0 &END CHARGE &CHARGE ATOM C CHARGE 0.0 &END CHARGE &NONBONDED &GENPOT atoms Cu C FUNCTION A*exp(-av*r)+B*exp(-ac*r)-C/(r^6) VARIABLES r PARAMETERS A av B ac C VALUES 4.13643 1.33747 115.82004 2.206825 75.40708524085266692113 RCUT 15 &END GENPOT &GENPOT atoms Cu H FUNCTION A*exp(-av*r)+B*exp(-ac*r)-C/(r^6) VARIABLES r PARAMETERS A av B ac C VALUES 0.878363 1.33747 24.594164 2.206825 21.32834305207502214234 RCUT 15 &END GENPOT &LENNARD-JONES atoms C H EPSILON 0.0 SIGMA 3.166 RCUT 15 &END LENNARD-JONES &LENNARD-JONES atoms H H EPSILON 0.0 SIGMA 3.166 RCUT 15 &END LENNARD-JONES &LENNARD-JONES atoms C C EPSILON 0.0 SIGMA 3.166 RCUT 15 &END LENNARD-JONES &EAM atoms Cu Cu PARM_FILE_NAME ../../Files/CU.pot &END EAM &END NONBONDED &END FORCEFIELD &POISSON &EWALD EWALD_TYPE none &END EWALD &END POISSON &END &SUBSYS &CELL ABC 40.764229 39.715716 70. &END CELL &TOPOLOGY COORD_FILE_NAME ./s.xyz COORDINATE XYZ CONNECTIVITY OFF &END TOPOLOGY &END SUBSYS &END ==== Third Section ==== In this section we specify the parameters for the DFT treatment of the molecule. Note that the simulation cell here is reduced with comparison to the simulation cell of the whole system. &FORCE_EVAL METHOD Quickstep &DFT &QS METHOD PM6 EXTRAPOLATION USE_GUESS &SE &COULOMB CUTOFF [angstrom] 20.0 &END &EXCHANGE CUTOFF [angstrom] 20.0 &END &END &END QS &SCF MAX_SCF 20 SCF_GUESS RESTART EPS_SCF 1.0E-6 &OT PRECONDITIONER FULL_SINGLE_INVERSE MINIMIZER DIIS N_DIIS 7 &END &OUTER_SCF MAX_SCF 10 EPS_SCF 1.0E-6 &END &PRINT &RESTART &EACH QS_SCF 0 &END ADD_LAST NUMERIC &END &RESTART_HISTORY OFF &END &END &END SCF &POISSON PERIODIC NONE POISSON_SOLVER WAVELET &WAVELET SCF_TYPE 60 &END &END POISSON &XC &XC_FUNCTIONAL BLYP &END XC_FUNCTIONAL &END XC ! &PRINT ! &MO_CUBES ! NHOMO 15 ! NLUMO 15 ! WRITE_CUBE T ! LOG_PRINT_KEY ! &END ! &END &END DFT &SUBSYS &CELL ABC 30 30 30 PERIODIC NONE &END CELL &TOPOLOGY COORD_FILE_NAME ./f.xyz COORDINATE xyz &CENTER_COORDINATES &END &END # &KIND H # BASIS_SET TZV2P-MOLOPT-GTH # POTENTIAL GTH-BLYP-q1 # &END KIND # &KIND C # BASIS_SET TZV2P-MOLOPT-GTH # POTENTIAL GTH-BLYP-q4 # &END KIND &END SUBSYS &END FORCE_EVAL ==== Fourth Section ==== In this section we define the target of the simulation as a //geometry optimization// this will be MD, or BAND in other examples. &GLOBAL PRINT_LEVEL LOW PROJECT INI RUN_TYPE GEO_OPT WALLTIME 28000 &END GLOBAL &MOTION &GEO_OPT MAX_FORCE 0.0001 MAX_ITER 500 OPTIMIZER LBFGS &LBFGS &END &END &END !&EXT_RESTART ! RESTART_FILE_NAME constr_3cc_2h_41_dft-1.restart !&END ==== Tasks ==== - First of all obtain the equilibrium geometry for the initial and the final states (in the directories ''INI'' and ''FIN'' you will find the input files (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/INI/geo.inp|INI/geo.inp]]''/''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/FIN/geo.inp|FIN/geo.inp]]'') the output files (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/INI/geo.inp|INI/out]]''/''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/FIN/geo.inp|FIN/out]]'') and the trajectory of the geometry optimization (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/INI/INI-pos-1.xyz|INI-pos-1.xyz]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/FIN/FIN-pos-1.xyz|FIN-pos-1.xyz]]''). - Please note that the geometry optimization of the final state is constrained with respect to the position of the final H2 molecule. - Perform a NEB simulation to find a //saddle point// between ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/INI/ini_eq.xyz|ini_eq.xyz]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/FIN/fin_eq.xyz|fin_eq.xzy]]''. - A linear guess for the path is not a good idea in this case; a clever guess can be obtained from a series of constrained geometry optimizations where the H-H distance is forced to vary from its initial value (more than 3 Å) to the H2 equilibrium distance. Such a guess is given, in the directory ''EX2'', with the files ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/ini_eq.xyz|ini_eq.xyz]]'', ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/due.xyz|due.xyz]]'',''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/tre.xyz|tre.xyz]]'',…,''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/tredici.xyz|tredici.xyz]]'',''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/fin_eq.xyz|fin_eq.xyz]]'').\\ Check that the initial step of the NEB calculation is reasonable and determine the activation barrier at the and of the optimization. In the directory ''EX2'' you will find the input for the calculation (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/neb.inp|neb.inp]]''), the output (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX2/out|out]]'') and the optimization trajectory of each //image// of the system (''NEB-pos-Replica_nr_XX-1.xyz'', 14 images are used in the example) The last section of the input described above is modified as follows: &GLOBAL PRINT_LEVEL LOW PROJECT NEB RUN_TYPE BAND WALLTIME 28000 &END GLOBAL &MOTION &BAND NPROC_REP 2 BAND_TYPE CI-NEB NUMBER_OF_REPLICA 14 K_SPRING 0.05 &CONVERGENCE_CONTROL MAX_FORCE 0.0030 RMS_FORCE 0.0050 MAX_DR 0.002 RMS_DR 0.005 &END ROTATE_FRAMES F ALIGN_FRAMES F &CI_NEB NSTEPS_IT 2 &END &OPTIMIZE_BAND OPT_TYPE DIIS OPTIMIZE_END_POINTS F &DIIS MAX_STEPS 1000 &END &END # &REPLICA COORD_FILE_NAME ini_eq.xyz &END &REPLICA COORD_FILE_NAME due.xyz &END . . . . . &REPLICA COORD_FILE_NAME fin_eq.xyz &END &PROGRAM_RUN_INFO INITIAL_CONFIGURATION_INFO &END &CONVERGENCE_INFO &END &END &END We declare that we need 14 replicas and each replica has to be computed with 2 CPUS (if we run the calculation with 14 cpus, then every group of 2 cpus will work on two replicas). The initial guess for the reaction path is given through 14 geometry files. ''[[inp>FORCE_EVAL/DFT/SCF#SCF_GUESS|SCF_GUESS RESTART]]'' in combination with ''[[inp>FORCE_EVAL/DFT/QS#EXTRAPOLATION|EXTRAPOLATION USE_GUESS]]'' has to be declared in the ''[[inp>FORCE_EVAL/DFT]]'' section to allow for an efficient guess of the wavefunctions at each step of the BAND optimization. {{ :exercises:2015_cecam_tutorial:distance_energy.jpg?direct&400 |}} ===== Exercise 2: Metadynamics ===== The files for this part of the exercise are found in the **''EX1''** folder. ==== Part 1 ==== Obtain two restart files for independent configurations of the system at the geometry of the initial state thermalized at 450 K. In the directory ''EQUIL'' the input file ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/EQUIL/inp|inp]]'' is used to run 3000 MD steps of MD in the NVT ensamble with a CSVR thermostat (a longer simulation should be used) two restart files obtained during the simulation (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/EQUIL/EQUIL-1_2000.restart|EQUIL-1_2000.restart]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/EQUIL/EQUIL-1_3000.restart|EQUIL-1_3000.restart]]'') will be used to run a Metadynamics simulation with two WALKERS. The trajectory of the MD should be also used to define the shape of the gaussians added in the metadynamics run. Trajectories are printed in dcd format (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/EQUIL/EQUIL-pos-1.dcd|EQUIL-pos-1.dcd]]'' use, e.g. ''vmd [[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/EQUIL/s.xyz|s.xyz]] [[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/EQUIL/EQUIL-pos-1.dcd|EQUIL-pos-1.dcd]]'' to visualize the trajectory). The ''[[inp>MOTION]]'' section will look like: &MOTION &MD ENSEMBLE NVT STEPS 3000 TIMESTEP 0.5 TEMPERATURE 450.0 &THERMOSTAT TYPE CSVR REGION MASSIVE &CSVR TIMECON [fs] 200.0 &END &END &END MD &PRINT &TRAJECTORY FORMAT DCD &EACH MD 100 &END &END &RESTART &EACH MD 1000 &END FILENAME EQUIL &END &RESTART_HISTORY &EACH MD 1000 &END &END &END &END ==== Part 2 ==== The two restart files are copied in the directory ''Files'' (''r1'' and ''r2'' respectively). In the directory also the geometry for the whole system in the initial configuration as well as the geometry of the molecular fragment are included (files ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/Files/s|s]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/Files/f|f]]'' respectively). We perform a metadynamics simulation with two collective variables: the sum of C-H distances (CV1) and the H-H distance (CV2). Walls have to be introduced to limit the range of variability of the two CVs. {{ :exercises:2015_cecam_tutorial:distances.jpg?direct&400 |}} To define the collective variables introduce a ''[[inp>FORCE_EVAL/SUBSYS/COLVAR|COLVAR]]'' card in the ''[[inp>FORCE_EVAL/SUBSYS|SUBSYS]]'' section of the first ''[[inp>FORCE_EVAL]]'': &SUBSYS &COLVAR &COMBINE_COLVAR &COLVAR &DISTANCE ATOMS 4 50 &END &END COLVAR &COLVAR &DISTANCE ATOMS 7 49 &END &END COLVAR FUNCTION CV1+CV2 VARIABLES CV1 CV2 ERROR_LIMIT 1.0E-8 &END &END &COLVAR &DISTANCE ATOMS 49 50 &END &END The ''[[inp>MOTION]]'' section has to be modified as follows to activate metadynamics on the two CVs: &MOTION &MD ENSEMBLE NVT STEPS 50000 TIMESTEP 0.5 TEMPERATURE 450.0 &THERMOSTAT TYPE CSVR REGION MASSIVE &CSVR TIMECON [fs] 200.0 &END &END &END MD &FREE_ENERGY &METADYN DO_HILLS NT_HILLS 50 WW 2.0e-3 &METAVAR SCALE 0.1 COLVAR 1 &WALL TYPE QUADRATIC POSITION [angstrom] 5 &QUADRATIC DIRECTION WALL_PLUS K [kcalmol] 40.0 &END &END &WALL TYPE QUADRATIC POSITION [angstrom] 1.90 &QUADRATIC DIRECTION WALL_MINUS K [kcalmol] 40.0 &END &END &END METAVAR &METAVAR SCALE 0.1 COLVAR 2 &WALL TYPE QUADRATIC POSITION [angstrom] 3.80 &QUADRATIC DIRECTION WALL_PLUS K [kcalmol] 40.0 &END &END &WALL TYPE QUADRATIC POSITION [angstrom] 0.75 &QUADRATIC DIRECTION WALL_MINUS K [kcalmol] 40.0 &END &END &END METAVAR # &METAVAR # SCALE 0.1 # COLVAR 3 # &WALL # TYPE QUADRATIC # POSITION [angstrom] 4.00 # &QUADRATIC # DIRECTION WALL_PLUS # K [kcalmol] 40.0 # &END # &END # &WALL # TYPE QUADRATIC # POSITION [angstrom] 1.30 # &QUADRATIC # DIRECTION WALL_MINUS # K [kcalmol] 40.0 # &END # &END # &END METAVAR &PRINT &COLVAR COMMON_ITERATION_LEVELS 4 &END &END &MULTIPLE_WALKERS NUMBER_OF_WALKERS 2 WALKER_ID 1 WALKER_COMM_FREQUENCY 4 &WALKERS_FILE_NAME ../WALK_DATA_FILES/WALKER_1.data ../WALK_DATA_FILES/WALKER_2.data &END &END &END METADYN &END &PRINT &TRAJECTORY FORMAT DCD &EACH MD 100 &END &END &RESTART &EACH MD 100 &END FILENAME META &END &VELOCITIES ON &EACH MD 5000 &END &END &RESTART_HISTORY OFF &END &END &END &EXT_RESTART RESTART_FILE_NAME ../../Files/r1 &END The section specific to the multiple walkers could be removed to run the simulation with a single walker: &MULTIPLE_WALKERS NUMBER_OF_WALKERS 2 WALKER_ID 1 WALKER_COMM_FREQUENCY 4 &WALKERS_FILE_NAME ../WALK_DATA_FILES/WALKER_1.data ../WALK_DATA_FILES/WALKER_2.data &END &END Here we declare that we are using two walkers, that the input belongs to the walker with ID 1, that the data relative to the different walkers are stored in the files contained in the directory ''WALK_DATA_FILES'' and that the history of the //gaussian hills deposited// by each walker should be exchanged every 4 hills deposited. We need two independent directories (''WALK1'' and ''WALK2'' in the example) belonging to each WALKER, each directory will contain an input in which the WALKER ID is modified (1 and 2). The calculation will run as a FARMING: we need a common input that specifies that we are running two cp2k problems: The input file for the calculation (''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/inp|inp]]'' in the directory ''EX1'') will be: &GLOBAL PROGRAM FARMING RUN_TYPE NONE &END GLOBAL &FARMING NGROUP 2 &JOB DIRECTORY WALK1 INPUT_FILE_NAME inp &END JOB &JOB DIRECTORY WALK2 INPUT_FILE_NAME inp &END JOB &END FARMING We declare that the cpus used for the calculation belongs to two groups of calculations, one job has to run in the directory ''WALK1'' according to the prescriptions contained in the input file ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK1/inp|WALK1/inp]]'' and a second job has to run in the directory ''WALK2'' (using ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK2/inp|WALK2/inp]]''). If we run the calculation with 8 cpus, 4 will be devoted to the JOB in directory ''WALK1'' and 4 to ''WALK2''. Each group of 10 cpus will be then partitioned according to partition instruction contained in each ''inp'' file (GROUP_PARTITION 1 3). During execution you can monitor the evolution of the CVs of each walker from the files ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK1/META-COLVAR.metadynLog|META-COLVAR.metadynLog]]'' and ''[[http://cp2k.org/static/exercises/2015_cecam_tutorial/NEB/EX1/WALK2/META-COLVAR.metadynLog|META-COLVAR.metadynLog]]'' e.g. plot 'WALK1/META-COLVAR.metadynLog' u 2:3 pt 7.0 ps 1.0 t "",\ 'WALK2/META-COLVAR.metadynLog' u 2:3 pt 7.0 ps 1.0 t "" You can reconstruct the free energy profile from a restart file with the command: fes.popt -cp2k -mathlab -file META-META-1.restart -ndim 2 -ndw 1 2 -out fes_12.dat {{ :exercises:2015_cecam_tutorial:fes.jpg?direct&400 |}} ===== References ===== ~~REFNOTES~~