├── tutorial-1 ├── getRDF.py ├── autocorr.py ├── ex-2 │ ├── h2o.xyz │ ├── input.xml │ └── cp2k.in ├── ex-1 │ ├── in.water │ ├── water-gas.pdb │ ├── data.water │ └── input.xml ├── ex-3 │ └── n.01 │ │ ├── in.lmp │ │ ├── data.lmp │ │ └── input.xml ├── ex-4 │ ├── n.001 │ │ ├── input.xml │ │ └── in.cp2k │ └── n.128 │ │ ├── input.xml │ │ └── in.cp2k └── checklist.py ├── tutorial-3 ├── ex-1 │ ├── precomputed-trajectories │ │ ├── cmd │ │ │ ├── .vv │ │ │ ├── .dpl │ │ │ └── post-avg │ │ ├── nve │ │ │ └── post-avg │ │ ├── rpmd │ │ │ └── post-avg │ │ └── trpmd │ │ │ └── post-avg │ ├── lammps_inputs │ │ ├── in.tip4pf │ │ └── in.tip4pf.bak │ ├── nve │ │ └── nve.xml │ ├── rpmd │ │ └── rpmd.xml │ ├── trpmd │ │ └── trpmd.xml │ └── cmd │ │ └── cmd.xml ├── tools │ ├── charges.tip4pf │ ├── post-vel │ ├── post-avg │ ├── post-dpl │ ├── get_imacf_from_real.py │ └── posforce2imaginaryvv.py ├── ex-3 │ └── convergedspecs │ │ ├── trpmd.imvacf │ │ ├── cmd.imvacf │ │ ├── nve.imvacf │ │ └── rpmd.imvacf └── ex-2 │ └── precomputed-imvacf │ └── conv.imvacf ├── tutorial-4 ├── solutions │ └── input │ │ ├── TS │ │ ├── ts.instanton_FINAL_12.ener │ │ ├── init.xyz │ │ ├── ts.instanton_FINAL_12.xyz │ │ ├── ts.instanton_FINAL_forces_12.xyz │ │ ├── ts.out │ │ ├── input.xml │ │ ├── ts.pos_0.xyz │ │ └── ts.instanton_FINAL.hess_12 │ │ ├── reactant │ │ ├── phonons │ │ │ ├── freq.dat │ │ │ ├── init.xyz │ │ │ ├── min.phonons.eigval │ │ │ ├── data.out │ │ │ ├── min.out │ │ │ ├── input.xml │ │ │ ├── min.phonons.eigvec │ │ │ ├── min.phonons.mode │ │ │ ├── min.phonons.hess │ │ │ ├── min.phonons_full.hess │ │ │ ├── min.phonons.dynmat │ │ │ └── min.xc.xyz │ │ └── minization │ │ │ ├── init.xyz │ │ │ ├── input.xml │ │ │ ├── min.out │ │ │ └── RESTART │ │ └── instanton │ │ ├── 40 │ │ ├── init.xyz │ │ ├── inst.out │ │ ├── inst.instanton_0.ener │ │ ├── inst.instanton_FINAL_7.ener │ │ ├── input.xml │ │ └── hessian.dat │ │ └── 80 │ │ ├── inst.out │ │ ├── input.xml │ │ ├── inst.instanton_0.ener │ │ └── inst.instanton_FINAL_6.ener └── input │ ├── reactant │ ├── phonons │ │ ├── init.xyz │ │ └── input.xml │ └── minization │ │ ├── init.xyz │ │ └── input.xml │ ├── TS │ ├── init.xyz │ └── input.xml │ └── instanton │ └── 40 │ └── input.xml ├── README.md ├── tutorial-2 ├── README.md ├── ex-4 │ ├── in.ice_short │ ├── in.ice_long │ ├── in.ice │ ├── highorder.xml │ └── ultimate.xml ├── ex-1 │ ├── in.water │ ├── base.xml │ └── data.water ├── ex-2 │ ├── in.water │ └── data.water ├── ex-3 │ ├── in.water │ ├── npt.xml │ └── data.water └── data │ └── water-32.pdb └── tools ├── compile.sh ├── autocorr.py └── getRDF.py /tutorial-1/getRDF.py: -------------------------------------------------------------------------------- 1 | ../tools/getRDF.py -------------------------------------------------------------------------------- /tutorial-1/autocorr.py: -------------------------------------------------------------------------------- 1 | ../tools/autocorr.py -------------------------------------------------------------------------------- /tutorial-3/ex-1/precomputed-trajectories/cmd/.vv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/precomputed-trajectories/cmd/.dpl: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tutorial-3/tools/charges.tip4pf: -------------------------------------------------------------------------------- 1 | O 0.0000 2 | M -1.1128 3 | H 0.5564 4 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/TS/ts.instanton_FINAL_12.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.6505827608614363 3 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # tutorials-schools 2 | This repository contains 4 tutorials related to the i-PI code. Similar versions of these tutorials have been conducted at Path Integral Quantum Mechanics schools in CECAM. 3 | 4 | The tutorials are in jupyter-notebook format and can be found directly in the tutorial-# folders. 5 | -------------------------------------------------------------------------------- /tutorial-2/README.md: -------------------------------------------------------------------------------- 1 | Advanced Path Integral Methods: Simulating Water Across its Phase Diagram 2 | ========================================================================= 3 | 4 | This set of exercises covers advanced PIMD techniques, applied to the 5 | equilibrium sampling of water at different thermodynamic state points. 6 | 7 | -------------------------------------------------------------------------------- /tutorial-1/ex-2/h2o.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 8.000 8.000 8.000 90.00000 90.00000 90.00000 Step: 0 Bead: 0 positions{angstrom} cell{angstrom} 3 | O 0.54044984 -0.97485007 -0.21657970 4 | H 1.54328720 -0.97927800 -0.26039502 5 | H 0.18385954 -1.25804198 -1.07875142 6 | -------------------------------------------------------------------------------- /tutorial-2/ex-4/in.ice_short: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 5 | bond_style class2 6 | angle_style harmonic 7 | 8 | read_data data.ice_short 9 | # dummy pair coefficients 10 | pair_coeff * * 0 0 11 | 12 | neighbor 2.0 bin 13 | 14 | timestep 0.00025 15 | 16 | fix 1 all ipi lammps_ice.short 32345 unix 17 | 18 | run 100000000 19 | 20 | -------------------------------------------------------------------------------- /tools/compile.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | f2py --fcompiler=gfortran --f90flags=-ffree-line-length-0 -m fortran -c fortran.f90 4 | cd ../tutorial-1/ 5 | ln -s ../tools/fortran.cpython*so . 6 | cd ../tutorial-2/ 7 | ln -s ../tools/fortran.cpython*so . 8 | cd ../tutorial-3/ 9 | ln -s ../tools/fortran.cpython*so . 10 | cd ../tutorial-4/ 11 | ln -s ../tools/fortran.cpython*so . 12 | cd ../tools/ 13 | -------------------------------------------------------------------------------- /tutorial-1/ex-1/in.water: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data data.water 10 | pair_coeff * * 0 0 11 | pair_coeff 1 1 0.000295147 5.96946 12 | 13 | neighbor 2.0 bin 14 | 15 | fix 1 all ipi 300K-G.0 32345 unix 16 | run 100000000 17 | 18 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/freq.dat: -------------------------------------------------------------------------------- 1 | 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 3.976285529205385869e-05 3.976420322961130211e-05 3.977044354305435631e-05 4.995169310794363485e-05 4.995680662875626226e-05 1.860872423826852209e-04 2.081326339419599673e-04 2.081545492704249057e-04 2.081642712449477211e-04 2 | -------------------------------------------------------------------------------- /tutorial-1/ex-1/water-gas.pdb: -------------------------------------------------------------------------------- 1 | TITLE positions{angstrom} cell{angstrom} 2 | CRYST1 8.000 8.000 8.000 90.00 90.00 90.00 P 1 1 3 | ATOM 1 O 1 1 0.540 -0.975 -0.217 0.00 0.00 0 4 | ATOM 2 H 1 1 1.743 -0.909 -0.100 0.00 0.00 0 5 | ATOM 3 H 1 1 0.184 -1.258 -1.079 0.00 0.00 0 6 | END 7 | -------------------------------------------------------------------------------- /tutorial-2/ex-1/in.water: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data data.water 10 | pair_coeff * * 0 0 11 | pair_coeff 1 1 0.000295147 5.96946 12 | 13 | neighbor 2.0 bin 14 | 15 | timestep 0.00025 16 | 17 | fix 1 all ipi water 32345 unix 18 | 19 | run 100000000 20 | -------------------------------------------------------------------------------- /tutorial-2/ex-4/in.ice_long: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut/coul/long 17.01 5 | bond_style harmonic 6 | angle_style harmonic 7 | kspace_style ewald 0.0001 8 | 9 | read_data data.ice_long 10 | pair_coeff * * 0 0 11 | pair_coeff 1 1 0.000295147 5.96946 12 | 13 | neighbor 2.0 bin 14 | 15 | timestep 0.00025 16 | 17 | fix 1 all ipi lammps_ice.long 32345 unix 18 | 19 | run 100000000 20 | 21 | -------------------------------------------------------------------------------- /tutorial-4/input/reactant/phonons/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 32 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 3 | H 1.63089e+00 1.36267e+00 1.15180e+00 4 | C 8.44945e-01 7.89704e-01 6.62032e-01 5 | H 1.29316e+00 6.34755e-02 -1.44336e-02 6 | H 2.02556e-01 1.46367e+00 9.72761e-02 7 | H 2.53301e-01 2.69000e-01 1.41347e+00 8 | H 5.82909e+00 2.17935e+00 1.85263e+00 9 | -------------------------------------------------------------------------------- /tutorial-4/input/reactant/minization/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 130.18034 170.29206 240.21758 90.00000 90.00000 90.00000 cell{atomic_unit} Traj: positions{angstrom} Step: 12 Bead: 0 3 | H 2.23738e+00 1.48469e+00 1.25544e+00 4 | C 6.45117e-01 7.89716e-01 6.62042e-01 5 | H 1.30858e+00 1.61593e-01 6.94713e-02 6 | H -1.37407e-02 1.34855e+00 -8.78892e-04 7 | H 4.84318e-02 1.64198e-01 1.32427e+00 8 | H 5.82817e+00 2.17911e+00 1.85243e+00 9 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 32 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 3 | H 1.63089e+00 1.36267e+00 1.15180e+00 4 | C 8.44945e-01 7.89704e-01 6.62032e-01 5 | H 1.29316e+00 6.34755e-02 -1.44336e-02 6 | H 2.02556e-01 1.46367e+00 9.72761e-02 7 | H 2.53301e-01 2.69000e-01 1.41347e+00 8 | H 5.82909e+00 2.17935e+00 1.85263e+00 9 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/minization/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 130.18034 170.29206 240.21758 90.00000 90.00000 90.00000 cell{atomic_unit} Traj: positions{angstrom} Step: 12 Bead: 0 3 | H 2.23738e+00 1.48469e+00 1.25544e+00 4 | C 6.45117e-01 7.89716e-01 6.62042e-01 5 | H 1.30858e+00 1.61593e-01 6.94713e-02 6 | H -1.37407e-02 1.34855e+00 -8.78892e-04 7 | H 4.84318e-02 1.64198e-01 1.32427e+00 8 | H 5.82817e+00 2.17911e+00 1.85243e+00 9 | -------------------------------------------------------------------------------- /tutorial-3/tools/post-vel: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | lag=2000 4 | dt=1.0 5 | echo $# 6 | 7 | if [ $# -ge 1 ]; then lag=$1; fi 8 | if [ $# -ge 2 ]; then dt=$2; fi 9 | 10 | awk '{if (NF==4) print $1, $2, $3, $4, $2, $3, $4; else print $0}' *.vc.xyz | trajworks -ixyz -vvac -raw -vvlag $lag -vvftpad 10000 -vvftbox true -ts $dt > vel.dat 11 | 12 | awk '{print $3, $4}' vel.dat > tmp.f 13 | 14 | #awk '!/#/{print $2}' vel.dat | fourier -raw -dt $dt -pad 10000 -win hanning > tmp.f 15 | 16 | awk '{print $1*5308.8375, $2}' tmp.f > vel.ft 17 | 18 | rm tmp.* 19 | -------------------------------------------------------------------------------- /tutorial-4/input/TS/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 130.18034 170.29206 240.21758 90.00000 90.00000 90.00000 cell{atomic_unit} Traj: positions{angstrom} Step: 12 Bead: 0 3 | H 1.3762859974402626 1.6475377505750781 1.3947309252535616 4 | C 0.5610492771673459 0.6910172235578630 0.5785825986233499 5 | H 0.0313332395759015 0.1474340996450444 1.3607366615876173 6 | H 1.3412729333952838 0.1418736998062487 0.0516893010969587 7 | H -0.0352236727959057 1.3786671745683925 -0.0209976311964991 8 | H 2.162629 2.651689 2.290930 9 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/TS/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 130.18034 170.29206 240.21758 90.00000 90.00000 90.00000 cell{atomic_unit} Traj: positions{angstrom} Step: 12 Bead: 0 3 | H 1.3762859974402626 1.6475377505750781 1.3947309252535616 4 | C 0.5610492771673459 0.6910172235578630 0.5785825986233499 5 | H 0.0313332395759015 0.1474340996450444 1.3607366615876173 6 | H 1.3412729333952838 0.1418736998062487 0.0516893010969587 7 | H -0.0352236727959057 1.3786671745683925 -0.0209976311964991 8 | H 2.162629 2.651689 2.290930 9 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/80/inst.out: -------------------------------------------------------------------------------- 1 | # column 1 --> step : The current simulation time step. 2 | # column 2 --> potential{electronvolt} : The physical system potential energy. 3 | 0.00000000e+00 6.18877098e-01 4 | 1.00000000e+00 6.18532498e-01 5 | 2.00000000e+00 6.18825292e-01 6 | 3.00000000e+00 6.18821105e-01 7 | 4.00000000e+00 6.18869103e-01 8 | 5.00000000e+00 6.18884274e-01 9 | 6.00000000e+00 6.18897996e-01 10 | 7.00000000e+00 6.18905280e-01 11 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/40/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | CELL(abcABC): 200.000000 200.000000 200.000000 90.000000 90.000000 90.000000 cell{atomic_unit} Traj: positions{angstrom} Bead: 0 3 | H 1.3384253255715128 1.6274017113145895 1.3889068156026712 4 | C 0.5982853188055953 0.7370620057626184 0.6191260188528143 5 | H 0.018252993834192818 0.12724588296258574 1.311973076085819 6 | H 1.3129952926415505 0.14128880735063695 0.05114876420112837 7 | H -0.04034313468639996 1.336324755510271 -0.030019349733218834 8 | H 1.8032591355546759 2.186266970192309 1.8719610572483019 9 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/TS/ts.instanton_FINAL_12.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | CELL(abcABC): 200.000000 200.000000 200.000000 90.000000 90.000000 90.000000 cell{atomic_unit} Traj: positions{angstrom} Bead: 0 3 | H 1.3384253255715128 1.6274017113145895 1.3889068156026712 4 | C 0.5982853188055953 0.7370620057626184 0.6191260188528143 5 | H 0.018252993834192818 0.12724588296258574 1.311973076085819 6 | H 1.3129952926415505 0.14128880735063695 0.05114876420112837 7 | H -0.04034313468639996 1.336324755510271 -0.030019349733218834 8 | H 1.8032591355546759 2.186266970192309 1.8719610572483019 9 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/lammps_inputs/in.tip4pf: -------------------------------------------------------------------------------- 1 | units real 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data ./data.tip4pf 10 | pair_coeff * 2 0 0 11 | pair_coeff 1 1 0.1852 3.1589022 12 | 13 | #tip4pf bond parameters 14 | bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577 15 | angle_coeff 1 43.93 107.4 16 | 17 | neighbor 2.0 bin 18 | 19 | timestep 0.00025 20 | 21 | fix 1 all ipi addr 32345 unix 22 | 23 | run 1000000000 24 | 25 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/lammps_inputs/in.tip4pf.bak: -------------------------------------------------------------------------------- 1 | units real 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 8 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data ./data.tip4pf 10 | pair_coeff * 2 0 0 11 | pair_coeff 1 1 0.1852 3.1589022 12 | 13 | #tip4pf bond parameters 14 | bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577 15 | angle_coeff 1 43.93 107.4 16 | 17 | neighbor 2.0 bin 18 | 19 | timestep 0.00025 20 | 21 | fix 1 all ipi addr 32345 unix 22 | 23 | run 1000000000 24 | 25 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.phonons.eigval: -------------------------------------------------------------------------------- 1 | # Eigenvalues (atomic units) 2 | -5.938963328909619e-09 3 | -3.634812594373227e-09 4 | -2.0950648590831742e-09 5 | -1.2856949370864437e-09 6 | -1.2501525226049213e-09 7 | -8.500735292415501e-14 8 | 6.643846599891028e-13 9 | 1.661003113535475e-12 10 | 1.0923227353225234e-08 11 | 3.976285552383113e-05 12 | 3.976420326757967e-05 13 | 3.9770443839122275e-05 14 | 4.9951693183278976e-05 15 | 4.995680671457014e-05 16 | 0.00018608724242523284 17 | 0.00020813263396113324 18 | 0.00020815454926272338 19 | 0.00020816427135329353 20 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/data.out: -------------------------------------------------------------------------------- 1 | 2 | We are ready to start. Reading RESTART ... (This can take a while) 3 | 4 | Temperature: 300.0 K 5 | NBEADS: 1 6 | atoms: 5 7 | ASR: poly 8 | 1/(betaP*hbar) = 0.00095 9 | Diagonalization ... 10 | 11 | 12 | Final lowest 10 frequencies (cm^-1) 13 | [1383.00 1383.02 1383.13 1550.10 1550.18 2991.87 3164.13 3164.29 3164.37] 14 | 15 | We are done. Reactants. Nbeads 160 16 | Qtras(bohr^-3) | Qrot | logQvib_rp 17 | 9.298 | 438.764 | -47.337 18 | 19 | A file with the frequencies in atomic units was generated 20 | 21 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/40/inst.out: -------------------------------------------------------------------------------- 1 | # column 1 --> step : The current simulation time step. 2 | # column 2 --> potential{electronvolt} : The physical system potential energy. 3 | 0.00000000e+00 6.50582761e-01 4 | 1.00000000e+00 6.29204774e-01 5 | 2.00000000e+00 6.27791662e-01 6 | 3.00000000e+00 6.15349564e-01 7 | 4.00000000e+00 6.19161970e-01 8 | 5.00000000e+00 6.18799930e-01 9 | 6.00000000e+00 6.18982866e-01 10 | 7.00000000e+00 6.18881630e-01 11 | 8.00000000e+00 6.18877053e-01 12 | -------------------------------------------------------------------------------- /tutorial-3/tools/post-avg: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | prefix=$1 4 | paste ${prefix}_*/dpl.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.dpl 5 | paste ${prefix}_*/vel.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.vv 6 | #paste ${prefix}-*/msdcent.dat | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ~rossi/${prefix}.msdcent 7 | -------------------------------------------------------------------------------- /tutorial-2/ex-4/in.ice: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | # Since one can only use Ewald with triclinic boxes, 5 | # and there is no TIP4P/Ewald in LAMMPS, this potential 6 | # is not exactly QTIP4P/f. Do **NOT** use this example 7 | # as a template for anything serious! 8 | pair_style lj/cut/coul/long 17.01 9 | bond_style class2 10 | angle_style harmonic 11 | kspace_style ewald 0.0001 12 | 13 | read_data data.ice 14 | pair_coeff * * 0 0 15 | pair_coeff 1 1 0.000295147 5.96946 16 | 17 | neighbor 2.0 bin 18 | 19 | timestep 0.00025 20 | 21 | fix 1 all ipi lammps_ice 32345 unix 22 | 23 | run 100000000 24 | 25 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/TS/ts.instanton_FINAL_forces_12.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | CELL(abcABC): 200.000000 200.000000 200.000000 90.000000 90.000000 90.000000 cell{atomic_unit} Traj: positions{atomic_unit} Bead: 0 3 | H 1.2740697385993371e-06 -1.462774346094875e-07 -8.470002477167781e-07 4 | C 3.1689373347631995e-06 -2.9889424268958464e-07 -2.331002058042486e-06 5 | H 6.076916747588257e-07 1.5374646000765322e-06 1.7959023157487761e-06 6 | H -1.967964680105183e-06 -1.9691359653961626e-06 -1.328043230941489e-06 7 | H -3.83248988100604e-07 4.6361248173809594e-07 6.84280410112592e-07 8 | H -2.6994628754550827e-06 4.1325276534109884e-07 2.0258406063788925e-06 9 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/precomputed-trajectories/cmd/post-avg: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | prefix=$1 4 | paste ${prefix}_*/dpl.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.dpl 5 | paste ${prefix}_*/vel.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.vv 6 | #paste ${prefix}-*/msdcent.dat | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ~rossi/${prefix}.msdcent 7 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/precomputed-trajectories/nve/post-avg: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | prefix=$1 4 | paste ${prefix}_*/dpl.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.dpl 5 | paste ${prefix}_*/vel.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.vv 6 | #paste ${prefix}-*/msdcent.dat | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ~rossi/${prefix}.msdcent 7 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/precomputed-trajectories/rpmd/post-avg: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | prefix=$1 4 | paste ${prefix}_*/dpl.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.dpl 5 | paste ${prefix}_*/vel.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.vv 6 | #paste ${prefix}-*/msdcent.dat | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ~rossi/${prefix}.msdcent 7 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/precomputed-trajectories/trpmd/post-avg: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | prefix=$1 4 | paste ${prefix}_*/dpl.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.dpl 5 | paste ${prefix}_*/vel.ft | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ${prefix}.vv 6 | #paste ${prefix}-*/msdcent.dat | awk '{t2=t=n=0; for (i=2; i<=NF; i+=2) { t+=$i; t2+=$i*$i; n++ } printf "%12.5e %12.5e %12.5e\n", $1, t/n, sqrt(t2/n-(t/n)*(t/n))/sqrt(n-1)}' > ~rossi/${prefix}.msdcent 7 | -------------------------------------------------------------------------------- /tutorial-1/ex-3/n.01/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | #pair_style lj/cut/coul/long 17.01 5 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 6 | #bond_style harmonic 7 | bond_style class2 8 | angle_style harmonic 9 | #kspace_style pppm 0.0001 10 | kspace_style pppm/tip4p 0.0001 11 | 12 | read_data data.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | 18 | timestep 0.00025 19 | 20 | #velocity all create 298.0 2345187 21 | 22 | #thermo_style multi 23 | #thermo 1 24 | 25 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 26 | #fix 1 all nve 27 | fix 1 all ipi driver.01 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /tutorial-2/ex-2/in.water: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | #pair_style lj/cut/coul/long 17.01 5 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 6 | #bond_style harmonic 7 | bond_style class2 8 | angle_style harmonic 9 | #kspace_style pppm 0.0001 10 | kspace_style pppm/tip4p 0.0001 11 | 12 | read_data data.water 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | 18 | timestep 0.00025 19 | 20 | #velocity all create 298.0 2345187 21 | 22 | #thermo_style multi 23 | #thermo 1 24 | 25 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 26 | #fix 1 all nve 27 | fix 1 all ipi water-gle 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /tutorial-2/ex-3/in.water: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | #pair_style lj/cut/coul/long 17.01 5 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 17.007 6 | #bond_style harmonic 7 | bond_style class2 8 | angle_style harmonic 9 | #kspace_style pppm 0.0001 10 | kspace_style pppm/tip4p 0.0001 11 | 12 | read_data data.water 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | 18 | timestep 0.00025 19 | 20 | #velocity all create 298.0 2345187 21 | 22 | #thermo_style multi 23 | #thermo 1 24 | 25 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 26 | #fix 1 all nve 27 | fix 1 all ipi water-npt 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/TS/ts.out: -------------------------------------------------------------------------------- 1 | # column 1 --> step : The current simulation time step. 2 | # column 2 --> potential{electronvolt} : The physical system potential energy. 3 | 0.00000000e+00 1.41494114e+00 4 | 1.00000000e+00 1.32894296e+00 5 | 2.00000000e+00 8.41733571e-01 6 | 3.00000000e+00 6.39981496e-01 7 | 4.00000000e+00 6.59012705e-01 8 | 5.00000000e+00 6.52906552e-01 9 | 6.00000000e+00 6.50658096e-01 10 | 7.00000000e+00 6.50586753e-01 11 | 8.00000000e+00 6.50586651e-01 12 | 9.00000000e+00 6.50584246e-01 13 | 1.00000000e+01 6.50583335e-01 14 | 1.10000000e+01 6.50582965e-01 15 | 1.20000000e+01 6.50582818e-01 16 | 1.30000000e+01 6.50582761e-01 17 | -------------------------------------------------------------------------------- /tutorial-1/ex-1/data.water: -------------------------------------------------------------------------------- 1 | LAMMPS Description 2 | 3 | 3 atoms 4 | 2 bonds 5 | 1 angles 6 | 7 | 2 atom types 8 | 1 bond types 9 | 1 angle types 10 | 11 | 0 35.233 xlo xhi 12 | 0 35.233 ylo yhi 13 | 0 35.233 zlo zhi 14 | 15 | Masses 16 | 17 | 1 15.9994 18 | 2 1.0080 19 | 20 | Bond Coeffs 21 | 22 | 1 1.78 0.2708585 -0.327738785 0.231328959 23 | 24 | Angle Coeffs 25 | 26 | 1 0.0700 107.400000 27 | 28 | Atoms 29 | 30 | 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 31 | 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 32 | 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 33 | 34 | Bonds 35 | 36 | 1 1 1 2 37 | 2 1 1 3 38 | 39 | Angles 40 | 41 | 1 1 2 1 3 42 | -------------------------------------------------------------------------------- /tutorial-1/ex-3/n.01/data.lmp: -------------------------------------------------------------------------------- 1 | LAMMPS Description 2 | 3 | 3 atoms 4 | 2 bonds 5 | 1 angles 6 | 7 | 2 atom types 8 | 1 bond types 9 | 1 angle types 10 | 11 | -17.6165 17.6165 xlo xhi 12 | -17.6165 17.6165 ylo yhi 13 | -17.6165 17.6165 zlo zhi 14 | 15 | Masses 16 | 17 | 1 15.9994 18 | 2 1.0080 19 | 20 | Bond Coeffs 21 | 22 | 1 1.78 0.2708585 -0.327738785 0.231328959 23 | 24 | Angle Coeffs 25 | 26 | 1 0.0700 107.400000 27 | 28 | Atoms 29 | 30 | 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 31 | 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 32 | 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 33 | 34 | Bonds 35 | 36 | 1 1 1 2 37 | 2 1 1 3 38 | 39 | Angles 40 | 41 | 1 1 2 1 3 42 | -------------------------------------------------------------------------------- /tutorial-3/tools/post-dpl: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | lag=2000 4 | dt=1.0 5 | echo $# 6 | 7 | if [ $# -ge 1 ]; then lag=$1; fi 8 | if [ $# -ge 2 ]; then dt=$2; fi 9 | cat *.vc.xyz | awk 'BEGIN {nh=0; g=0.73612; } 10 | !/[OH]/{print $0}; /O/{ox=$2; oy=$2; oz=$3;} 11 | /H/{nh++; print $0; if (nh%2==1) {h1x=$2; h1y=$3; h1z=$3} else { 12 | h2x=$2; h2y=$3; h2z=$4; 13 | print "M", g*ox+(1-g)/2.0*(h1x+h2x), g*oz+(1-g)/2.0*(h1z+h2z), g*oz+(1-g)/2.0*(h1z+h2z);} } 14 | ' | trajworks -ixyz -qat ./charges.tip4pf -dpl -ts $dt > dpl.dat 15 | 16 | awk '!/#/{print $2}' dpl.dat | autocorr -raw -maxlag $lag -timestep $dt > tmp.x 17 | awk '!/#/{print $3}' dpl.dat | autocorr -raw -maxlag $lag -timestep $dt > tmp.y 18 | awk '!/#/{print $4}' dpl.dat | autocorr -raw -maxlag $lag -timestep $dt > tmp.z 19 | 20 | for w in x y z; do 21 | awk '!/#/{print $2}' tmp.$w | fourier -raw -dt $dt -pad 10000 -win hanning > tmp.f$w 22 | done 23 | 24 | paste tmp.f? | awk '{print $1*5308.8375, ($2+$4+$6)/3}' > dpl.ft 25 | 26 | rm tmp.* 27 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.out: -------------------------------------------------------------------------------- 1 | # column 1 --> step : The current simulation time step. 2 | # column 2 --> potential{electronvolt} : The physical system potential energy. 3 | 0.00000000e+00 1.95221318e-04 4 | 1.00000000e+00 1.95221318e-04 5 | 2.00000000e+00 1.95221318e-04 6 | 3.00000000e+00 1.95221318e-04 7 | 4.00000000e+00 1.95221318e-04 8 | 5.00000000e+00 1.95221318e-04 9 | 6.00000000e+00 1.95221318e-04 10 | 7.00000000e+00 1.95221318e-04 11 | 8.00000000e+00 1.95221318e-04 12 | 9.00000000e+00 1.95221318e-04 13 | 1.00000000e+01 1.95221318e-04 14 | 1.10000000e+01 1.95221318e-04 15 | 1.20000000e+01 1.95221318e-04 16 | 1.30000000e+01 1.95221318e-04 17 | 1.40000000e+01 1.95221318e-04 18 | 1.50000000e+01 1.95221318e-04 19 | 1.60000000e+01 1.95221318e-04 20 | 1.70000000e+01 1.95221318e-04 21 | 1.80000000e+01 1.95221318e-04 22 | -------------------------------------------------------------------------------- /tutorial-4/input/reactant/phonons/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | 6 | 400 7 | 8 |
localhost
9 | 10 | 11 | 12 | init.xyz 13 | [200.0, 200.0, 200.0 ] 14 | 15 | 16 | 17 | 18 | 19 | 20 | 0.01 21 | phonons 22 | none 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | 6 | 400 7 | 8 |
localhost
9 | 10 | 11 | 12 | init.xyz 13 | [200.0, 200.0, 200.0 ] 14 | 15 | 16 | 17 | 18 | 19 | 20 | 0.01 21 | phonons 22 | none 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/40/inst.instanton_0.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.6099210091280085 3 | 1 0.6107417129035733 4 | 2 0.6123523747553932 5 | 3 0.6146913055422606 6 | 4 0.6176672375903108 7 | 5 0.6211617287991036 8 | 6 0.6250328962223357 9 | 7 0.6291207211415983 10 | 8 0.6332540175769278 11 | 9 0.637258913608358 12 | 10 0.6409683937574521 13 | 11 0.6442321491178662 14 | 12 0.6469257538495115 15 | 13 0.6489581054266015 16 | 14 0.6502761801760413 17 | 15 0.6508664693977846 18 | 16 0.6507529247152485 19 | 17 0.6499917581084249 20 | 18 0.6486638969487577 21 | 19 0.6468661867982417 22 | 20 0.6447025095957888 23 | 21 0.6422758460970978 24 | 22 0.6396820143115354 25 | 23 0.6370054457205423 26 | 24 0.6343170041983944 27 | 25 0.6316735750485235 28 | 26 0.629118985677331 29 | 27 0.6266857661327697 30 | 28 0.6243972948586768 31 | 29 0.6222699686229605 32 | 30 0.6203151518861799 33 | 31 0.6185407728932505 34 | 32 0.6169525253035735 35 | 33 0.6155546979865117 36 | 34 0.6143506923215224 37 | 35 0.613343301084332 38 | 36 0.6125348227156027 39 | 37 0.6119270753901783 40 | 38 0.6115213624187255 41 | 39 0.6113184275782758 42 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/40/inst.instanton_FINAL_7.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.5909982141580981 3 | 1 0.5925910331144739 4 | 2 0.5957046990496287 5 | 3 0.6001953010546319 6 | 4 0.6058481117473732 7 | 5 0.6123816875018043 8 | 6 0.6194571975775096 9 | 7 0.6266948830728482 10 | 8 0.6336983288578081 11 | 9 0.6400852269558983 12 | 10 0.6455209648115944 13 | 11 0.6497494889044808 14 | 12 0.6526153748821057 15 | 13 0.6540724194751824 16 | 14 0.6541771221369291 17 | 15 0.6530691048997508 18 | 16 0.650943451708177 19 | 17 0.6480211305338738 20 | 18 0.6445229237435552 21 | 19 0.6406502888887574 22 | 20 0.6365741829861314 23 | 21 0.6324310111118613 24 | 22 0.6283238425545109 25 | 23 0.6243267857533278 26 | 24 0.620490710232827 27 | 25 0.6168490324380612 28 | 26 0.6134228118622519 29 | 27 0.610224822272334 30 | 28 0.607262563988344 31 | 29 0.604540366354895 32 | 30 0.6020607708693129 33 | 31 0.5998253824126056 34 | 32 0.5978353559842007 35 | 33 0.5960916480046169 36 | 34 0.594595124818584 37 | 35 0.5933465912947099 38 | 36 0.5923467796717761 39 | 37 0.5915963227021556 40 | 38 0.5910957244438957 41 | 39 0.5908453354638681 42 | -------------------------------------------------------------------------------- /tutorial-4/input/reactant/minization/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | 6 | 400 7 | 8 |
localhost
9 | 10 | 11 | 12 | init.xyz 13 | [200.0, 200.0, 200.0 ] 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 5e-5 22 | 5e-5 23 | 5e-5 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/minization/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | 6 | 400 7 | 8 |
localhost
9 | 10 | 11 | 12 | init.xyz 13 | [200.0, 200.0, 200.0 ] 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 5e-5 22 | 5e-5 23 | 5e-5 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /tutorial-1/ex-4/n.001/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 1.00000000e-04
driver.ch5.001
4 | 5 | 80000 6 | 7 | [ step, time{femtosecond}, conserved, temperature, kinetic_cv, 8 | potential, kinetic_cv(H), kinetic_cv(C) ] 9 | positions{angstrom} 10 | 11 | 12 | 18885 13 | 14 | 15 | 16 | init.chk 17 | [ 25., 25.0, 25.0 ] 18 | 100 19 | 20 | 21 | 22 | 23 | 0.25 24 | 100 25 | 26 | 27 | 28 | 29 | 100.0 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /tutorial-1/ex-4/n.128/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 1.00000000e-04
driver.ch5.128
4 | 5 | 80000 6 | 7 | [ step, time{femtosecond}, conserved, temperature, kinetic_cv, 8 | potential, kinetic_cv(H), kinetic_cv(C) ] 9 | positions{angstrom} 10 | 11 | 12 | 18885 13 | 14 | 15 | 16 | init.chk 17 | [ 25., 25.0, 25.0 ] 18 | 100 19 | 20 | 21 | 22 | 23 | 0.25 24 | 100 25 | 26 | 27 | 28 | 29 | 100.0 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/nve/nve.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] 4 | x_centroid{angstrom} 5 | v_centroid 6 | 7 | 8 | 20000 9 | 32xxx845 10 | 11 |
nve-h2o-xxx
12 | 13 | 14 | 15 | ../../checkpoint-nvt/h2o-ice-nvt.restart_xxx 16 | 200 17 | 18 | 19 | 20 | 21 | 22 | 23 | 0.5 24 | 25 | 26 | 27 | 200 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /tutorial-1/ex-3/n.01/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ time{picosecond}, conserved, temperature{kelvin}, kinetic_cv(O){electronvolt}, kinetic_cv(H){electronvolt}, potential{electronvolt} ] 4 | positions{angstrom} 5 | 6 | 7 | 40000 8 | 23658 9 | 10 |
driver.01
11 | 31400 0.001 400 12 | 13 | 14 | 15 | init.chk 16 | 17 | 18 | 19 | 300 20 | 21 | 22 | False 23 | 24 | 0.25 25 | 26 | 100 27 | 28 | 29 | 30 | 31 | 32 | -------------------------------------------------------------------------------- /tutorial-1/ex-1/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | [ step, time{picosecond}, conserved, temperature{kelvin}, potential ] 5 | 6 | x_centroid{angstrom} 7 | 8 | 9 | 3924 10 | 800000 11 | 12 |
300K-G.0
13 | 14 | 15 | 16 | water-gas.pdb 17 | 300 18 | 19 | 20 | 21 | 22 | 23 | 300 24 | 25 | 26 | False 27 | 28 | 0.5 29 | 30 | 100 31 | 0.1 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | -------------------------------------------------------------------------------- /tutorial-1/ex-2/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | [ step, time{picosecond}, conserved, temperature{kelvin}, potential ] 5 | 6 | x_centroid{angstrom} 7 | 8 | 9 | 3924 10 | 800000 11 | 12 | 1.00000000e-02 13 | 4 14 | 20614 15 | 6.00000000e+02 16 |
localhost
17 | 18 | 19 | 20 | h2o.xyz 21 | 300 22 | 23 | 24 | 25 | 26 | 27 | 300 28 | 29 | 30 | True 31 | 32 | 1.0 33 | 34 | 100 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/rpmd/rpmd.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] 4 | 5 | x_centroid{angstrom} 6 | v_centroid 7 | forces 8 | positions{angstrom} 9 | 10 | 20000 11 | 32xxx45 12 | 13 | 0.0001 14 | 8 15 |
h2o-rpmd-xxx
16 | 17 | 18 | 19 | ../../checkpoint-pimd/h2o-ice-pimd.restart_xxx 20 | 200 21 | 22 | 23 | 24 | 25 | 26 | 27 | 0.25 28 | 29 | 30 | 31 | 200 32 | 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/minization/min.out: -------------------------------------------------------------------------------- 1 | # column 1 --> step : The current simulation time step. 2 | # column 2 --> potential{electronvolt} : The physical system potential energy. 3 | 0.00000000e+00 3.26575622e+00 4 | 1.00000000e+00 1.12604684e+00 5 | 2.00000000e+00 3.40436178e-01 6 | 3.00000000e+00 8.57059022e-02 7 | 4.00000000e+00 3.98682446e-02 8 | 5.00000000e+00 2.09743660e-02 9 | 6.00000000e+00 1.23134988e-02 10 | 7.00000000e+00 7.26008108e-03 11 | 8.00000000e+00 4.39016595e-03 12 | 9.00000000e+00 2.68821675e-03 13 | 1.00000000e+01 1.69475986e-03 14 | 1.10000000e+01 1.10017689e-03 15 | 1.20000000e+01 7.46520693e-04 16 | 1.30000000e+01 5.32457399e-04 17 | 1.40000000e+01 4.03076065e-04 18 | 1.50000000e+01 3.23866644e-04 19 | 1.60000000e+01 2.75338454e-04 20 | 1.70000000e+01 2.45320020e-04 21 | 1.80000000e+01 2.26721261e-04 22 | 1.90000000e+01 2.15112551e-04 23 | 2.00000000e+01 2.07851923e-04 24 | 2.10000000e+01 2.03282852e-04 25 | 2.20000000e+01 2.00399843e-04 26 | 2.30000000e+01 1.98569134e-04 27 | 2.40000000e+01 1.97401612e-04 28 | 2.50000000e+01 1.96650222e-04 29 | 2.60000000e+01 1.96162526e-04 30 | 2.70000000e+01 1.95840616e-04 31 | 2.80000000e+01 1.95624421e-04 32 | 2.90000000e+01 1.95474479e-04 33 | 3.00000000e+01 1.95367135e-04 34 | 3.10000000e+01 1.95286148e-04 35 | 3.20000000e+01 1.95222276e-04 36 | -------------------------------------------------------------------------------- /tutorial-2/ex-4/highorder.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, kinetic_opsc, kinetic_tdsc, potential_opsc, potential_tdsc] 4 | positions{angstrom} 5 | 6 | 7 | 100000 8 | 31415 9 | 10 |
lammps_ice
11 | 12 | 13 | 14 | ../data/ice-96.pdb 15 | 100 16 | [ 25.6156, 0, 0, 0, 29.5783, 0, 0, 0, 27.8867 ] 17 | 18 | 19 | 20 | 100 21 | 22 | 23 | 24 | 25 | 100 26 | 0.5 27 | 28 | 0.25 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /tutorial-1/ex-2/cp2k.in: -------------------------------------------------------------------------------- 1 | &GLOBAL 2 | PRINT_LEVEL LOW 3 | WALLTIME 2682000 4 | PROJECT H2O 5 | RUN_TYPE DRIVER 6 | SEED 1 7 | &END GLOBAL 8 | 9 | &MOTION 10 | 11 | &DRIVER 12 | HOST localhost 13 | UNIX FALSE 14 | PORT 20614 15 | &END DRIVER 16 | &END MOTION 17 | 18 | &FORCE_EVAL 19 | METHOD Quickstep 20 | 21 | &DFT 22 | WFN_RESTART_FILE_NAME H2O-RESTART.wfn 23 | 24 | BASIS_SET_FILE_NAME ./basis/GTH_BASIS_SETS 25 | POTENTIAL_FILE_NAME ./basis/GTH_POTENTIALS 26 | 27 | &MGRID 28 | CUTOFF 250 29 | &END MGRID 30 | 31 | &QS 32 | MAP_CONSISTENT 33 | &END QS 34 | 35 | &SCF 36 | SCF_GUESS RESTART 37 | EPS_SCF 5.e-7 38 | MAX_SCF 20 39 | &OT 40 | MINIMIZER DIIS 41 | N_DIIS 7 42 | PRECONDITIONER FULL_ALL 43 | &END OT 44 | 45 | &OUTER_SCF 46 | TYPE NONE 47 | OPTIMIZER NONE 48 | EPS_SCF 5.0E-7 49 | MAX_SCF 25 50 | 51 | &END OUTER_SCF 52 | &END SCF 53 | 54 | &XC 55 | &XC_FUNCTIONAL BLYP 56 | &END XC_FUNCTIONAL 57 | &XC_GRID 58 | XC_DERIV SPLINE2 59 | &END XC_GRID 60 | &END XC 61 | &END DFT 62 | STRESS_TENSOR DIAGONAL_ANALYTICAL 63 | 64 | &SUBSYS 65 | &CELL 66 | ABC 8 8 8 67 | &END CELL 68 | 69 | &KIND H 70 | BASIS_SET DZVP-GTH 71 | POTENTIAL GTH-BLYP-q1 72 | ELEMENT H 73 | &END KIND 74 | 75 | &KIND O 76 | BASIS_SET DZVP-GTH 77 | POTENTIAL GTH-BLYP-q6 78 | &END KIND 79 | 80 | &COORD 81 | O 1.8374 3.36775 12.3092 82 | H 2.9612 4.19864 11.1874 83 | H 1.56927 4.83071 13.4077 84 | &END COORD 85 | 86 | &END SUBSYS 87 | &END FORCE_EVAL 88 | 89 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/trpmd/trpmd.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] 4 | 5 | x_centroid{angstrom} 6 | v_centroid 7 | forces 8 | positions{angstrom} 9 | 10 | 20000 11 | 32xxx45 12 | 13 | 0.0001 14 | 8 15 |
h2o-trpmd-xxx
16 | 17 | 18 | 19 | ../../checkpoint-pimd/h2o-ice-pimd.restart_xxx 20 | 200 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 1000 29 | 0.5 30 | 31 | 0.50 32 | 33 | 34 | 35 | 200 36 | 37 | 38 | 39 | 40 | -------------------------------------------------------------------------------- /tutorial-4/input/TS/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | positions{angstrom} 4 | [ step, potential{electronvolt}] 5 | 6 | 20 7 | 8 |
localhost
9 | 10 | 11 | 12 | init.xyz 13 | [200.0, 200.0, 200.0 ] 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 5e-6 22 | 5e-6 23 | 1e-3 24 | 25 | -1 26 | powell 27 | poly 28 | true 29 | true 30 | 0.3 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/TS/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | positions{angstrom} 4 | [ step, potential{electronvolt}] 5 | 6 | 20 7 | 8 |
localhost
9 | 10 | 11 | 12 | init.xyz 13 | [200.0, 200.0, 200.0 ] 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 5e-6 22 | 5e-6 23 | 1e-3 24 | 25 | -1 26 | powell 27 | poly 28 | true 29 | true 30 | 0.3 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /tutorial-3/ex-1/cmd/cmd.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal}] 4 | 5 | x_centroid{angstrom} 6 | v_centroid 7 | forces 8 | positions{angstrom} 9 | 10 | 200000 11 | 32xxx45 12 | 13 | 0.0001 14 | 8 15 |
h2o-cmd-xxx
16 | 17 | 18 | 19 | [13000] 20 | 21 | 22 | ../../checkpoint-pimd/h2o-ice-pimd.restart_xxx 23 | 200 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 1000 32 | 0.01 33 | 34 | 0.025 35 | 36 | 37 | 38 | 200 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /tutorial-1/checklist.py: -------------------------------------------------------------------------------- 1 | ### CHECKING IF FILES AND DIRECTORIES ARE IN PLACE 2 | 3 | import os 4 | dirs = ['ex-1','ex-2','ex-3','ex-4'] 5 | ex1files = ['data.water','in.water','input.xml','water-gas.pdb'] 6 | ex1dirs = [] 7 | ex1dirfs = [] 8 | ex2files = ['cp2k.in','h2o.xyz','input.xml'] 9 | ex2dirs = ['basis'] 10 | ex2dirfs = [] 11 | ex3files = ['extract-gOH.bash','extract-pot.bash','extract-kin.bash'] 12 | ex3dirs = ['n.01','n.02','n.04','n.08','n.16','n.32','n.64'] 13 | ex3dirfs = ['boxfile','data.lmp','in.lmp','init.chk','input.xml'] 14 | ex4files = [] 15 | ex4dirs = ['n.001','n.128'] 16 | ex4dirfs = ['boxfile','in.cp2k','init.chk','input.xml','start.chk'] 17 | 18 | def fileChecker(): 19 | 20 | misses = [] 21 | for dr in dirs: 22 | 23 | if(os.path.isdir(dr)==False): 24 | globals()[dr]=False 25 | misses.extend([dr+'/']) 26 | else: 27 | globals()[dr]=True 28 | if not all([os.path.isfile(dr+'/'+ff) for ff in globals()[dr[:2]+dr[-1]+'files']]): 29 | misses.extend([dr+'/'+ff for ff in globals()[dr[:2]+dr[-1]+'files'] 30 | if os.path.isfile(dr+'/'+ff)==False]) 31 | globals()[dr]=False 32 | if not all([os.path.isdir(dr+'/'+dd) for dd in globals()[dr[:2]+dr[-1]+'dirs']]): 33 | misses.extend([dr+'/'+dd+'/' for dd in globals()[dr[:2]+dr[-1]+'dirs'] 34 | if os.path.isdir(dr+'/'+dd)==False]) 35 | globals()[dr]=False 36 | if not all([os.path.isfile(dr+'/'+dd+'/'+df) for dd in globals()[dr[:2]+dr[-1]+'dirs'] 37 | for df in globals()[dr[:2]+dr[-1]+'dirfs']]): 38 | misses.extend([dr+'/'+dd+'/'+df for dd in globals()[dr[:2]+dr[-1]+'dirs'] 39 | for df in globals()[dr[:2]+dr[-1]+'dirfs'] 40 | if os.path.isfile(dr+'/'+dd+'/'+df)==False]) 41 | globals()[dr]=False 42 | 43 | if misses: 44 | print(*['You are missing the following files or directories:', 45 | '---------------------------------------------------', 46 | *misses],sep='\n') 47 | 48 | if all([globals()[dr] for dr in dirs]): 49 | print('Everything is ready, you can start the tutorial.') 50 | -------------------------------------------------------------------------------- /tutorial-2/ex-1/base.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential] 5 | positions{angstrom} 6 | 7 | 8 | 40000 9 | 10 | 32345 11 | 12 | 13 | 14 |
water
0.001 15 | 16 | 17 | 18 | 19 | 20 | ../data/water-32.pdb 21 | 600 22 | 23 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 50 33 | 0.5 34 | 35 | 0.25 36 | 37 | 38 | 39 | 300 40 | 41 | 42 | 43 | 44 | 45 | -------------------------------------------------------------------------------- /tutorial-4/input/instanton/40/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | 5 | 20 6 | 7 |
localhost
8 | 9 | 10 | 11 | init.xyz 12 | [200.0, 200.0, 200.0 ] 13 | 14 | 15 | 16 | 17 | 18 | 300 19 | 20 | 21 | [ 0,1,2,3,4,5 ] 22 | 23 | 24 | 25 | 10 26 | 27 | 5e-6 28 | 5e-6 29 | 1e-3 30 | 31 | 0.1 32 | nichols 33 | powell 34 | poly 35 | true 36 | 0.3 37 | hessian.dat 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/40/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | 5 | 20 6 | 7 |
localhost
8 | 9 | 10 | 11 | init.xyz 12 | [200.0, 200.0, 200.0 ] 13 | 14 | 15 | 16 | 17 | 18 | 300 19 | 20 | 21 | [ 0,1,2,3,4,5 ] 22 | 23 | 24 | 25 | 10 26 | 27 | 5e-6 28 | 5e-6 29 | 1e-3 30 | 31 | 0.1 32 | nichols 33 | powell 34 | poly 35 | true 36 | 0.3 37 | hessian.dat 38 | 39 | 40 | 41 | 42 | -------------------------------------------------------------------------------- /tutorial-3/ex-3/convergedspecs/trpmd.imvacf: -------------------------------------------------------------------------------- 1 | 0.0 0.0012258868748501357 2 | 0.015625 0.0009283210314750146 3 | 0.03125 0.0007166629618679823 4 | 0.046875 0.000564450024045865 5 | 0.0625 0.00045360841143794246 6 | 0.078125 0.00037175538391194236 7 | 0.09375 0.00031037657132195753 8 | 0.109375 0.00026359280064982275 9 | 0.125 0.00022732452263715815 10 | 0.140625 0.00019872471098023514 11 | 0.15625 0.00017579326833645783 12 | 0.171875 0.00015711430723264108 13 | 0.1875 0.00014167673373755257 14 | 0.203125 0.000128751395467077 15 | 0.21875 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/tutorial-3/ex-3/convergedspecs/cmd.imvacf: -------------------------------------------------------------------------------- 1 | 0.0 0.0011991072529851572 2 | 0.015625 0.0009154005318615556 3 | 0.03125 0.0007114596099151171 4 | 0.046875 0.0005633758532525385 5 | 0.0625 0.000454610696664819 6 | 0.078125 0.0003736922901029405 7 | 0.09375 0.00031263786319174296 8 | 0.109375 0.00026587188100788155 9 | 0.125 0.0002294832352907468 10 | 0.140625 0.00020071450755138997 11 | 0.15625 0.00017761025300958795 12 | 0.171875 0.00015877437079219267 13 | 0.1875 0.00014320239631774573 14 | 0.203125 0.0001301653195831168 15 | 0.21875 0.00011912889120296749 16 | 0.234375 0.00010969741044177607 17 | 0.25 0.00010157443421500026 18 | 0.265625 9.453520612672569e-05 19 | 0.28125 8.840722311500288e-05 20 | 0.296875 8.305646834252423e-05 21 | 0.3125 7.83776025340002e-05 22 | 0.32812500000000006 7.428693134700222e-05 23 | 0.34375 7.07173283562899e-05 24 | 0.35937499999999994 6.761454303195556e-05 25 | 0.375 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localhost
8 | 9 | 10 | 11 | init.xyz 12 | [200.0, 200.0, 200.0 ] 13 | 14 | 15 | 16 | 17 | 18 | 300 19 | 20 | 21 | [ 0,1,2,3,4,5 ] 22 | 23 | 24 | 25 | 10 26 | 27 | 5e-6 28 | 5e-6 29 | 1e-3 30 | 31 | 0.1 32 | nichols 33 | powell 34 | poly 35 | true 36 | 0.3 37 | hessian.dat 38 | hessian.dat 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /tutorial-3/ex-3/convergedspecs/nve.imvacf: -------------------------------------------------------------------------------- 1 | 0.0 0.0012832225522636316 2 | 0.015625 0.0009639741439184458 3 | 0.03125 0.0007389547820025012 4 | 0.046875 0.0005785933875240918 5 | 0.0625 0.00046283630927006225 6 | 0.078125 0.0003780492323973607 7 | 0.09375 0.0003149334945864318 8 | 0.109375 0.00026712353801017056 9 | 0.125 0.00023024196144508992 10 | 0.140625 0.00020126218004940611 11 | 0.15625 0.00017807800456699552 12 | 0.171875 0.00015921251750158368 13 | 0.1875 0.00014362080745371298 14 | 0.203125 0.00013055601148167863 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-------------------------------------------------------------------------------- /tutorial-3/ex-3/convergedspecs/rpmd.imvacf: -------------------------------------------------------------------------------- 1 | 0.0 0.0011880325584435777 2 | 0.015625 0.0008994287401572361 3 | 0.03125 0.0006941763073299191 4 | 0.046875 0.0005466175085051827 5 | 0.0625 0.00043921597801774645 6 | 0.078125 0.0003599508363009044 7 | 0.09375 0.00030055354756703686 8 | 0.109375 0.0002553135641717246 9 | 0.125 0.00022026820173874607 10 | 0.140625 0.00019265232529340725 11 | 0.15625 0.00017052390056077494 12 | 0.171875 0.000152508724816275 13 | 0.1875 0.00013762602567322688 14 | 0.203125 0.00012516901001430775 15 | 0.21875 0.00011462281181041032 16 | 0.234375 0.00010560794006805234 17 | 0.25 9.784115031312553e-05 18 | 0.265625 9.110824991751078e-05 19 | 0.28125 8.52451001748373e-05 20 | 0.296875 8.012426670011183e-05 21 | 0.3125 7.564557689716414e-05 22 | 0.32812500000000006 7.172939209318538e-05 23 | 0.34375 6.83117757228469e-05 24 | 0.35937499999999994 6.53409939501033e-05 25 | 0.375 6.277495944679112e-05 26 | 0.39062500000000006 6.0579348517525844e-05 27 | 0.40625 5.872620387701694e-05 28 | 0.42187499999999994 5.7192892036436976e-05 29 | 0.4375 5.5961323524474715e-05 30 | 0.45312500000000006 5.5017371565783186e-05 31 | 0.46875 5.4350444131035476e-05 32 | 0.48437499999999994 5.395317804615481e-05 33 | 0.5 5.3821233896421625e-05 34 | 0.515625 5.395317804615481e-05 35 | 0.53125 5.4350444131035476e-05 36 | 0.546875 5.5017371565783186e-05 37 | 0.5625 5.5961323524474715e-05 38 | 0.578125 5.7192892036436976e-05 39 | 0.59375 5.872620387701694e-05 40 | 0.609375 6.0579348517525844e-05 41 | 0.625 6.277495944679112e-05 42 | 0.640625 6.53409939501033e-05 43 | 0.6562500000000001 6.831177572284692e-05 44 | 0.671875 7.172939209318538e-05 45 | 0.6875 7.564557689716414e-05 46 | 0.703125 8.012426670011185e-05 47 | 0.7187499999999999 8.524510017483727e-05 48 | 0.734375 9.110824991751078e-05 49 | 0.75 9.784115031312553e-05 50 | 0.765625 0.00010560794006805235 51 | 0.7812500000000001 0.00011462281181041036 52 | 0.796875 0.00012516901001430775 53 | 0.8125 0.00013762602567322688 54 | 0.828125 0.00015250872481627504 55 | 0.8437499999999999 0.00017052390056077489 56 | 0.859375 0.00019265232529340717 57 | 0.875 0.00022026820173874607 58 | 0.890625 0.0002553135641717247 59 | 0.9062500000000001 0.00030055354756703713 60 | 0.921875 0.00035995083630090423 61 | 0.9375 0.00043921597801774645 62 | 0.953125 0.000546617508505183 63 | 0.9687499999999999 0.0006941763073299183 64 | 0.984375 0.0008994287401572354 65 | 1.0 0.0011880325584435777 66 | 67 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/80/inst.instanton_0.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.589301831535524 3 | 1 0.5897112818272886 4 | 2 0.5905255460888933 5 | 3 0.5917354570972517 6 | 4 0.5933273018116361 7 | 5 0.595282816215065 8 | 6 0.5975792147343889 9 | 7 0.600189233054066 10 | 8 0.6030812401567015 11 | 9 0.6062194178768131 12 | 10 0.6095640414277683 13 | 11 0.6130718635706566 14 | 12 0.6166966196997 15 | 13 0.6203896706807484 16 | 14 0.6241007766045193 17 | 15 0.6277789907052763 18 | 16 0.6313736559660247 19 | 17 0.6348354825211348 20 | 18 0.63811765328156 21 | 19 0.6411769106667765 22 | 20 0.6439745922478165 23 | 21 0.6464775370713217 24 | 22 0.6486588295388963 25 | 23 0.650498332057522 26 | 24 0.6519829781609238 27 | 25 0.6531068153488984 28 | 26 0.6538707932493264 29 | 27 0.6542823096681524 30 | 28 0.6543545641899634 31 | 29 0.6541057419018372 32 | 30 0.6535580945049684 33 | 31 0.6527369609637322 34 | 32 0.6516697890761088 35 | 33 0.650385196937412 36 | 34 0.6489121122590723 37 | 35 0.6472790259999983 38 | 36 0.6455133742310998 39 | 37 0.643641047396001 40 | 38 0.641686037795431 41 | 39 0.6396702074145004 42 | 40 0.63761317331786 43 | 41 0.6355322827926807 44 | 42 0.6334426675986254 45 | 43 0.6313573519748664 46 | 44 0.629287409692236 47 | 45 0.6272421357615923 48 | 46 0.6252292463754392 49 | 47 0.6232550696442266 50 | 48 0.621324737941516 51 | 49 0.6194423638314792 52 | 50 0.6176112074309209 53 | 51 0.6158338236547134 54 | 52 0.6141121931115947 55 | 53 0.6124478353109047 56 | 54 0.6108419013243169 57 | 55 0.6092952569281556 58 | 56 0.6078085477809184 59 | 57 0.6063822537666362 60 | 58 0.6050167303363695 61 | 59 0.6037122429460582 62 | 60 0.6024689934455935 63 | 61 0.6012871383698096 64 | 62 0.6001668058115888 65 | 63 0.5991081031082767 66 | 64 0.5981111277293214 67 | 65 0.597175966357255 68 | 66 0.5963027033302465 69 | 67 0.5954914217918733 70 | 68 0.5947422014595803 71 | 69 0.5940551193947237 72 | 70 0.5934302487950152 73 | 71 0.5928676615626204 74 | 72 0.5923674233629824 75 | 73 0.5919295938039811 76 | 74 0.5915542244137765 77 | 75 0.5912413594380386 78 | 76 0.59099103621102 79 | 77 0.590803280653768 80 | 78 0.5906781082180488 81 | 79 0.5906155237980176 82 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/instanton/80/inst.instanton_FINAL_6.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.590888265664242 3 | 1 0.5912886784943733 4 | 2 0.5920850158370303 5 | 3 0.5932682970048133 6 | 4 0.5948250452245629 7 | 5 0.5967372928265928 8 | 6 0.5989826076667027 9 | 7 0.601534156218289 10 | 8 0.6043608209706735 11 | 9 0.6074273908048093 12 | 10 0.610694842628482 13 | 11 0.6141207305174317 14 | 12 0.6176596947592575 15 | 13 0.6212640975038133 16 | 14 0.6248847842940306 17 | 15 0.6284719619030212 18 | 16 0.6319761731741566 19 | 17 0.6353493397152065 20 | 18 0.6385458342514132 21 | 19 0.6415235372394571 22 | 20 0.6442448279635626 23 | 21 0.646677459607783 24 | 22 0.6487952712078865 25 | 23 0.6505786969907023 26 | 24 0.6520150449501108 27 | 25 0.653098530633571 28 | 26 0.6538300676919363 29 | 27 0.654216832216716 30 | 28 0.6542716317096341 31 | 29 0.6540121203733228 32 | 30 0.6534599093523296 33 | 31 0.652639623189848 34 | 32 0.651577952206281 35 | 33 0.6503027453368219 36 | 34 0.6488421800963636 37 | 35 0.6472240368469818 38 | 36 0.6454750945132869 39 | 37 0.6436206552790702 40 | 38 0.6416841973410929 41 | 39 0.6396871479709791 42 | 40 0.6376487641609996 43 | 41 0.6355861050051566 44 | 42 0.6335140785135547 45 | 43 0.6314455455034641 46 | 44 0.6293914642219895 47 | 45 0.6273610610939531 48 | 46 0.6253620151555805 49 | 47 0.6234006460643272 50 | 48 0.6214820978771374 51 | 49 0.6196105129155274 52 | 50 0.6177891919097783 53 | 51 0.6160207381814253 54 | 52 0.614307184879978 55 | 53 0.6126501052579366 56 | 54 0.6110507066619189 57 | 55 0.6095099093899573 58 | 56 0.6080284118497933 59 | 57 0.606606743588227 60 | 58 0.6052453077936669 61 | 59 0.6039444148207367 62 | 60 0.602704308182357 63 | 61 0.6015251843216904 64 | 62 0.6004072073263657 65 | 63 0.5993505195918941 66 | 64 0.5983552492940863 67 | 65 0.597421515389165 68 | 66 0.5965494307362493 69 | 67 0.5957391038240575 70 | 68 0.5949906394874614 71 | 69 0.5943041389195148 72 | 70 0.5936796992126181 73 | 71 0.5931174126109668 74 | 72 0.592617365606705 75 | 73 0.5921796379794451 76 | 74 0.5918043018482261 77 | 75 0.5914914207855811 78 | 76 0.5912410490253771 79 | 77 0.5910532307844935 80 | 78 0.5909279997125009 81 | 79 0.5908653784751736 82 | -------------------------------------------------------------------------------- /tutorial-2/ex-4/ultimate.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, kinetic_opsc, kinetic_tdsc, potential_opsc, potential_tdsc] 4 | [ pot_component(0), pot_component(1) ] 5 | positions{angstrom} 6 | 7 | 8 | 100000 9 | 31415 10 | 12 | 13 |
lammps_ice.short
14 | 15 | 16 |
lammps_ice.long
17 | 18 | 19 | 20 | ../data/ice-96.pdb 21 | 100 22 | [ 25.6156, 0, 0, 0, 29.5783, 0, 0, 0, 27.8867 ] 23 | 24 | 28 | 29 | 30 | 31 | 32 | 33 | 100 34 | 35 | 36 | 37 | 38 | 100 39 | 0.5 40 | 41 | 0.25 42 | 43 | 44 | 45 | 46 | -------------------------------------------------------------------------------- /tutorial-3/ex-2/precomputed-imvacf/conv.imvacf: -------------------------------------------------------------------------------- 1 | 0.0 0.0012143 2 | 0.010417 0.0010010050000000001 3 | 0.020833 0.0008336445 4 | 0.03125 0.000702198 5 | 0.041667 0.000597402 6 | 0.052083 0.0005128915000000001 7 | 0.0625 0.0004448275 8 | 0.072917 0.00038911999999999996 9 | 0.083333 0.000343305 10 | 0.09375 0.000305635 11 | 0.104167 0.000274092 12 | 0.114583 0.000247363 13 | 0.125 0.0002246645 14 | 0.135417 0.00020517449999999998 15 | 0.145833 0.0001883555 16 | 0.15625 0.000173835 17 | 0.166667 0.000161309 18 | 0.177083 0.0001503765 19 | 0.1875 0.0001410115 20 | 0.197917 0.0001327575 21 | 0.208333 0.0001247845 22 | 0.21875 0.0001176965 23 | 0.229167 0.0001115295 24 | 0.239583 0.0001058655 25 | 0.25 0.0001004835 26 | 0.260417 9.605245e-05 27 | 0.270833 9.222825e-05 28 | 0.28125 8.85676e-05 29 | 0.291667 8.52425e-05 30 | 0.302083 8.20297e-05 31 | 0.3125 7.885554999999999e-05 32 | 0.322917 7.566834999999999e-05 33 | 0.333333 7.27904e-05 34 | 0.34375 7.038030000000001e-05 35 | 0.354167 6.826170000000001e-05 36 | 0.364583 6.660975e-05 37 | 0.375 6.513995e-05 38 | 0.385417 6.39613e-05 39 | 0.395833 6.272025e-05 40 | 0.40625 6.187435e-05 41 | 0.416667 6.13378e-05 42 | 0.427083 6.07559e-05 43 | 0.4375 6.00607e-05 44 | 0.447917 5.944535e-05 45 | 0.458333 5.8952e-05 46 | 0.46875 5.8387e-05 47 | 0.479167 5.818925e-05 48 | 0.489583 5.8000850000000006e-05 49 | 0.5 5.76947e-05 50 | 0.510417 5.8000850000000006e-05 51 | 0.520833 5.818925e-05 52 | 0.53125 5.8387e-05 53 | 0.541667 5.8952e-05 54 | 0.552083 5.944535e-05 55 | 0.5625 6.00607e-05 56 | 0.572917 6.07559e-05 57 | 0.583333 6.13378e-05 58 | 0.59375 6.187435e-05 59 | 0.604167 6.272025e-05 60 | 0.614583 6.39613e-05 61 | 0.625 6.513995e-05 62 | 0.635417 6.660975e-05 63 | 0.645833 6.826170000000001e-05 64 | 0.65625 7.038030000000001e-05 65 | 0.666667 7.27904e-05 66 | 0.677083 7.566834999999999e-05 67 | 0.6875 7.885554999999999e-05 68 | 0.697917 8.20297e-05 69 | 0.708333 8.52425e-05 70 | 0.71875 8.85676e-05 71 | 0.729167 9.222825e-05 72 | 0.739583 9.605245e-05 73 | 0.75 0.0001004835 74 | 0.760417 0.0001058655 75 | 0.770833 0.0001115295 76 | 0.78125 0.0001176965 77 | 0.791667 0.0001247845 78 | 0.802083 0.0001327575 79 | 0.8125 0.0001410115 80 | 0.822917 0.0001503765 81 | 0.833333 0.000161309 82 | 0.84375 0.000173835 83 | 0.854167 0.0001883555 84 | 0.864583 0.00020517449999999998 85 | 0.875 0.0002246645 86 | 0.885417 0.000247363 87 | 0.895833 0.000274092 88 | 0.90625 0.000305635 89 | 0.916667 0.000343305 90 | 0.927083 0.00038911999999999996 91 | 0.9375 0.0004448275 92 | 0.947917 0.0005128915000000001 93 | 0.958333 0.000597402 94 | 0.96875 0.000702198 95 | 0.979167 0.0008336445 96 | 0.989583 0.0010010050000000001 97 | 1.0 0.0012143 98 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/minization/RESTART: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt} ] 4 | x_centroid{angstrom} 5 | 6 | 32 7 | 400 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 1.00000000e+00 17 | 18 | [ -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, 19 | -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, -1.00000000e+00 ] 20 | 21 | [ 1.00000000e+00 ] 22 | 23 | 24 | 25 | 26 | 9.66918009e-06 27 | 28 | 29 | 5.00000000e-05 30 | 5.00000000e-05 31 | 5.00000000e-05 32 | 33 | 34 | 35 | 36 | 37 | [ 3.08193707e+00, 2.57506676e+00, 2.17658472e+00, 1.59671482e+00, 1.49232344e+00, 38 | 1.25105918e+00, 2.44371128e+00, 1.19951333e-01, -2.72755494e-02, 3.82774455e-01, 39 | 2.76592781e+00, 1.83825153e-01, 4.78669560e-01, 5.08335946e-01, 2.67106918e+00, 40 | 1.10153821e+01, 4.11836602e+00, 3.50096686e+00 ] 41 | 42 |

43 | [ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 44 | 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 45 | 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 46 | 0.00000000e+00, 0.00000000e+00, 0.00000000e+00 ] 47 |

48 | 49 | [ 1.83736223e+03, 2.18941669e+04, 1.83736223e+03, 1.83736223e+03, 1.83736223e+03, 50 | 1.83736223e+03 ] 51 | 52 | 53 | [ H, C, H, H, H, 54 | H ] 55 | 56 | 57 | 58 | [ 2.00000000e+02, 1.22464680e-14, 1.22464680e-14, 0.00000000e+00, 2.00000000e+02, 59 | 1.22464680e-14, 0.00000000e+00, 0.00000000e+00, 2.00000000e+02 ] 60 | 61 | 62 | 63 | -------------------------------------------------------------------------------- /tutorial-2/ex-3/npt.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, volume, pressure_cv{gigapascal}] 4 | positions{angstrom} 5 | 6 | 7 | 40000 8 | 9 | 32345 10 | 11 | 12 |
water-npt
0.001 13 | 14 | 15 | 16 | ../data/water-32.pdb 17 | 750 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 50 26 | 27 | 28 | [ 4.498098855452e-3, 6.594810718477e-6, 2.788030342989e-4, -8.808265165053e-4, 5.605371493938e-3, 29 | -6.726802271646e-6, 2.079069559861e-9, 1.746169548818e-5, -4.800164465960e-6, 1.025830873432e-5, 30 | -3.586191452340e-4, -1.746169548818e-5, 3.287481976399e-5, 1.245698716799e-4, -2.417657162526e-4, 31 | -2.508912543565e-4, 4.800164465960e-6, -1.245698716799e-4, 6.449207766266e-4, 2.783583234046e-4, 32 | 5.273493443008e-3, -1.025830873432e-5, 2.417657162526e-4, -2.783583234046e-4, 7.488477456790e-3 33 | ] 34 | 35 | 36 | 37 | 38 | 41 | 50 42 | 0.5 43 | 44 | 0.25 45 | 46 | 47 | 48 | 750 49 | 10 50 | 51 | 52 | 53 | 54 | -------------------------------------------------------------------------------- /tutorial-3/tools/get_imacf_from_real.py: -------------------------------------------------------------------------------- 1 | import scipy.integrate 2 | from sys import argv 3 | from numpy import exp, pi, arange, sum, array,sinh,cosh, interp 4 | 5 | def g(lamb, omega, beta): 6 | hbar=1.0 7 | if omega==0.0: 8 | fac=(beta-lamb)*lamb*hbar**2/(2.*pi) 9 | else: 10 | fac=beta*hbar/(2.*pi*omega*sinh(beta*hbar*omega/2.))*(cosh(beta*hbar*omega/2.)-cosh(beta*hbar*omega/2. - lamb*hbar*omega)) 11 | return fac 12 | 13 | def f(lamb, omega, beta): 14 | hbar=1.0 15 | if omega==0.0: 16 | fac=1./(pi) 17 | else: 18 | fac=beta*hbar*omega*cosh(beta*hbar*omega/2.-lamb*hbar*omega)/(2.*pi*sinh(beta*hbar*omega/2.)) 19 | return fac 20 | 21 | def t(lamb, omega, beta): 22 | hbar=1.0 23 | if omega==0.0: 24 | fac=0.0 25 | else: 26 | fac=beta*hbar*(omega**3)*cosh(beta*hbar*omega/2.-lamb*hbar*omega)/(4.*pi*sinh(beta*hbar*omega/2.)) 27 | return fac 28 | 29 | def integrate(dx, func, fact): 30 | numarray=[i*j for i,j in zip(func,fact)] 31 | integ=dx*0.5*sum(array([(numarray[i]+numarray[i+1]) for i in range(len(numarray)-1)])) 32 | return integ 33 | 34 | 35 | inp=open(argv[1]) # PRIOR 36 | temperature=float(argv[2]) # T in kelvin 37 | beta=1./(temperature*3.1668152e-06) # convert beta to atomic units so hbar is 1 38 | nbeads=int(argv[3]) 39 | omfac=4.5563353e-06 #invcm to atomic frequency 40 | facatomic=0.024188843/(2.*pi) # factor to account for fs and atomic time mix in fourier transforms, as well as fourier transform conventions (2 pis) 41 | dl=beta/nbeads 42 | lamb=arange(0, (beta)+dl, dl) 43 | 44 | 45 | whole=[line.split()[:] for line in inp] 46 | 47 | inp.close() 48 | 49 | freq=[float(i[0])*omfac for i in whole if float(i[0])<4500.0] 50 | 51 | fftfull=[float(i[1])/facatomic for i in whole] 52 | fftfull=fftfull[:len(freq)] 53 | 54 | # clean small numbers 55 | fft=[i if i>max(fftfull)/10000. else 0.0 for i in fftfull] 56 | 57 | #fft=fftfull 58 | 59 | dx=freq[1] 60 | 61 | # displacement 62 | #for l in lamb: 63 | # gf=array([g(l, i, beta) for i in freq]) 64 | # filetemp=open('f_displ_'+str(l), 'w') 65 | # trash=[filetemp.write('%f %f\n' %(i,j)) for i,j in zip(freq, gf)] 66 | # filetemp.close() 67 | # integrate 68 | # number2=integrate(freq[1], fft[1:], gf) 69 | # numarray=[i*j for i,j in zip(fft,gf)] 70 | # number=scipy.integrate.simps(numarray, x=freq) 71 | # print l, number 72 | 73 | #print ' ' 74 | 75 | # cvv 76 | for l in lamb: 77 | fplus=array([f(l, i, beta) for i in freq]) 78 | # filetemp=open('f_vv_'+str(l), 'w') 79 | # trash=[filetemp.write('%f %f\n' %(i,j)) for i,j in zip(freq, fplus)] 80 | # filetemp.close() 81 | # integrate 82 | numarray=[i*j for i,j in zip(fft,fplus)] 83 | number=scipy.integrate.simps(numarray, x=freq) 84 | number=integrate(freq[1], fft[1:], fplus) 85 | print(l/beta, number) 86 | 87 | print(' ') 88 | 89 | ## force 90 | #for l in lamb: 91 | # gffplus=array([t(l, i, beta) for i in freq]) 92 | ## filetemp=open('f_ff_'+str(l), 'w') 93 | ## trash=[filetemp.write('%f %f\n' %(i,j)) for i,j in zip(freq, gffplus)] 94 | ## filetemp.close() 95 | # number=integrate(freq[1], fft, gffplus) 96 | # print l, number 97 | # 98 | # 99 | -------------------------------------------------------------------------------- /tools/autocorr.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | def autoCorr(infile,nbead,columns,mlag,nequi,dt,verbosity,ncol): 4 | 5 | data = np.genfromtxt(infile,skip_header = ncol+nequi,usecols = columns) 6 | if (len(columns)>1): data = np.sum(data,axis=-1) 7 | 8 | autocorr = np.zeros((mlag),float) 9 | autoerror = np.zeros((mlag),float) 10 | block = np.zeros((mlag), float) 11 | blockerror = np.zeros((mlag), float) 12 | times = np.arange(mlag) 13 | 14 | # Calculates the mean, variance and stadard deviation 15 | mean = np.mean(data) 16 | var = np.mean(data**2)-mean**2 17 | std = np.sqrt(var) if(abs(var)>1.0e-15) else 0. 18 | 19 | # Calculates the normalized autocorrelation function 20 | for tt in range(mlag): 21 | autocorr[tt] = np.dot(data[:len(data)-tt]-mean,data[tt:len(data)]-mean) / (len(data)-tt) 22 | autocorr /= autocorr[0] 23 | 24 | # Estimating the autocorrelation time (integral of the autocorrelation function) 25 | tau = sum(autocorr) - autocorr[0]*0.5*dt 26 | tau2 = sum(autocorr**2) - autocorr[0]*0.5*dt 27 | # Calculating the standard error in the mean value 28 | error = std/np.sqrt(len(data)*dt*0.5/tau) 29 | 30 | # printing the information 31 | if(verbosity>0): 32 | title = str(nbead)+' bead' if nbead<2 else str(nbead)+' beads' 33 | print('==================================', title, '=============================================') 34 | print(' mean = %8.4e | variance: = %8.4e | st.dev. = %8.4e'%(mean,var,std)) 35 | print(' = %8.4e | = %8.4e | error = %8.4e'%(tau,tau2,error)) 36 | 37 | # Calculating the block correlation function 38 | block[0]=0. 39 | block[1]=autocorr[0]*0.5 40 | vtimesm = autocorr[1] 41 | for m in range(2,mlag): 42 | block[m]=block[m-1]+vtimesm*(1./(m-1)-1./(m)) 43 | vtimesm+=autocorr[m]*m 44 | block *= 2*dt 45 | 46 | # here we compute the errors on ACF, assuming that the AC is a gaussian 47 | # distributed random variable. see Zwanzig and Ailawadi¸ PR 182 (1969) 48 | # ********************************************************************** 49 | 50 | tau2 *= 2./(len(data)*dt) 51 | tau2 = np.sqrt(tau2) if tau2>0 else 0. 52 | 53 | for i in range(mlag): 54 | autoerror[i]=tau2*(1-autocorr[i]); 55 | 56 | # Calculating the block error 57 | # //the errors on blocking averages can be computed in a similar way 58 | # //!BEWARE THIS FORMULA NEED CHECK!!!!!!!!!!!!!!!! 59 | 60 | for i in range(mlag): 61 | blockerror[i]=tau2*abs(block[i]-i*dt/2.) 62 | 63 | if(verbosity>1): 64 | # printing the information 65 | print(' time acf Dacf block Dblock ') 66 | print('---------------------------------------------------------------------------------------') 67 | for i in range(mlag): 68 | print('%15.8f %15.8f %15.8f %15.8f %15.8f'%(times[i], autocorr[i], autoerror[i], block[i], blockerror[i])) 69 | if(verbosity>0): print('=======================================================================================\n') 70 | return mean, error 71 | -------------------------------------------------------------------------------- /tutorial-3/tools/posforce2imaginaryvv.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | """ posforce2imaginary.py 3 | 4 | Reads beads positions and forces from an i-PI run and computes the 5 | imaginary time velocity autocorrelation functions for each particle, 6 | in a single file 7 | 8 | Assumes the input files are in xyz format and atomic units, 9 | with prefix.pos_*.xyz and prefix.for_*.xyz naming scheme. 10 | 11 | Syntax: 12 | posforce2imaginaryvv.py prefix temperature[K] 13 | """ 14 | 15 | import numpy as np 16 | import sys, glob 17 | from ipi.utils.io import read_file 18 | #from ipi.utils.io.inputs.io_xyz import * 19 | from ipi.engine.beads import Beads 20 | from ipi.utils.depend import * 21 | from ipi.utils.units import * 22 | 23 | def main(prefix, temp): 24 | 25 | temp = unit_to_internal("energy","kelvin",float(temp)) 26 | 27 | ipos=[] 28 | for filename in sorted(glob.glob(prefix+".pos*")): 29 | ipos.append(open(filename,"r")) 30 | 31 | ifor=[] 32 | for filename in sorted(glob.glob(prefix+".for*")): 33 | ifor.append(open(filename,"r")) 34 | 35 | ivacfim=open(prefix+".imvacf","w") 36 | 37 | nbeads = len(ipos) 38 | 39 | if (nbeads!=len(ifor)): raise ValueError("Mismatch between number of output files for forces and positions") 40 | natoms = 0 41 | ifr = 0 42 | while True: 43 | try: 44 | for i in range(nbeads): 45 | ret = read_file("xyz", ipos[i]) 46 | pos = ret["atoms"] 47 | ret = read_file("xyz", ifor[i]) 48 | force = ret["atoms"] 49 | if natoms == 0: 50 | natoms = pos.natoms 51 | beads = Beads(natoms,nbeads) 52 | forces = Beads(natoms,nbeads) 53 | beads[i].q = pos.q 54 | beads[i].m = pos.m 55 | forces[i].q = force.q 56 | except EOFError: # finished reading files 57 | break 58 | 59 | if (ifr==0): 60 | cim = np.zeros((natoms,nbeads+1),float) 61 | 62 | q = dstrip(beads.q) 63 | f = dstrip(forces.q) 64 | m = dstrip(beads.m) 65 | qc = dstrip(beads.qc) 66 | 67 | for j in range(nbeads+1): 68 | for i in range(natoms): 69 | dummy=[(q[(j+k)%nbeads, 3*i:3*(i+1)]-qc[3*i:3*(i+1)])*(-f[k, 3*i:3*(i+1)]) for k in range(nbeads)] 70 | cim[i,j]=cim[i,j]+np.sum(dummy)/(nbeads*m[i]) 71 | cim[i,j]+=3.*Constants.kb*temp/m[i] 72 | 73 | ifr+=1 74 | print('Frame: ', ifr) 75 | 76 | cim[:,:]=cim[:,:]/ifr 77 | 78 | fullcim=np.zeros(len(cim)) 79 | for j in range(nbeads+1): 80 | fullcim[j]=np.sum([i for i in cim[:,j]]) 81 | 82 | ivacfim.write("# Imaginary time autocorrelation, averaged through the whole simulation -- beta*hbar is %f \n" % (Constants.hbar/(Constants.kb*temp))) 83 | 84 | for islice in range(nbeads+1): 85 | ivacfim.write("%f %12.5e \n" % (float(islice)/float(nbeads), fullcim[islice])) 86 | 87 | # for iatom in range(natoms): 88 | # ivacfim.write("\n# Imvacf for atom %d %s \n" % (iatom, pos.names[iatom])) 89 | # for islice in range(nbeads+1): 90 | # ivacfim.write("%f %12.5e \n" % (float(islice)/float(nbeads), cim[iatom, islice])) 91 | 92 | # could add the full imvacf in another file, as well as other types of imvacf 93 | 94 | 95 | if __name__ == '__main__': 96 | main(*sys.argv[1:]) 97 | -------------------------------------------------------------------------------- /tutorial-1/ex-4/n.001/in.cp2k: -------------------------------------------------------------------------------- 1 | &GLOBAL 2 | PROJECT_NAME CH5+ 3 | RUN_TYPE DRIVER 4 | PRINT_LEVEL LOW 5 | &END GLOBAL 6 | &MOTION 7 | 8 | &DRIVER 9 | HOST driver.ch5.001 10 | UNIX TRUE 11 | &END DRIVER 12 | &END MOTION 13 | 14 | &FORCE_EVAL 15 | METHOD FIST 16 | &MM 17 | &FORCEFIELD 18 | &BEND 19 | ATOMS H C H 20 | K 1.0 21 | KIND LEGENDRE 22 | LEGENDRE 0.0190931 0.0139452 0.0673905 0.008298 0.0410469 0.0127439 0.0256356 0.00554186 0.00991002 0.00108887 0.00173833 23 | THETA0 2.00 24 | &END BEND 25 | &BOND 26 | KIND QUARTIC 27 | ATOMS C H 28 | K 0.315808 -0.451771 0.206022 29 | R0 2.13514 30 | &END BOND 31 | &CHARGE 32 | ATOM C 33 | CHARGE 0.0 34 | &END CHARGE 35 | &CHARGE 36 | ATOM H 37 | CHARGE 0.0 38 | &END CHARGE 39 | &NONBONDED 40 | &LENNARD-JONES 41 | ATOMS C C 42 | EPSILON 0.D0 43 | SIGMA 1.D0 44 | &END LENNARD-JONES 45 | &LENNARD-JONES 46 | ATOMS C H 47 | EPSILON 0.D0 48 | SIGMA 1.D0 49 | &END LENNARD-JONES 50 | &LENNARD-JONES 51 | ATOMS H H 52 | EPSILON 0.D0 53 | SIGMA 1.D0 54 | &END LENNARD-JONES 55 | &END NONBONDED 56 | &END FORCEFIELD 57 | &POISSON 58 | PERIODIC NONE 59 | &EWALD 60 | EWALD_TYPE NONE 61 | &END EWALD 62 | POISSON_SOLVER PERIODIC 63 | &END POISSON 64 | &PRINT 65 | &FF_INFO ON 66 | &EACH 67 | MD 10 68 | &END EACH 69 | &END FF_INFO 70 | &END PRINT 71 | &END MM 72 | &SUBSYS 73 | &CELL 74 | ABC 16.D0 16.D0 16.D0 75 | PERIODIC NONE 76 | &END CELL 77 | &COORD 78 | C 0.0000000000 0.0000000000 0.0000000000 79 | H 1.1298793646 0.0000000000 0.0000000000 80 | H -0.3550935874 1.0726303769 0.0000000000 81 | H -0.5623498407 -0.5610608244 -0.8034928709 82 | H -0.5158867801 0.1260633904 0.9972944563 83 | H -0.1636419371 -0.7234934097 0.8522945358 84 | &END COORD 85 | &TOPOLOGY 86 | &GENERATE 87 | &BOND ADD 88 | ATOMS 1 2 89 | &END BOND 90 | &BOND ADD 91 | ATOMS 1 3 92 | &END BOND 93 | &BOND ADD 94 | ATOMS 1 4 95 | &END BOND 96 | &BOND ADD 97 | ATOMS 1 5 98 | &END BOND 99 | &BOND ADD 100 | ATOMS 1 6 101 | &END BOND 102 | &ANGLE ADD 103 | ATOMS 2 1 3 104 | &END ANGLE 105 | &ANGLE ADD 106 | ATOMS 2 1 4 107 | &END ANGLE 108 | &ANGLE ADD 109 | ATOMS 2 1 5 110 | &END ANGLE 111 | &ANGLE ADD 112 | ATOMS 2 1 6 113 | &END ANGLE 114 | &ANGLE ADD 115 | ATOMS 3 1 4 116 | &END ANGLE 117 | &ANGLE ADD 118 | ATOMS 3 1 5 119 | &END ANGLE 120 | &ANGLE ADD 121 | ATOMS 3 1 6 122 | &END ANGLE 123 | &ANGLE ADD 124 | ATOMS 4 1 5 125 | &END ANGLE 126 | &ANGLE ADD 127 | ATOMS 4 1 6 128 | &END ANGLE 129 | &ANGLE ADD 130 | ATOMS 5 1 6 131 | &END ANGLE 132 | &END GENERATE 133 | &END TOPOLOGY 134 | &END SUBSYS 135 | &END FORCE_EVAL 136 | -------------------------------------------------------------------------------- /tutorial-1/ex-4/n.128/in.cp2k: -------------------------------------------------------------------------------- 1 | &GLOBAL 2 | PROJECT_NAME CH5+ 3 | RUN_TYPE DRIVER 4 | PRINT_LEVEL LOW 5 | &END GLOBAL 6 | &MOTION 7 | 8 | &DRIVER 9 | HOST driver.ch5.128 10 | UNIX TRUE 11 | &END DRIVER 12 | &END MOTION 13 | 14 | &FORCE_EVAL 15 | METHOD FIST 16 | &MM 17 | &FORCEFIELD 18 | &BEND 19 | ATOMS H C H 20 | K 1.0 21 | KIND LEGENDRE 22 | LEGENDRE 0.0190931 0.0139452 0.0673905 0.008298 0.0410469 0.0127439 0.0256356 0.00554186 0.00991002 0.00108887 0.00173833 23 | THETA0 2.00 24 | &END BEND 25 | &BOND 26 | KIND QUARTIC 27 | ATOMS C H 28 | K 0.315808 -0.451771 0.206022 29 | R0 2.13514 30 | &END BOND 31 | &CHARGE 32 | ATOM C 33 | CHARGE 0.0 34 | &END CHARGE 35 | &CHARGE 36 | ATOM H 37 | CHARGE 0.0 38 | &END CHARGE 39 | &NONBONDED 40 | &LENNARD-JONES 41 | ATOMS C C 42 | EPSILON 0.D0 43 | SIGMA 1.D0 44 | &END LENNARD-JONES 45 | &LENNARD-JONES 46 | ATOMS C H 47 | EPSILON 0.D0 48 | SIGMA 1.D0 49 | &END LENNARD-JONES 50 | &LENNARD-JONES 51 | ATOMS H H 52 | EPSILON 0.D0 53 | SIGMA 1.D0 54 | &END LENNARD-JONES 55 | &END NONBONDED 56 | &END FORCEFIELD 57 | &POISSON 58 | PERIODIC NONE 59 | &EWALD 60 | EWALD_TYPE NONE 61 | &END EWALD 62 | POISSON_SOLVER PERIODIC 63 | &END POISSON 64 | &PRINT 65 | &FF_INFO ON 66 | &EACH 67 | MD 10 68 | &END EACH 69 | &END FF_INFO 70 | &END PRINT 71 | &END MM 72 | &SUBSYS 73 | &CELL 74 | ABC 16.D0 16.D0 16.D0 75 | PERIODIC NONE 76 | &END CELL 77 | &COORD 78 | C 0.0000000000 0.0000000000 0.0000000000 79 | H 1.1298793646 0.0000000000 0.0000000000 80 | H -0.3550935874 1.0726303769 0.0000000000 81 | H -0.5623498407 -0.5610608244 -0.8034928709 82 | H -0.5158867801 0.1260633904 0.9972944563 83 | H -0.1636419371 -0.7234934097 0.8522945358 84 | &END COORD 85 | &TOPOLOGY 86 | &GENERATE 87 | &BOND ADD 88 | ATOMS 1 2 89 | &END BOND 90 | &BOND ADD 91 | ATOMS 1 3 92 | &END BOND 93 | &BOND ADD 94 | ATOMS 1 4 95 | &END BOND 96 | &BOND ADD 97 | ATOMS 1 5 98 | &END BOND 99 | &BOND ADD 100 | ATOMS 1 6 101 | &END BOND 102 | &ANGLE ADD 103 | ATOMS 2 1 3 104 | &END ANGLE 105 | &ANGLE ADD 106 | ATOMS 2 1 4 107 | &END ANGLE 108 | &ANGLE ADD 109 | ATOMS 2 1 5 110 | &END ANGLE 111 | &ANGLE ADD 112 | ATOMS 2 1 6 113 | &END ANGLE 114 | &ANGLE ADD 115 | ATOMS 3 1 4 116 | &END ANGLE 117 | &ANGLE ADD 118 | ATOMS 3 1 5 119 | &END ANGLE 120 | &ANGLE ADD 121 | ATOMS 3 1 6 122 | &END ANGLE 123 | &ANGLE ADD 124 | ATOMS 4 1 5 125 | &END ANGLE 126 | &ANGLE ADD 127 | ATOMS 4 1 6 128 | &END ANGLE 129 | &ANGLE ADD 130 | ATOMS 5 1 6 131 | &END ANGLE 132 | &END GENERATE 133 | &END TOPOLOGY 134 | &END SUBSYS 135 | &END FORCE_EVAL 136 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.phonons.eigvec: -------------------------------------------------------------------------------- 1 | # Eigenvector matrix (normalized) 2 | 0.015849824233458557 -0.05321222034738475 -0.41002012854342496 -0.0062067645366760075 -0.003167952544333553 0.039114741862806175 -0.08713508096219878 0.23531233955257994 0.08224924634078226 -0.087382654863889 0.3809137427712294 0.00982072752701828 -0.029778238010871556 0.34476075158763314 0.3608537573604485 -0.34133035267253553 0.48030119909085767 0.08664638764202162 3 | -0.3952406821469548 0.15718419217356777 0.30465916686257366 0.026715205627331328 -0.02547073150586391 -0.1649224752225552 -0.17184163781423395 -0.0465063967065959 -0.004428340878699616 -0.02530872354969331 -0.3004750606374026 -0.3692788994479508 0.347274555161909 -0.2452889918378666 0.26309163627004517 -0.23046957512924443 0.3645909641189993 0.05165101700547224 4 | 0.43663822788977574 -0.09741577322715178 0.32316322967169436 -0.018319722447077507 -0.02065219389528027 -0.17427894852610773 0.1425950749041421 0.07677261188864903 -0.004056154106063361 -0.010717889496655822 -0.2732625829951288 0.41862720062911835 -0.3584881416460639 -0.2662989723411873 0.2248921560828685 -0.19677298091044 0.3068902454456054 0.0714211913697543 5 | -0.0011715033695391807 0.004362234377467115 0.029234445736043262 -0.002469917947217361 0.07038790455549754 0.13457153721077847 -0.29583837955690817 0.77305322362492 0.19900148521983022 -0.26718720304974036 -0.297462614383343 -0.002694573184111634 -1.445741462916048e-05 -8.212036603411095e-06 -0.00013822288978770705 -0.05386434520560848 -0.2932049697470778 -0.05070359399207569 6 | -0.010181702455849304 -0.0013756619054917654 0.007375674410279937 0.14255518242199294 -0.14496312533436342 -0.5649232519926679 -0.6062632854462675 -0.13355450642583183 0.051480578262437966 -0.22224294122970625 0.1971887779089626 0.267616434009652 1.1881066685853317e-05 -4.7920353549995224e-05 7.760199414297927e-05 0.22452393188604153 -0.00623291323607753 -0.20243392912038433 7 | 0.012725934582960546 -0.0016648175860295785 0.019067735246764878 -0.15254355653433097 -0.13504834549409234 -0.606003611505718 0.4995871691145435 0.2964054375163531 0.04423928795300424 -0.19776998637462395 0.18032157754872574 -0.29709081592295483 -9.268465156606062e-06 -3.711960376517357e-05 0.00010910752906470597 0.195232170471497 -0.07369866478000482 0.21882457540636924 8 | -0.010112190614137581 0.05234862692861977 0.5620027875884527 0.007541011170033566 0.05156029718892301 0.038906219764448 -0.08381330100531681 0.20899366251589452 0.025247104083249414 0.4791038430801219 0.17447387459142769 0.007045318322655994 -0.006197538993690235 0.4557266438541826 0.20596469768428657 0.33374395226546866 0.0609451638353306 0.021529729683347997 9 | 0.24270262685162675 0.3504556335927597 0.15860136274054124 0.045594473263746105 -0.032613293827779534 -0.16431141137656072 -0.17875189533980124 -0.045294553982941695 0.0039020716578903763 0.13841748250364824 0.11516146615301277 -0.3789651189031233 -0.3428304428978704 0.1459342385727888 -0.3337655751921736 -0.5312398585604454 -0.13224971813248299 -0.05469216324397961 10 | -0.2665136927562236 -0.3433018172195185 0.20429144448194414 -0.04333386945934442 -0.02854203818613374 -0.17489928720757694 0.1493297484131083 0.08304959798908887 0.003169298232636054 0.11601260302704364 0.11192878496381682 0.40988438220252743 0.36395077321582703 0.14523722429101815 -0.31088922091689014 -0.4958025327693894 -0.1279123766037388 -0.02259197058073629 11 | 0.23876859477461662 -0.430725215851756 -0.008752093616777059 0.01941257234788566 0.019530156040383616 0.04093118420089483 -0.08588887610882019 0.2259856866726453 0.06210370387939606 0.2573800990365162 0.22278986725900649 -0.2994731067342871 0.11249921872587583 -0.3877236581025334 -0.2948443771489303 0.11106781865940434 0.32185235309298704 -0.3482009699209483 12 | 0.39847092641201504 -0.08432278104134458 -0.24788504217019156 0.05539160857522468 -0.05550906321759392 -0.16260700013833643 -0.17963527331843437 -0.03267098935557671 0.03074314826523618 0.4317424305036099 -0.07334571289114827 -0.055521740902055236 0.37140572078279593 -0.12756482358686913 0.30934317390324956 -0.10483275715975099 -0.35952044647102777 0.3475267922677998 13 | 0.2107547367136748 0.3907357909189884 -0.27326205735737036 -0.05026505071873951 -0.05427160769849491 -0.1765199138646644 0.14015817276438858 0.09072950153138701 0.026640990638307275 0.1743100122293045 -0.4210538968947285 0.14820142933527933 0.31525688310399 0.28877119980705906 -0.2592058688029788 0.11453458145287511 0.2957699702934118 -0.2877902106150093 14 | -0.24586500891955998 0.4366341908748153 -0.1094568060072628 -0.02361075742733845 0.01363754683428527 0.03698331249794668 -0.08597225291347559 0.22550408662692814 0.060995166592235035 0.27319456058581093 0.2486493150770557 0.29190983727020925 -0.07647479993074002 -0.41271972079158714 -0.2714916462834057 0.08245006877189305 0.14903689996220235 0.41505234542777425 15 | -0.25771931836754947 -0.42495153581619644 -0.20680948814987615 0.037493359772956925 -0.05438473297344503 -0.1627772461886523 -0.17229161060868659 -0.030288903111802424 0.029460883228876612 0.22230890193869002 -0.4220181516394256 -0.1200197513968379 -0.3758934388674178 0.2270911200451115 -0.23893628266265776 0.09149563868423882 0.14869547014122164 0.3543066923978275 16 | -0.3661680408335771 0.048114259513204 -0.2321100058257111 -0.06485241189641958 -0.053024952622828525 -0.17652225378021302 0.1468260292673872 0.09291336732320647 0.025529778542196305 0.4030752026292417 -0.0400658538556464 0.04881780162844607 -0.3206854314438393 -0.16757562726644268 0.34482671685894645 -0.09589174768448347 -0.22034311014968366 -0.5164108940621799 17 | 0.0014856454694643162 -0.004945289482568265 -0.029196533277849233 0.012721584403847361 -0.31505204566000117 0.03894530460337926 -0.08595645185172947 0.22607294212303594 -0.9163443920832476 1.6065426171521673e-05 -1.3768861456325673e-05 -6.075159931508153e-07 1.2661655625650657e-06 -1.5671689974313604e-05 -5.686241178377567e-06 5.544926073775075e-06 -6.467389614860499e-06 -1.1835691220639584e-06 18 | 0.025322645989715474 -0.01976998395402071 -0.03986659045247524 -0.6601268451221909 0.6680613181346399 -0.16376745947803933 -0.1748998090610627 -0.038565717406766745 -0.23750400255993134 2.2979065545561147e-06 -4.451207471243629e-06 -2.390091563951671e-06 2.594666894558787e-06 -6.1162580006062845e-06 -7.132024123871468e-07 9.747205336490327e-07 -5.781526917496085e-07 -3.851486831717771e-07 19 | -0.027908385049489427 0.016120791320148452 -0.057957933601222034 0.7093877629373414 0.6262938599550718 -0.17513169924122932 0.14388684432906645 0.08527780293792858 -0.20366708878371292 2.008499308570308e-06 -3.890941654704061e-06 2.4403081863115785e-06 -2.0905620198403595e-06 -5.70372298379059e-06 -6.183218038126255e-07 8.331536042399049e-07 -5.929083635455797e-07 1.9762787586328383e-07 20 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.phonons.mode: -------------------------------------------------------------------------------- 1 | # Phonon modes (mass-scaled) 2 | 0.015851762888994758 -0.05321279783758215 -0.4102593451098902 -0.006334550940171787 -0.0032341152592273636 0.06568272075622203 -0.14635303129616928 0.39454115021789876 0.0839671081130822 -0.09458390872226564 0.41230271340971086 0.01063002998685629 -0.029778238016819534 0.3447607521784949 0.36085376348131354 -0.3565900123586995 0.5017766413360726 0.09052033563770696 3 | -0.39528902561911516 0.15718589802853067 0.30483691306273686 0.027265224888670208 -0.026002687942450555 -0.2769430749271699 -0.28862708703882445 -0.07797588211480205 -0.0045208314223662656 -0.027394429727843932 -0.3252355294703893 -0.3997102825473491 0.34727455523127443 -0.24528899225825052 0.26309164073265184 -0.24077304581959086 0.38089271853453144 0.05396032682494378 4 | 0.43669163486169843 -0.09741683044020817 0.32335177163055995 -0.018696893424117123 -0.021083515134314983 -0.2926547630016006 0.23950424134200393 0.1287223383923379 -0.004140871138636445 -0.011601156813398138 -0.2957806237773464 0.4531252581602094 -0.3584881417176692 -0.2662989727975788 0.2248921598975289 -0.20556999735100856 0.32061205949512683 0.07461442294796419 5 | -0.0003394140685535392 0.00126370845062871 0.008473861273724707 -0.0007302410944022516 0.020816515931065066 0.0654631741826528 -0.14394493188219834 0.37548291487767793 0.058852750852554966 -0.08378009652798472 -0.09327282324576783 -0.0008449168899679283 -4.1881653276141625e-06 -2.3789431171330047e-06 -4.004175981974327e-05 -0.01630154738816373 -0.08873629201312262 -0.015345025661584494 6 | -0.0029498959586439287 -0.000398519525717768 0.0021379041120597143 0.04214700838213215 -0.042871388585811666 -0.2748104837882809 -0.29498717325638124 -0.064869317965812 0.015224879567495842 -0.06968722624571866 0.06183080877602061 0.0839144568278962 3.441823647251379e-06 -1.3882036911646052e-05 2.2480505332935468e-05 0.0679500976285154 -0.0018863445919287494 -0.061264963537163784 7 | 0.0036870241650673857 -0.0004822858815400108 0.005526950801259323 -0.045100111035323624 -0.039939192013099714 -0.2947942841224975 0.2430821894546644 0.14396832490052888 0.0130833384932604 -0.06201340617993464 0.05654190414808016 -0.09315651536494242 -2.684979673392101e-06 -1.0753170029853975e-05 3.160733710635503e-05 0.05908521613855596 -0.02230434990422232 0.06622545781509805 8 | -0.010113427476706432 0.05234919504659532 0.5623306748501546 0.007696267373236685 0.05263713441896697 0.06533256380501419 -0.14077373349073727 0.35041341288796996 0.025774416331026045 0.5185870609328858 0.188851290556757 0.007625906006529803 -0.006197538994928147 0.45572664463522117 0.2059647011778961 0.3486644511136105 0.06367017128596411 0.02249232091679953 9 | 0.24273231278279334 0.35045943694266135 0.15869389496223066 0.046533183556883614 -0.03329442273709197 -0.2759169570480987 -0.3002336308640684 -0.075944021724553 0.003983570516932701 0.14982454528399985 0.12465127834372802 -0.4101947199767028 -0.3428304429663481 0.14593423882289547 -0.3337655808535641 -0.5549896932583737 -0.1381629267379914 -0.05713744229074226 10 | -0.2665462911143079 -0.34330554293201276 0.20441063350342173 -0.044226037882206935 -0.029138138887949867 -0.29369645547990303 0.25081587234002645 0.13924677294038643 0.003235492350163957 0.12557326705665142 0.12115220998195851 0.4436619651619443 0.3639507732885234 0.14523722453993024 -0.3108892261902479 -0.5179680913327015 -0.13363165205298067 -0.023602054457647736 11 | 0.23879779951855026 -0.430729890334202 -0.008757199819225767 0.019812243188994518 0.01993804350960812 0.06873294860333216 -0.14425989204738518 0.3789034307428847 0.06340080486887649 0.278590938122867 0.24114873389129834 -0.3241519628850773 0.11249921874834669 -0.3877236587670263 -0.2948443821501326 0.11603326372327502 0.336243159598193 -0.36376898707930877 12 | 0.39851966498829994 -0.08432369616157732 -0.2480296648473189 0.056532024713431314 -0.0566683704585617 -0.2730548553932619 -0.30171736214113376 -0.05477846909182471 0.03138525115996887 0.46732256764103014 -0.07938972278076108 -0.060097153605737544 0.37140572085698137 -0.1275648238054937 0.309343179150383 -0.10951945491661527 -0.3755954856314065 0.36306466703662477 13 | 0.21078051497033512 0.39074003141276137 -0.2734214856550456 -0.0512999200157663 -0.05540507067078815 -0.29641786339666554 0.23541119395871438 0.15212343713446186 0.027197415668685405 0.18867499862248738 -0.45575059308293714 0.16041435154318892 0.3152568831669602 0.2887712003019642 -0.2592058731996744 0.11965501308628704 0.30899456962176686 -0.30065727108838997 14 | -0.24589508165435373 0.4366389294849209 -0.1095206659972646 -0.024096861541264874 0.01392236711186857 0.06210355665807415 -0.14439993263685108 0.3780959463740517 0.06226911461784644 0.2957086783654836 0.2691391141414063 0.31596542263328475 -0.07647479994601528 -0.41271972149891906 -0.27149165088849486 0.08613611655729746 0.1557007045573241 0.4336092783297829 15 | -0.25775084105044993 -0.4249561476392833 -0.20693014626449943 0.038265282337772856 -0.05552055856803424 -0.2733407379850982 -0.2893828662467134 -0.0507844964496593 0.03007620467349373 0.24062950389718055 -0.4567943066669219 -0.12991028952320197 -0.37589343894249966 0.22709112043430738 -0.2389362867155371 0.09558608155917757 0.15534400857332914 0.3701476955628204 16 | -0.3662128283144404 0.04811478167734304 -0.23224542493021483 -0.06618760939348921 -0.05413237919363281 -0.296421792657406 0.24661059838556137 0.15578505948314217 0.026062994742515163 0.43629285735340934 -0.04336745673594962 0.052840758871999766 -0.3206854315078938 -0.16757562755363903 0.34482672270795794 -0.10017872487511309 -0.2301951899385901 -0.5394995536410131 17 | 0.001485827184716914 -0.004945343151747653 -0.029213567306076646 0.012983499530179228 -0.3216319102198409 0.06539819631181505 -0.1443733930013942 0.3790497293425475 -0.9354832057679232 1.7389387000868657e-05 -1.4903476303334465e-05 -6.575799203186596e-07 1.2661655628179726e-06 -1.5671690001172236e-05 -5.686241274828592e-06 5.792819893378986e-06 -6.756562434778788e-06 -1.2364863336517967e-06 18 | 0.025325743304052604 -0.019770198509471724 -0.03988984967372029 -0.6737176998889091 0.6820137842479301 -0.2750035356894531 -0.29376362478290874 -0.06466198302041982 -0.2424645227460431 2.487278329400468e-06 -4.818006578054979e-06 -2.587053242872362e-06 2.594666895077052e-06 -6.116258011088519e-06 -7.132024244846118e-07 1.0182968037232914e-06 -6.040033137428206e-07 -4.02368627474343e-07 19 | -0.027911798635935924 0.016120966272422592 -0.057991747789624834 0.7239928136644996 0.6393740123614169 -0.29408672917160517 0.24167391134156935 0.14298273742532583 -0.20792088953767404 2.1740208690895903e-06 -4.211572389806998e-06 2.641408095917198e-06 -2.090562020257933e-06 -5.703722993565809e-06 -6.183218143007089e-07 8.704009230542358e-07 -6.194187477422664e-07 2.0646379083247086e-07 20 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/TS/ts.pos_0.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 0 Bead: 0 positions{angstrom} cell{angstrom} 3 | H 1.37629e+00 1.64754e+00 1.39473e+00 4 | C 5.61049e-01 6.91017e-01 5.78583e-01 5 | H 3.13332e-02 1.47434e-01 1.36074e+00 6 | H 1.34127e+00 1.41874e-01 5.16893e-02 7 | H -3.52237e-02 1.37867e+00 -2.09976e-02 8 | H 2.16263e+00 2.65169e+00 2.29093e+00 9 | 6 10 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 1 Bead: 0 positions{angstrom} cell{angstrom} 11 | H 1.39721e+00 1.67919e+00 1.42513e+00 12 | C 5.69338e-01 7.01209e-01 5.87510e-01 13 | H 3.29840e-02 1.48801e-01 1.35847e+00 14 | H 1.34221e+00 1.46816e-01 5.58967e-02 15 | H -3.22640e-02 1.37801e+00 -1.85140e-02 16 | H 2.03738e+00 2.49294e+00 2.14973e+00 17 | 6 18 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 2 Bead: 0 positions{angstrom} cell{angstrom} 19 | H 1.34656e+00 1.62781e+00 1.38493e+00 20 | C 5.87348e-01 7.22722e-01 6.06064e-01 21 | H 2.35438e-02 1.36646e-01 1.33422e+00 22 | H 1.32039e+00 1.37503e-01 4.85440e-02 23 | H -3.99889e-02 1.35326e+00 -2.64634e-02 24 | H 1.91240e+00 2.33418e+00 2.00838e+00 25 | 6 26 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 3 Bead: 0 positions{angstrom} cell{angstrom} 27 | H 1.31409e+00 1.59309e+00 1.35687e+00 28 | C 6.01530e-01 7.39970e-01 6.21096e-01 29 | H 2.28943e-02 1.34963e-01 1.32112e+00 30 | H 1.31061e+00 1.38861e-01 5.01251e-02 31 | H -3.90250e-02 1.34153e+00 -2.57337e-02 32 | H 1.78536e+00 2.17543e+00 1.86811e+00 33 | 6 34 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 4 Bead: 0 positions{angstrom} cell{angstrom} 35 | H 1.34250e+00 1.62971e+00 1.38970e+00 36 | C 5.99258e-01 7.37593e-01 6.19224e-01 37 | H 2.26188e-02 1.33906e-01 1.31972e+00 38 | H 1.31341e+00 1.41684e-01 5.21687e-02 39 | H -3.80846e-02 1.34175e+00 -2.57846e-02 40 | H 1.78056e+00 2.16515e+00 1.85700e+00 41 | 6 42 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 5 Bead: 0 positions{angstrom} cell{angstrom} 43 | H 1.33302e+00 1.62666e+00 1.39108e+00 44 | C 5.97532e-01 7.36395e-01 6.18637e-01 45 | H 1.56237e-02 1.23664e-01 1.30963e+00 46 | H 1.31543e+00 1.43297e-01 5.25629e-02 47 | H -4.13159e-02 1.33527e+00 -3.17596e-02 48 | H 1.81881e+00 2.19758e+00 1.87829e+00 49 | 6 50 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 6 Bead: 0 positions{angstrom} cell{angstrom} 51 | H 1.33962e+00 1.63112e+00 1.39320e+00 52 | C 5.97638e-01 7.36481e-01 6.18694e-01 53 | H 1.75726e-02 1.26041e-01 1.31113e+00 54 | H 1.31472e+00 1.42379e-01 5.18937e-02 55 | H -4.04700e-02 1.33619e+00 -3.06815e-02 56 | H 1.80886e+00 2.18973e+00 1.87357e+00 57 | 6 58 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 7 Bead: 0 positions{angstrom} cell{angstrom} 59 | H 1.33632e+00 1.62657e+00 1.38901e+00 60 | C 5.98243e-01 7.37181e-01 6.19295e-01 61 | H 1.75985e-02 1.26090e-01 1.31078e+00 62 | H 1.31398e+00 1.42183e-01 5.17694e-02 63 | H -4.04361e-02 1.33577e+00 -3.05888e-02 64 | H 1.80564e+00 2.18650e+00 1.87099e+00 65 | 6 66 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 8 Bead: 0 positions{angstrom} cell{angstrom} 67 | H 1.33786e+00 1.62766e+00 1.38959e+00 68 | C 5.98186e-01 7.37080e-01 6.19198e-01 69 | H 1.79553e-02 1.26579e-01 1.31124e+00 70 | H 1.31380e+00 1.41980e-01 5.16210e-02 71 | H -4.02721e-02 1.33608e+00 -3.03363e-02 72 | H 1.80443e+00 2.18602e+00 1.87100e+00 73 | 6 74 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 9 Bead: 0 positions{angstrom} cell{angstrom} 75 | H 1.33807e+00 1.62742e+00 1.38914e+00 76 | C 5.98222e-01 7.37076e-01 6.19177e-01 77 | H 1.80990e-02 1.26854e-01 1.31154e+00 78 | H 1.31351e+00 1.41717e-01 5.14360e-02 79 | H -4.02748e-02 1.33620e+00 -3.02090e-02 80 | H 1.80395e+00 2.18617e+00 1.87146e+00 81 | 6 82 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 10 Bead: 0 positions{angstrom} cell{angstrom} 83 | H 1.33827e+00 1.62743e+00 1.38904e+00 84 | C 5.98248e-01 7.37070e-01 6.19156e-01 85 | H 1.81479e-02 1.27001e-01 1.31172e+00 86 | H 1.31329e+00 1.41542e-01 5.13167e-02 87 | H -4.03075e-02 1.33625e+00 -3.01370e-02 88 | H 1.80363e+00 2.18621e+00 1.87167e+00 89 | 6 90 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 11 Bead: 0 positions{angstrom} cell{angstrom} 91 | H 1.33835e+00 1.62742e+00 1.38897e+00 92 | C 5.98265e-01 7.37065e-01 6.19141e-01 93 | H 1.82043e-02 1.27127e-01 1.31185e+00 94 | H 1.31315e+00 1.41423e-01 5.12375e-02 95 | H -4.03203e-02 1.33629e+00 -3.00758e-02 96 | H 1.80345e+00 2.18624e+00 1.87182e+00 97 | 6 98 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 12 Bead: 0 positions{angstrom} cell{angstrom} 99 | H 1.33839e+00 1.62741e+00 1.38893e+00 100 | C 5.98278e-01 7.37064e-01 6.19132e-01 101 | H 1.82318e-02 1.27198e-01 1.31192e+00 102 | H 1.31305e+00 1.41338e-01 5.11811e-02 103 | H -4.03360e-02 1.33631e+00 -3.00423e-02 104 | H 1.80333e+00 2.18626e+00 1.87190e+00 105 | 6 106 | # CELL(abcABC): 105.83544 105.83544 105.83544 90.00000 90.00000 90.00000 Step: 13 Bead: 0 positions{angstrom} cell{angstrom} 107 | H 1.33843e+00 1.62740e+00 1.38891e+00 108 | C 5.98285e-01 7.37062e-01 6.19126e-01 109 | H 1.82530e-02 1.27246e-01 1.31197e+00 110 | H 1.31300e+00 1.41289e-01 5.11488e-02 111 | H -4.03431e-02 1.33632e+00 -3.00193e-02 112 | H 1.80326e+00 2.18627e+00 1.87196e+00 113 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.phonons.hess: -------------------------------------------------------------------------------- 1 | # Hessian matrix (atomic units) 2 | 0.20233210579201358 0.11405165187272637 0.0974895301986134 -0.19020625463550545 -0.10374515302391528 -0.08867983153360014 0.009998452760173748 0.009661674099659122 0.008384425931318162 -0.011527412913103774 -0.012563910745111428 -0.006585174905371361 -0.010592862420555349 -0.007403469504119187 -0.010608240536003065 -5.200839758856546e-06 -1.1463052729254741e-06 -9.836575998178887e-07 3 | 0.11405165187272637 0.1290341219983837 0.07106983446192315 -0.10374734807361286 -0.12353790809771503 -0.06464223240021383 -0.01732886820149382 -0.009493992259024251 -0.00795344068382775 0.016719846201995733 0.010821890605861027 0.01061505036648036 -0.009694579305996596 -0.006825577325564326 -0.009089091701497408 -1.1352030426792228e-06 4.1869285816176216e-07 -1.895705814547455e-07 4 | 0.0974895301986134 0.07106983446192315 0.10664232802382045 -0.08868177928111896 -0.06464220325685943 -0.10317041249097157 -0.016114451439896982 -0.008994019279340291 -0.007537923341072172 -0.010800531718979654 -0.010705084874107483 -0.006324214346653533 0.018107914612208727 0.013271690413318995 0.010388659377191798 -9.744982598647312e-07 -1.8998691508897994e-07 4.77118344832661e-07 5 | -0.19020625463550545 -0.10374734807361286 -0.08868177928111896 0.5559310894964752 1.5311363288361478e-06 -4.767297667740422e-06 -0.09417648119680598 0.07497522672150757 0.06983669836868599 -0.1429798687779815 0.09975519493776731 -0.08358753633697089 -0.12855399605937734 -0.07098099802371748 0.10244062750852655 -1.0303424780033765e-05 -3.2809865935234943e-06 -2.8109459204728182e-06 6 | -0.10374515302391528 -0.12353790809771503 -0.06464220325685943 1.5311363288361478e-06 0.5558740223676749 -5.610845121850616e-05 0.0749740883265737 -0.16939560823492347 -0.1131566468304257 0.09975249140592446 -0.1525591658557701 0.08769881390535693 -0.07098004017880298 -0.11037762481791445 0.09015704294235148 -3.2554514639571157e-06 5.867528685143952e-07 -7.785438960183911e-07 7 | -0.08867983153360014 -0.06464223240021383 -0.10317041249097157 -4.767297667740422e-06 -5.610845121850616e-05 0.5558908428016095 0.06983549932781939 -0.11315699238734211 -0.1533165065736863 -0.08358666217511689 0.08769873355296551 -0.12139222058116239 0.10243814491106562 0.09015720600635821 -0.17800828144842737 -2.7891577936145495e-06 -7.788214517745474e-07 8.275324869799761e-07 8 | 0.009998452760173748 -0.01732886820149382 -0.016114451439896982 -0.09417648119680598 0.0749740883265737 0.06983549932781939 0.09676070777953073 -0.08242164603600165 -0.07677282795603979 -0.006540845365332616 0.011488307388729522 0.013599481402115643 -0.00604244473900728 0.01328852861082197 0.009452496285700105 -4.850286838831154e-07 -2.6909030559352237e-07 -2.381428387820961e-07 9 | 0.009661674099659122 -0.009493992259024251 -0.008994019279340291 0.07497522672150757 -0.16939560823492347 -0.11315699238734211 -0.08242164603600165 0.17944865371433136 0.12440427687998577 0.006125007723234432 -0.011198799387823753 -0.014564654898796547 -0.008339714613336824 0.010638716296806903 0.01231104579391129 -3.833044992518353e-07 -8.479328350574633e-08 -1.3739009929736312e-07 10 | 0.008384425931318162 -0.00795344068382775 -0.007537923341072172 0.06983669836868599 -0.1131566468304257 -0.1533165065736863 -0.07677282795603979 0.12440427687998577 0.16177116007876077 -0.008831944064979778 0.013682978361462261 0.010708932074443565 0.007384204914195892 -0.01697745569129161 -0.011626631740702107 -3.431976924872515e-07 -1.4002687898084787e-07 -5.037636974236648e-08 11 | -0.011527412913103774 0.016719846201995733 -0.010800531718979654 -0.1429798687779815 0.09975249140592446 -0.08358666217511689 -0.006540845365332616 0.006125007723234432 -0.008831944064979778 0.15040945766653377 -0.10966224303632366 0.09188968669304741 0.01063802768097588 -0.012934912446693758 0.011329163718265532 -3.151645611154663e-07 -5.898059818321145e-08 -9.645062526431047e-08 12 | -0.012563910745111428 0.010821890605861027 -0.010705084874107483 0.09975519493776731 -0.1525591658557701 0.08769873355296551 0.011488307388729522 -0.011198799387823753 0.013682978361462261 -0.10966224303632366 0.1609369842947572 -0.09641134487980985 0.010983079029580622 -0.008002006834928466 0.005734723668160412 7.355227538141663e-08 4.565792188770956e-08 1.5265566588595902e-08 13 | -0.006585174905371361 0.01061505036648036 -0.006324214346653533 -0.08358753633697089 0.08769881390535693 -0.12139222058116239 0.013599481402115643 -0.014564654898796547 0.010708932074443565 0.09188968669304741 -0.09641134487980985 0.12667505516761327 -0.01531625562489758 0.012662592363543723 -0.009668545547514285 -1.6056600493641326e-07 -3.4555691641458e-08 -2.2898349882893857e-08 14 | -0.010592862420555349 -0.009694579305996596 0.018107914612208727 -0.12855399605937734 -0.07098004017880298 0.10243814491106562 -0.00604244473900728 -0.008339714613336824 0.007384204914195892 0.01063802768097588 0.010983079029580622 -0.01531625562489758 0.13455063313516644 0.07803112184179282 -0.11261369892157091 -3.1641356201816967e-07 -1.0935696792557795e-07 -4.218847493575595e-08 15 | -0.007403469504119187 -0.006825577325564326 0.013271690413318995 -0.07098099802371748 -0.11037762481791445 0.09015720600635821 0.01328852861082197 0.010638716296806903 -0.01697745569129161 -0.012934912446693758 -0.008002006834928466 0.012662592363543723 0.07803112184179282 0.11456543463905788 -0.09911359871717097 -1.6459056340067948e-07 -2.9282132274488504e-08 -2.6784130469081905e-08 16 | -0.010608240536003065 -0.009089091701497408 0.010388659377191798 0.10244062750852655 0.09015704294235148 -0.17800828144842737 0.009452496285700105 0.01231104579391129 -0.011626631740702107 0.011329163718265532 0.005734723668160412 -0.009668545547514285 -0.11261369892157091 -0.09911359871717097 0.18891362252304583 9.561795799584161e-08 2.525757381022231e-08 4.8155923693116165e-08 17 | -5.200839758856546e-06 -1.1352030426792228e-06 -9.744982598647312e-07 -1.0303424780033765e-05 -3.2554514639571157e-06 -2.7891577936145495e-06 -4.850286838831154e-07 -3.833044992518353e-07 -3.431976924872515e-07 -3.151645611154663e-07 7.355227538141663e-08 -1.6056600493641326e-07 -3.1641356201816967e-07 -1.6459056340067948e-07 9.561795799584161e-08 1.6620871345907062e-05 4.865691183297827e-06 4.172079348663261e-06 18 | -1.1463052729254741e-06 4.1869285816176216e-07 -1.8998691508897994e-07 -3.2809865935234943e-06 5.867528685143952e-07 -7.788214517745474e-07 -2.6909030559352237e-07 -8.479328350574633e-08 -1.4002687898084787e-07 -5.898059818321145e-08 4.565792188770956e-08 -3.4555691641458e-08 -1.0935696792557795e-07 -2.9282132274488504e-08 2.525757381022231e-08 4.865691183297827e-06 -9.381384558082573e-07 1.1168843627729075e-06 19 | -9.836575998178887e-07 -1.895705814547455e-07 4.77118344832661e-07 -2.8109459204728182e-06 -7.785438960183911e-07 8.275324869799761e-07 -2.381428387820961e-07 -1.3739009929736312e-07 -5.037636974236648e-08 -9.645062526431047e-08 1.5265566588595902e-08 -2.2898349882893857e-08 -4.218847493575595e-08 -2.6784130469081905e-08 4.8155923693116165e-08 4.172079348663261e-06 1.1168843627729075e-06 -1.2803647031489618e-06 20 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.phonons_full.hess: -------------------------------------------------------------------------------- 1 | # Hessian matrix (atomic units) 2 | 0.20233210579201358 0.11405165187272637 0.0974895301986134 -0.19020625463550545 -0.10374515302391528 -0.08867983153360014 0.009998452760173748 0.009661674099659122 0.008384425931318162 -0.011527412913103774 -0.012563910745111428 -0.006585174905371361 -0.010592862420555349 -0.007403469504119187 -0.010608240536003065 -5.200839758856546e-06 -1.1463052729254741e-06 -9.836575998178887e-07 3 | 0.11405165187272637 0.1290341219983837 0.07106983446192315 -0.10374734807361286 -0.12353790809771503 -0.06464223240021383 -0.01732886820149382 -0.009493992259024251 -0.00795344068382775 0.016719846201995733 0.010821890605861027 0.01061505036648036 -0.009694579305996596 -0.006825577325564326 -0.009089091701497408 -1.1352030426792228e-06 4.1869285816176216e-07 -1.895705814547455e-07 4 | 0.0974895301986134 0.07106983446192315 0.10664232802382045 -0.08868177928111896 -0.06464220325685943 -0.10317041249097157 -0.016114451439896982 -0.008994019279340291 -0.007537923341072172 -0.010800531718979654 -0.010705084874107483 -0.006324214346653533 0.018107914612208727 0.013271690413318995 0.010388659377191798 -9.744982598647312e-07 -1.8998691508897994e-07 4.77118344832661e-07 5 | -0.19020625463550545 -0.10374734807361286 -0.08868177928111896 0.5559310894964752 1.5311363288361478e-06 -4.767297667740422e-06 -0.09417648119680598 0.07497522672150757 0.06983669836868599 -0.1429798687779815 0.09975519493776731 -0.08358753633697089 -0.12855399605937734 -0.07098099802371748 0.10244062750852655 -1.0303424780033765e-05 -3.2809865935234943e-06 -2.8109459204728182e-06 6 | -0.10374515302391528 -0.12353790809771503 -0.06464220325685943 1.5311363288361478e-06 0.5558740223676749 -5.610845121850616e-05 0.0749740883265737 -0.16939560823492347 -0.1131566468304257 0.09975249140592446 -0.1525591658557701 0.08769881390535693 -0.07098004017880298 -0.11037762481791445 0.09015704294235148 -3.2554514639571157e-06 5.867528685143952e-07 -7.785438960183911e-07 7 | -0.08867983153360014 -0.06464223240021383 -0.10317041249097157 -4.767297667740422e-06 -5.610845121850616e-05 0.5558908428016095 0.06983549932781939 -0.11315699238734211 -0.1533165065736863 -0.08358666217511689 0.08769873355296551 -0.12139222058116239 0.10243814491106562 0.09015720600635821 -0.17800828144842737 -2.7891577936145495e-06 -7.788214517745474e-07 8.275324869799761e-07 8 | 0.009998452760173748 -0.01732886820149382 -0.016114451439896982 -0.09417648119680598 0.0749740883265737 0.06983549932781939 0.09676070777953073 -0.08242164603600165 -0.07677282795603979 -0.006540845365332616 0.011488307388729522 0.013599481402115643 -0.00604244473900728 0.01328852861082197 0.009452496285700105 -4.850286838831154e-07 -2.6909030559352237e-07 -2.381428387820961e-07 9 | 0.009661674099659122 -0.009493992259024251 -0.008994019279340291 0.07497522672150757 -0.16939560823492347 -0.11315699238734211 -0.08242164603600165 0.17944865371433136 0.12440427687998577 0.006125007723234432 -0.011198799387823753 -0.014564654898796547 -0.008339714613336824 0.010638716296806903 0.01231104579391129 -3.833044992518353e-07 -8.479328350574633e-08 -1.3739009929736312e-07 10 | 0.008384425931318162 -0.00795344068382775 -0.007537923341072172 0.06983669836868599 -0.1131566468304257 -0.1533165065736863 -0.07677282795603979 0.12440427687998577 0.16177116007876077 -0.008831944064979778 0.013682978361462261 0.010708932074443565 0.007384204914195892 -0.01697745569129161 -0.011626631740702107 -3.431976924872515e-07 -1.4002687898084787e-07 -5.037636974236648e-08 11 | -0.011527412913103774 0.016719846201995733 -0.010800531718979654 -0.1429798687779815 0.09975249140592446 -0.08358666217511689 -0.006540845365332616 0.006125007723234432 -0.008831944064979778 0.15040945766653377 -0.10966224303632366 0.09188968669304741 0.01063802768097588 -0.012934912446693758 0.011329163718265532 -3.151645611154663e-07 -5.898059818321145e-08 -9.645062526431047e-08 12 | -0.012563910745111428 0.010821890605861027 -0.010705084874107483 0.09975519493776731 -0.1525591658557701 0.08769873355296551 0.011488307388729522 -0.011198799387823753 0.013682978361462261 -0.10966224303632366 0.1609369842947572 -0.09641134487980985 0.010983079029580622 -0.008002006834928466 0.005734723668160412 7.355227538141663e-08 4.565792188770956e-08 1.5265566588595902e-08 13 | -0.006585174905371361 0.01061505036648036 -0.006324214346653533 -0.08358753633697089 0.08769881390535693 -0.12139222058116239 0.013599481402115643 -0.014564654898796547 0.010708932074443565 0.09188968669304741 -0.09641134487980985 0.12667505516761327 -0.01531625562489758 0.012662592363543723 -0.009668545547514285 -1.6056600493641326e-07 -3.4555691641458e-08 -2.2898349882893857e-08 14 | -0.010592862420555349 -0.009694579305996596 0.018107914612208727 -0.12855399605937734 -0.07098004017880298 0.10243814491106562 -0.00604244473900728 -0.008339714613336824 0.007384204914195892 0.01063802768097588 0.010983079029580622 -0.01531625562489758 0.13455063313516644 0.07803112184179282 -0.11261369892157091 -3.1641356201816967e-07 -1.0935696792557795e-07 -4.218847493575595e-08 15 | -0.007403469504119187 -0.006825577325564326 0.013271690413318995 -0.07098099802371748 -0.11037762481791445 0.09015720600635821 0.01328852861082197 0.010638716296806903 -0.01697745569129161 -0.012934912446693758 -0.008002006834928466 0.012662592363543723 0.07803112184179282 0.11456543463905788 -0.09911359871717097 -1.6459056340067948e-07 -2.9282132274488504e-08 -2.6784130469081905e-08 16 | -0.010608240536003065 -0.009089091701497408 0.010388659377191798 0.10244062750852655 0.09015704294235148 -0.17800828144842737 0.009452496285700105 0.01231104579391129 -0.011626631740702107 0.011329163718265532 0.005734723668160412 -0.009668545547514285 -0.11261369892157091 -0.09911359871717097 0.18891362252304583 9.561795799584161e-08 2.525757381022231e-08 4.8155923693116165e-08 17 | -5.200839758856546e-06 -1.1352030426792228e-06 -9.744982598647312e-07 -1.0303424780033765e-05 -3.2554514639571157e-06 -2.7891577936145495e-06 -4.850286838831154e-07 -3.833044992518353e-07 -3.431976924872515e-07 -3.151645611154663e-07 7.355227538141663e-08 -1.6056600493641326e-07 -3.1641356201816967e-07 -1.6459056340067948e-07 9.561795799584161e-08 1.6620871345907062e-05 4.865691183297827e-06 4.172079348663261e-06 18 | -1.1463052729254741e-06 4.1869285816176216e-07 -1.8998691508897994e-07 -3.2809865935234943e-06 5.867528685143952e-07 -7.788214517745474e-07 -2.6909030559352237e-07 -8.479328350574633e-08 -1.4002687898084787e-07 -5.898059818321145e-08 4.565792188770956e-08 -3.4555691641458e-08 -1.0935696792557795e-07 -2.9282132274488504e-08 2.525757381022231e-08 4.865691183297827e-06 -9.381384558082573e-07 1.1168843627729075e-06 19 | -9.836575998178887e-07 -1.895705814547455e-07 4.77118344832661e-07 -2.8109459204728182e-06 -7.785438960183911e-07 8.275324869799761e-07 -2.381428387820961e-07 -1.3739009929736312e-07 -5.037636974236648e-08 -9.645062526431047e-08 1.5265566588595902e-08 -2.2898349882893857e-08 -4.218847493575595e-08 -2.6784130469081905e-08 4.8155923693116165e-08 4.172079348663261e-06 1.1168843627729075e-06 -1.2803647031489618e-06 20 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.phonons.dynmat: -------------------------------------------------------------------------------- 1 | # Dynamical matrix (atomic units) 2 | 0.00011012096687953914 6.207358011359646e-05 5.305950473890186e-05 -2.9989083183991332e-05 -1.635709630018307e-05 -1.3981805433789568e-05 5.4417428264278466e-06 5.258448180355268e-06 4.563295017725659e-06 -6.273892374330137e-06 -6.838015121841889e-06 -3.584037366742988e-06 -5.765255332105253e-06 -4.029401151465541e-06 -5.773625002036077e-06 -2.830601206807775e-09 -6.238863797692449e-10 -5.35364002397628e-10 3 | 6.207358011359646e-05 7.022791671787808e-05 3.868036096535643e-05 -1.635744238516382e-05 -1.9477743302491202e-05 -1.0191890315929941e-05 -9.431383683804485e-06 -5.167185914554337e-06 -4.3287276366435464e-06 9.099918288467872e-06 5.889905866976141e-06 5.777331310105723e-06 -5.276357118351387e-06 -3.7148784255467926e-06 -4.946815347508717e-06 -6.178438966722063e-10 2.2787714379707166e-10 -1.0317539888193567e-10 4 | 5.305950473890186e-05 3.868036096535643e-05 5.8040992685262814e-05 -1.3982112527594003e-05 -1.0191885721010173e-05 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__version__ = '1.0' 5 | 6 | """ get_rdf.py 7 | The script reads simulation time, potential energy, positions and forces from 8 | standard i-PI output files and computes a conventional and PPI radial distribution function (RDF) estimators. 9 | The output is saved to two files which are created in the folder which contains the input files. 10 | The results are printed out in the format: "distance", "RDF". 11 | 12 | The script assumes that the input files are in 'xyz' format, with prefix.pos_*.xyz (positions) and 13 | prefix.for_*.xyz (forces) naming scheme. 14 | This would require the following lines in input.xml file: 15 | positions 16 | where n is the same integer number. 17 | 18 | Syntax: 19 | python rdf_ppi.py "prefix" "simulation temperature (in Kelvin)" "element A" "element B" "number of bins for RDF" 20 | "minimum distance (in Angstroms)" "maximum distance (in Angstroms) "number of time frames to skip in the beginning 21 | of each file (default 0)" 22 | 23 | WARNING: 24 | Since the python code for computing RDF is inefficient the fortran function in f90 folder must be compiled to 25 | compute RDFs. 26 | """ 27 | 28 | import numpy as np 29 | import sys 30 | import glob 31 | import os 32 | from ipi.utils.units import unit_to_internal, unit_to_user, Constants, Elements 33 | from ipi.utils.io import read_file 34 | 35 | 36 | def RDF(prefix, filetype, A, B, nbins, r_min, r_max, width, ss=0, unit='angstrom'): 37 | 38 | # Adding fortran functions (when exist) 39 | try: 40 | import fortran 41 | except: 42 | print('WARNING: No compiled fortran module for fast calculations have been found.\n' 43 | 'Proceeding the calculations is not possible.') 44 | sys.exit(0) 45 | 46 | skipSteps = int(ss) # steps to skip 47 | nbins = int(nbins) 48 | 49 | fns_pos = sorted(glob.glob(prefix + ".pos*")) 50 | #print(fns_pos) 51 | fn_out_rdf = prefix + '.' + A + B + ".rdf.dat" 52 | fn_out_rdf2 = prefix + '.' + A + B + ".rdf2.dat" 53 | fn_out_rdf3 = prefix + '.' + A + B + ".rdf3.dat" 54 | fn_out_rdf4 = prefix + '.' + A + B + ".rdf4.dat" 55 | fn_out_rdf5 = prefix + '.' + A + B + ".rdf5.dat" 56 | 57 | # check that we found the same number of positions files 58 | nbeads = len(fns_pos) 59 | 60 | # open input and output files 61 | ipos = [open(fn, "r") for fn in fns_pos] 62 | 63 | # Species for RDF 64 | species = (A, B) 65 | speciesMass = np.array([Elements.mass(species[0]), Elements.mass(species[1])], order='F') 66 | 67 | r_min = unit_to_internal('length', unit, float(r_min)) # Minimal distance for RDF 68 | r_max = unit_to_internal('length', unit, float(r_max)) # Maximal distance for RDF 69 | width = unit_to_internal('length', unit, float(width)) # Maximal distance for RDF 70 | dr = (r_max - r_min) / nbins # RDF step 71 | rdf = np.array([[r_min + (0.5 + i) * dr, 0] for i in range(nbins)], order='F') # conventional RDF 72 | 73 | # Kernel Density Estimation (use Gaussian instead of spikes for the datapoints) 74 | forma = np.zeros((nbins,nbins)) 75 | for bin in range(nbins): 76 | forma[bin] = 1.0/(np.sqrt(2.0)*np.pi)/width*np.exp(-0.5*(rdf[:, 0]-rdf[bin, 0])**2/width**2) 77 | rdfG = np.copy(rdf) 78 | 79 | # RDF auxiliary variables 80 | cell = None # simulation cell matrix 81 | inverseCell = None # inverse simulation sell matrix 82 | cellVolume = None # simulation cell volume 83 | natomsA = 0 # the total number of A type particles in the system 84 | natomsB = 0 # the total number of B type particles in the system 85 | # Here A and B are the types of elements used for RDF calculations 86 | 87 | natoms = 0 # total number of atoms 88 | ifr = 0 # time frame number 89 | pos, mass = None, None # positions, and mass arrays 90 | noteof = True # end of file test variable 91 | 92 | while noteof: # Reading input files and calculating PPI correction 93 | 94 | if ifr % 100 == 0: 95 | print('\r number of beads = {:d}, Processing frame {:d}'.format(nbeads, ifr), end=" ") 96 | sys.stdout.flush() 97 | 98 | try: 99 | for i in range(nbeads): 100 | ret = read_file(filetype, ipos[i], dimension='length') 101 | if natoms == 0: 102 | mass, natoms = ret["atoms"].m, ret["atoms"].natoms 103 | pos = np.zeros((nbeads, 3 * natoms), order='F') 104 | cell = ret["cell"].h 105 | inverseCell = ret["cell"].get_ih() 106 | cellVolume = ret["cell"].get_volume() 107 | pos[i, :] = ret["atoms"].q 108 | except EOFError: # finished reading files 109 | noteof = False 110 | 111 | if noteof: 112 | if ifr >= skipSteps: # RDF calculations 113 | 114 | species_A = [3 * i + j for i in np.where(mass == speciesMass[0])[0] for j in range(3)] 115 | species_B = [3 * i + j for i in np.where(mass == speciesMass[1])[0] for j in range(3)] 116 | natomsA = len(species_A) 117 | natomsB = len(species_B) 118 | posA = np.zeros((nbeads, natomsA), order='F') 119 | posB = np.zeros((nbeads, natomsB), order='F') 120 | for bead in range(nbeads): 121 | posA[bead, :] = pos[bead, species_A] 122 | posB[bead, :] = pos[bead, species_B] 123 | 124 | fortran.updaterdf(rdf, posA, posB, natomsA / 3, natomsB / 3, nbins, r_min, r_max, cell, 125 | inverseCell, nbeads, speciesMass[0], speciesMass[1])#, forma.T) 126 | 127 | ifr += 1 128 | 129 | else: 130 | ifr += 1 131 | 132 | 133 | # if ifr > skipSteps and ifr % 1000 == 0: 134 | # 135 | # rdfG[:, 1] = np.sum(forma * rdf.T[1].astype(int), axis=1) 136 | # 137 | # # Some constants 138 | # if(A==B): 139 | # const = 2./(natomsA*(natomsB-1)) 140 | # else: 141 | # const = 1./(natomsA*natomsB) 142 | # const /= float(ifr - skipSteps) 143 | # 144 | # # # Normalization 145 | # _rdf = np.copy(rdfG) 146 | # _rdf[:, 1] *= const / nbeads 147 | # 148 | # # Creating RDF from N(r) 149 | # const, dr = cellVolume / (4 * np.pi / 3.0), _rdf[1, 0] - _rdf[0, 0] 150 | # _rdf[:, 1] = const * _rdf[:, 1] * dr / ((_rdf[:, 0] + 0.5 * dr)**3 - (_rdf[:, 0] - 0.5 * dr)**3) 151 | # _rdf[:, 0] = unit_to_user('length', unit, _rdf[:, 0]) 152 | # 153 | # # Writing the results into files 154 | # np.savetxt(fn_out_rdf, _rdf) 155 | 156 | else: 157 | # Get the kernel density smoothed RDF by summing the contrbutions. 158 | rdfG[:, 1] = np.sum(forma * rdf.T[1].astype(int), axis=1) 159 | 160 | # Some constants 161 | if(A==B): 162 | const = 2./(natomsA*(natomsB-1)) 163 | else: 164 | const = 1./(natomsA*natomsB) 165 | const /= float(ifr - skipSteps) 166 | 167 | # # Normalization 168 | _rdf = np.copy(rdfG) 169 | _rdf[:, 1] *= const / nbeads 170 | 171 | # Creating RDF from N(r) 172 | const, dr = cellVolume / (4 * np.pi / 3.0), _rdf[1, 0] - _rdf[0, 0] 173 | _rdf[:, 1] = const * _rdf[:, 1] * dr / ((_rdf[:, 0] + 0.5 * dr)**3 - (_rdf[:, 0] - 0.5 * dr)**3) 174 | _rdf[:, 0] = unit_to_user('length', unit, _rdf[:, 0]) 175 | 176 | # Writing the results into files 177 | np.savetxt(fn_out_rdf, _rdf) 178 | 179 | def main(*arg): 180 | 181 | RDF(*arg) 182 | 183 | if __name__ == '__main__': 184 | 185 | main(*sys.argv[1:]) 186 | -------------------------------------------------------------------------------- /tutorial-2/data/water-32.pdb: -------------------------------------------------------------------------------- 1 | TITLE positions{angstrom} cell{angstrom} 2 | CRYST1 10.260 10.260 10.260 90.00 90.00 90.00 P 1 1 3 | ATOM 1 O 1 1 3.756 4.710 -0.766 0.00 0.00 0 4 | ATOM 2 H 1 1 4.604 4.272 -0.589 0.00 0.00 0 5 | ATOM 3 H 1 1 3.998 5.320 -1.472 0.00 0.00 0 6 | ATOM 4 O 1 1 9.933 8.841 0.366 0.00 0.00 0 7 | ATOM 5 H 1 1 10.132 8.196 1.120 0.00 0.00 0 8 | ATOM 6 H 1 1 9.368 8.449 -0.316 0.00 0.00 0 9 | ATOM 7 O 1 1 0.321 1.492 5.796 0.00 0.00 0 10 | ATOM 8 H 1 1 -0.287 1.993 5.241 0.00 0.00 0 11 | ATOM 9 H 1 1 0.791 2.061 6.364 0.00 0.00 0 12 | ATOM 10 O 1 1 -2.225 -0.525 4.307 0.00 0.00 0 13 | ATOM 11 H 1 1 -3.057 -0.471 4.847 0.00 0.00 0 14 | ATOM 12 H 1 1 -1.624 -0.953 4.920 0.00 0.00 0 15 | ATOM 13 O 1 1 -4.597 -1.178 10.920 0.00 0.00 0 16 | ATOM 14 H 1 1 -3.882 -0.539 11.074 0.00 0.00 0 17 | ATOM 15 H 1 1 -5.047 -1.269 11.812 0.00 0.00 0 18 | ATOM 16 O 1 1 -2.130 0.215 11.461 0.00 0.00 0 19 | ATOM 17 H 1 1 -2.064 -0.065 12.378 0.00 0.00 0 20 | ATOM 18 H 1 1 -1.322 -0.161 11.078 0.00 0.00 0 21 | ATOM 19 O 1 1 8.177 4.165 0.716 0.00 0.00 0 22 | ATOM 20 H 1 1 7.895 5.066 0.840 0.00 0.00 0 23 | ATOM 21 H 1 1 7.722 3.562 1.341 0.00 0.00 0 24 | ATOM 22 O 1 1 -3.919 3.256 -0.582 0.00 0.00 0 25 | ATOM 23 H 1 1 -3.127 3.423 -0.071 0.00 0.00 0 26 | ATOM 24 H 1 1 -3.753 2.398 -0.910 0.00 0.00 0 27 | ATOM 25 O 1 1 10.396 -2.462 2.738 0.00 0.00 0 28 | ATOM 26 H 1 1 10.254 -1.960 3.584 0.00 0.00 0 29 | ATOM 27 H 1 1 10.574 -3.355 2.966 0.00 0.00 0 30 | ATOM 28 O 1 1 5.027 2.563 6.169 0.00 0.00 0 31 | ATOM 29 H 1 1 5.538 3.336 6.262 0.00 0.00 0 32 | ATOM 30 H 1 1 5.313 2.031 6.922 0.00 0.00 0 33 | ATOM 31 O 1 1 -3.096 2.542 2.418 0.00 0.00 0 34 | ATOM 32 H 1 1 -4.012 2.467 2.667 0.00 0.00 0 35 | ATOM 33 H 1 1 -2.876 1.681 2.057 0.00 0.00 0 36 | ATOM 34 O 1 1 3.336 -1.209 3.265 0.00 0.00 0 37 | ATOM 35 H 1 1 2.818 -1.919 2.787 0.00 0.00 0 38 | ATOM 36 H 1 1 2.733 -0.466 3.398 0.00 0.00 0 39 | ATOM 37 O 1 1 1.476 1.420 0.819 0.00 0.00 0 40 | ATOM 38 H 1 1 1.060 0.568 0.631 0.00 0.00 0 41 | ATOM 39 H 1 1 1.582 1.509 1.770 0.00 0.00 0 42 | ATOM 40 O 1 1 1.222 4.946 3.218 0.00 0.00 0 43 | ATOM 41 H 1 1 2.111 4.703 3.522 0.00 0.00 0 44 | ATOM 42 H 1 1 1.342 4.956 2.245 0.00 0.00 0 45 | ATOM 43 O 1 1 -3.470 6.491 4.488 0.00 0.00 0 46 | ATOM 44 H 1 1 -3.177 5.755 5.074 0.00 0.00 0 47 | ATOM 45 H 1 1 -3.513 7.293 4.975 0.00 0.00 0 48 | ATOM 46 O 1 1 -0.930 3.465 4.430 0.00 0.00 0 49 | ATOM 47 H 1 1 -0.286 3.956 3.918 0.00 0.00 0 50 | ATOM 48 H 1 1 -1.677 3.143 3.966 0.00 0.00 0 51 | ATOM 49 O 1 1 -2.776 4.543 6.379 0.00 0.00 0 52 | ATOM 50 H 1 1 -2.656 4.450 7.328 0.00 0.00 0 53 | ATOM 51 H 1 1 -2.019 4.098 5.987 0.00 0.00 0 54 | ATOM 52 O 1 1 0.448 5.701 8.219 0.00 0.00 0 55 | ATOM 53 H 1 1 0.573 4.840 7.871 0.00 0.00 0 56 | ATOM 54 H 1 1 0.720 5.651 9.123 0.00 0.00 0 57 | ATOM 55 O 1 1 10.996 4.082 0.545 0.00 0.00 0 58 | ATOM 56 H 1 1 11.292 3.147 0.501 0.00 0.00 0 59 | ATOM 57 H 1 1 10.010 3.978 0.476 0.00 0.00 0 60 | ATOM 58 O 1 1 4.229 2.582 3.562 0.00 0.00 0 61 | ATOM 59 H 1 1 4.650 2.364 4.424 0.00 0.00 0 62 | ATOM 60 H 1 1 4.306 3.526 3.496 0.00 0.00 0 63 | ATOM 61 O 1 1 14.009 5.318 3.591 0.00 0.00 0 64 | ATOM 62 H 1 1 13.837 5.600 2.690 0.00 0.00 0 65 | ATOM 63 H 1 1 14.779 5.812 3.831 0.00 0.00 0 66 | ATOM 64 O 1 1 0.242 8.540 5.195 0.00 0.00 0 67 | ATOM 65 H 1 1 0.243 9.452 5.454 0.00 0.00 0 68 | ATOM 66 H 1 1 0.725 8.102 5.864 0.00 0.00 0 69 | ATOM 67 O 1 1 6.065 10.503 8.171 0.00 0.00 0 70 | ATOM 68 H 1 1 6.685 9.900 8.559 0.00 0.00 0 71 | ATOM 69 H 1 1 5.235 10.240 8.586 0.00 0.00 0 72 | ATOM 70 O 1 1 7.362 8.029 9.049 0.00 0.00 0 73 | ATOM 71 H 1 1 6.719 7.831 8.312 0.00 0.00 0 74 | ATOM 72 H 1 1 6.813 7.839 9.757 0.00 0.00 0 75 | ATOM 73 O 1 1 1.971 1.171 3.631 0.00 0.00 0 76 | ATOM 74 H 1 1 1.520 1.399 4.474 0.00 0.00 0 77 | ATOM 75 H 1 1 2.821 1.577 3.533 0.00 0.00 0 78 | ATOM 76 O 1 1 7.674 6.605 2.134 0.00 0.00 0 79 | ATOM 77 H 1 1 7.143 6.490 2.918 0.00 0.00 0 80 | ATOM 78 H 1 1 8.563 6.681 2.409 0.00 0.00 0 81 | ATOM 79 O 1 1 2.769 7.384 7.275 0.00 0.00 0 82 | ATOM 80 H 1 1 2.353 8.088 7.748 0.00 0.00 0 83 | ATOM 81 H 1 1 2.249 6.554 7.408 0.00 0.00 0 84 | ATOM 82 O 1 1 2.253 13.051 7.349 0.00 0.00 0 85 | ATOM 83 H 1 1 2.718 13.490 8.076 0.00 0.00 0 86 | ATOM 84 H 1 1 2.955 12.931 6.707 0.00 0.00 0 87 | ATOM 85 O 1 1 3.652 9.953 9.290 0.00 0.00 0 88 | ATOM 86 H 1 1 4.114 9.509 9.983 0.00 0.00 0 89 | ATOM 87 H 1 1 3.199 10.639 9.784 0.00 0.00 0 90 | ATOM 88 O 1 1 5.263 6.708 7.589 0.00 0.00 0 91 | ATOM 89 H 1 1 4.318 7.082 7.707 0.00 0.00 0 92 | ATOM 90 H 1 1 5.455 7.057 6.733 0.00 0.00 0 93 | ATOM 91 O 1 1 3.507 6.721 1.020 0.00 0.00 0 94 | ATOM 92 H 1 1 4.097 7.303 0.607 0.00 0.00 0 95 | ATOM 93 H 1 1 3.586 5.984 0.419 0.00 0.00 0 96 | ATOM 94 O 1 1 5.455 9.196 5.888 0.00 0.00 0 97 | ATOM 95 H 1 1 5.473 9.602 6.758 0.00 0.00 0 98 | ATOM 96 H 1 1 4.549 9.238 5.484 0.00 0.00 0 99 | END 100 | -------------------------------------------------------------------------------- /tutorial-2/ex-1/data.water: -------------------------------------------------------------------------------- 1 | LAMMPS Description 2 | 3 | 96 atoms 4 | 64 bonds 5 | 32 angles 6 | 7 | 2 atom types 8 | 1 bond types 9 | 1 angle types 10 | 11 | 0 35.233 xlo xhi 12 | 0 35.233 ylo yhi 13 | 0 35.233 zlo zhi 14 | 15 | Masses 16 | 17 | 1 15.9994 18 | 2 1.0080 19 | 20 | Bond Coeffs 21 | 22 | 1 1.78 0.2708585 -0.327738785 0.231328959 23 | 24 | Angle Coeffs 25 | 26 | 1 0.0700 107.400000 27 | 28 | Atoms 29 | 30 | 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 31 | 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 32 | 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 33 | 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000 34 | 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 35 | 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 36 | 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 37 | 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 38 | 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 39 | 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 40 | 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 41 | 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 42 | 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 43 | 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 44 | 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 45 | 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001 46 | 17 6 2 0.5564 2.39200001 2.89799999 34.84600000 47 | 18 6 2 0.5564 0.81400000 0.53200001 35.83600000 48 | 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999 49 | 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000 50 | 21 7 2 0.5564 30.91999999 11.59399999 1.67700000 51 | 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000 52 | 23 8 2 0.5564 0.30500000 10.64300001 2.79300000 53 | 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000 54 | 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000 55 | 26 9 2 0.5564 33.61600000 7.67300000 8.85700000 56 | 27 9 2 0.5564 35.11500000 5.25999999 7.61800001 57 | 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999 58 | 29 10 2 0.5564 31.62400000 6.90800001 23.52100001 59 | 30 10 2 0.5564 32.54400000 4.99000000 24.98200000 60 | 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000 61 | 32 11 2 0.5564 1.85600000 10.17500000 25.57899999 62 | 33 11 2 0.5564 0.51900000 8.09899999 26.38599999 63 | 34 12 1 -1.1128 2.05400000 8.66000000 32.51499999 64 | 35 12 2 0.5564 2.16699999 8.72700000 30.49400000 65 | 36 12 2 0.5564 2.37400001 10.51300000 33.03799999 66 | 37 13 1 -1.1128 3.40200000 16.63900001 3.00800000 67 | 38 13 2 0.5564 4.12700001 15.87200001 4.44600001 68 | 39 13 2 0.5564 2.90500001 18.33899999 3.15999999 69 | 40 14 1 -1.1128 4.22200000 15.44400000 8.07200000 70 | 41 14 2 0.5564 5.21100000 16.75600000 8.29900001 71 | 42 14 2 0.5564 2.56000000 15.49200001 8.86000000 72 | 43 15 1 -1.1128 2.83100000 9.24599999 16.48800000 73 | 44 15 2 0.5564 2.86900001 8.02300001 18.05000000 74 | 45 15 2 0.5564 3.96000000 8.46700001 15.15400000 75 | 46 16 1 -1.1128 5.56300000 6.00300000 20.90700000 76 | 47 16 2 0.5564 4.65300000 4.63800000 21.48000000 77 | 48 16 2 0.5564 6.40500000 6.20800000 22.52899999 78 | 49 17 1 -1.1128 2.08700001 13.37000000 22.91299999 79 | 50 17 2 0.5564 2.83200000 14.80400001 23.42200000 80 | 51 17 2 0.5564 1.43400000 13.50900000 21.19599999 81 | 52 18 1 -1.1128 3.36900000 17.88600000 25.10900001 82 | 53 18 2 0.5564 3.65500000 17.20000000 26.76599999 83 | 54 18 2 0.5564 4.77200001 18.97699999 24.49999999 84 | 55 19 1 -1.1128 34.76400000 20.80300000 0.94800001 85 | 56 19 2 0.5564 35.20999999 21.26700001 2.81599999 86 | 57 19 2 0.5564 35.96200001 21.72599999 0.13099999 87 | 58 20 1 -1.1128 2.83600000 24.17799999 15.22900000 88 | 59 20 2 0.5564 2.79500000 22.34599999 14.87600001 89 | 60 20 2 0.5564 2.41399999 24.11500000 17.13000001 90 | 61 21 1 -1.1128 33.00000000 24.48100000 15.23000000 91 | 62 21 2 0.5564 34.63999999 24.80400001 15.01299999 92 | 63 21 2 0.5564 32.40100000 25.76400000 14.29500001 93 | 64 22 1 -1.1128 0.40399999 26.77900001 23.39999999 94 | 65 22 2 0.5564 1.35300001 27.24800000 24.98700001 95 | 66 22 2 0.5564 1.54600001 28.05000000 22.31700001 96 | 67 23 1 -1.1128 34.22200000 21.38000000 25.41799999 97 | 68 23 2 0.5564 35.66899999 20.15100000 25.31700001 98 | 69 23 2 0.5564 32.96000000 21.18000000 23.99200000 99 | 70 24 1 -1.1128 33.25900000 17.43800000 32.48000000 100 | 71 24 2 0.5564 33.31399999 18.78200000 33.88300001 101 | 72 24 2 0.5564 32.74300001 18.18100001 30.87100000 102 | 73 25 1 -1.1128 4.46300000 21.97900000 3.93600000 103 | 74 25 2 0.5564 5.85600000 23.08400001 3.39999999 104 | 75 25 2 0.5564 3.98600000 22.18000000 5.60200000 105 | 76 26 1 -1.1128 6.25800000 25.85100001 8.52000000 106 | 77 26 2 0.5564 5.76700000 27.69300001 8.47600000 107 | 78 26 2 0.5564 7.20200001 25.50600000 10.18600000 108 | 79 27 1 -1.1128 0.60099999 29.73699999 12.74700001 109 | 80 27 2 0.5564 -0.68500000 30.84200000 12.34999999 110 | 81 27 2 0.5564 1.33600000 30.71600000 14.03099999 111 | 82 28 1 -1.1128 7.56300000 28.19100001 24.33300000 112 | 83 28 2 0.5564 9.20100000 28.82800000 24.68400000 113 | 84 28 2 0.5564 7.38100001 27.62100000 22.79900000 114 | 85 29 1 -1.1128 3.65300000 27.10900001 27.77200001 115 | 86 29 2 0.5564 5.12600000 27.01500000 26.77200001 116 | 87 29 2 0.5564 3.03099999 28.75600000 27.69800000 117 | 88 30 1 -1.1128 2.59600001 23.99100001 32.47600000 118 | 89 30 2 0.5564 2.87900000 24.79099999 30.85899999 119 | 90 30 2 0.5564 4.00300000 22.91299999 32.70099999 120 | 91 31 1 -1.1128 3.08300000 31.31700001 3.64399999 121 | 92 31 2 0.5564 4.13300000 30.58900001 2.53900001 122 | 93 31 2 0.5564 4.21800000 32.17300001 5.03700001 123 | 94 32 1 -1.1128 4.66100001 30.55500000 9.36799999 124 | 95 32 2 0.5564 3.18400001 29.84300000 10.13200000 125 | 96 32 2 0.5564 4.35800000 32.44800000 9.12600000 126 | 127 | Bonds 128 | 129 | 1 1 1 2 130 | 2 1 1 3 131 | 3 1 4 5 132 | 4 1 4 6 133 | 5 1 7 8 134 | 6 1 7 9 135 | 7 1 10 11 136 | 8 1 10 12 137 | 9 1 13 14 138 | 10 1 13 15 139 | 11 1 16 17 140 | 12 1 16 18 141 | 13 1 19 20 142 | 14 1 19 21 143 | 15 1 22 23 144 | 16 1 22 24 145 | 17 1 25 26 146 | 18 1 25 27 147 | 19 1 28 29 148 | 20 1 28 30 149 | 21 1 31 32 150 | 22 1 31 33 151 | 23 1 34 35 152 | 24 1 34 36 153 | 25 1 37 38 154 | 26 1 37 39 155 | 27 1 40 41 156 | 28 1 40 42 157 | 29 1 43 44 158 | 30 1 43 45 159 | 31 1 46 47 160 | 32 1 46 48 161 | 33 1 49 50 162 | 34 1 49 51 163 | 35 1 52 53 164 | 36 1 52 54 165 | 37 1 55 56 166 | 38 1 55 57 167 | 39 1 58 59 168 | 40 1 58 60 169 | 41 1 61 62 170 | 42 1 61 63 171 | 43 1 64 65 172 | 44 1 64 66 173 | 45 1 67 68 174 | 46 1 67 69 175 | 47 1 70 71 176 | 48 1 70 72 177 | 49 1 73 74 178 | 50 1 73 75 179 | 51 1 76 77 180 | 52 1 76 78 181 | 53 1 79 80 182 | 54 1 79 81 183 | 55 1 82 83 184 | 56 1 82 84 185 | 57 1 85 86 186 | 58 1 85 87 187 | 59 1 88 89 188 | 60 1 88 90 189 | 61 1 91 92 190 | 62 1 91 93 191 | 63 1 94 95 192 | 64 1 94 96 193 | 194 | Angles 195 | 196 | 1 1 2 1 3 197 | 2 1 5 4 6 198 | 3 1 8 7 9 199 | 4 1 11 10 12 200 | 5 1 14 13 15 201 | 6 1 17 16 18 202 | 7 1 20 19 21 203 | 8 1 23 22 24 204 | 9 1 26 25 27 205 | 10 1 29 28 30 206 | 11 1 32 31 33 207 | 12 1 35 34 36 208 | 13 1 38 37 39 209 | 14 1 41 40 42 210 | 15 1 44 43 45 211 | 16 1 47 46 48 212 | 17 1 50 49 51 213 | 18 1 53 52 54 214 | 19 1 56 55 57 215 | 20 1 59 58 60 216 | 21 1 62 61 63 217 | 22 1 65 64 66 218 | 23 1 68 67 69 219 | 24 1 71 70 72 220 | 25 1 74 73 75 221 | 26 1 77 76 78 222 | 27 1 80 79 81 223 | 28 1 83 82 84 224 | 29 1 86 85 87 225 | 30 1 89 88 90 226 | 31 1 92 91 93 227 | 32 1 95 94 96 228 | -------------------------------------------------------------------------------- /tutorial-2/ex-2/data.water: -------------------------------------------------------------------------------- 1 | LAMMPS Description 2 | 3 | 96 atoms 4 | 64 bonds 5 | 32 angles 6 | 7 | 2 atom types 8 | 1 bond types 9 | 1 angle types 10 | 11 | 0 35.233 xlo xhi 12 | 0 35.233 ylo yhi 13 | 0 35.233 zlo zhi 14 | 15 | Masses 16 | 17 | 1 15.9994 18 | 2 1.0080 19 | 20 | Bond Coeffs 21 | 22 | 1 1.78 0.2708585 -0.327738785 0.231328959 23 | 24 | Angle Coeffs 25 | 26 | 1 0.0700 107.400000 27 | 28 | Atoms 29 | 30 | 1 1 1 -1.1128 3.84600000 5.67200001 1.32300000 31 | 2 1 2 0.5564 2.97900000 7.05400000 0.85700000 32 | 3 1 2 0.5564 5.52500001 5.69700001 0.45100000 33 | 4 2 1 -1.1128 34.55700001 34.34100000 3.07800000 34 | 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 35 | 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 36 | 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 37 | 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 38 | 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 39 | 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 40 | 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 41 | 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 42 | 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 43 | 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 44 | 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 45 | 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001 46 | 17 6 2 0.5564 2.39200001 2.89799999 34.84600000 47 | 18 6 2 0.5564 0.81400000 0.53200001 35.83600000 48 | 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999 49 | 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000 50 | 21 7 2 0.5564 30.91999999 11.59399999 1.67700000 51 | 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000 52 | 23 8 2 0.5564 0.30500000 10.64300001 2.79300000 53 | 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000 54 | 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000 55 | 26 9 2 0.5564 33.61600000 7.67300000 8.85700000 56 | 27 9 2 0.5564 35.11500000 5.25999999 7.61800001 57 | 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999 58 | 29 10 2 0.5564 31.62400000 6.90800001 23.52100001 59 | 30 10 2 0.5564 32.54400000 4.99000000 24.98200000 60 | 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000 61 | 32 11 2 0.5564 1.85600000 10.17500000 25.57899999 62 | 33 11 2 0.5564 0.51900000 8.09899999 26.38599999 63 | 34 12 1 -1.1128 2.05400000 8.66000000 32.51499999 64 | 35 12 2 0.5564 2.16699999 8.72700000 30.49400000 65 | 36 12 2 0.5564 2.37400001 10.51300000 33.03799999 66 | 37 13 1 -1.1128 3.40200000 16.63900001 3.00800000 67 | 38 13 2 0.5564 4.12700001 15.87200001 4.44600001 68 | 39 13 2 0.5564 2.90500001 18.33899999 3.15999999 69 | 40 14 1 -1.1128 4.22200000 15.44400000 8.07200000 70 | 41 14 2 0.5564 5.21100000 16.75600000 8.29900001 71 | 42 14 2 0.5564 2.56000000 15.49200001 8.86000000 72 | 43 15 1 -1.1128 2.83100000 9.24599999 16.48800000 73 | 44 15 2 0.5564 2.86900001 8.02300001 18.05000000 74 | 45 15 2 0.5564 3.96000000 8.46700001 15.15400000 75 | 46 16 1 -1.1128 5.56300000 6.00300000 20.90700000 76 | 47 16 2 0.5564 4.65300000 4.63800000 21.48000000 77 | 48 16 2 0.5564 6.40500000 6.20800000 22.52899999 78 | 49 17 1 -1.1128 2.08700001 13.37000000 22.91299999 79 | 50 17 2 0.5564 2.83200000 14.80400001 23.42200000 80 | 51 17 2 0.5564 1.43400000 13.50900000 21.19599999 81 | 52 18 1 -1.1128 3.36900000 17.88600000 25.10900001 82 | 53 18 2 0.5564 3.65500000 17.20000000 26.76599999 83 | 54 18 2 0.5564 4.77200001 18.97699999 24.49999999 84 | 55 19 1 -1.1128 34.76400000 20.80300000 0.94800001 85 | 56 19 2 0.5564 35.20999999 21.26700001 2.81599999 86 | 57 19 2 0.5564 35.96200001 21.72599999 0.13099999 87 | 58 20 1 -1.1128 2.83600000 24.17799999 15.22900000 88 | 59 20 2 0.5564 2.79500000 22.34599999 14.87600001 89 | 60 20 2 0.5564 2.41399999 24.11500000 17.13000001 90 | 61 21 1 -1.1128 33.00000000 24.48100000 15.23000000 91 | 62 21 2 0.5564 34.63999999 24.80400001 15.01299999 92 | 63 21 2 0.5564 32.40100000 25.76400000 14.29500001 93 | 64 22 1 -1.1128 0.40399999 26.77900001 23.39999999 94 | 65 22 2 0.5564 1.35300001 27.24800000 24.98700001 95 | 66 22 2 0.5564 1.54600001 28.05000000 22.31700001 96 | 67 23 1 -1.1128 34.22200000 21.38000000 25.41799999 97 | 68 23 2 0.5564 35.66899999 20.15100000 25.31700001 98 | 69 23 2 0.5564 32.96000000 21.18000000 23.99200000 99 | 70 24 1 -1.1128 33.25900000 17.43800000 32.48000000 100 | 71 24 2 0.5564 33.31399999 18.78200000 33.88300001 101 | 72 24 2 0.5564 32.74300001 18.18100001 30.87100000 102 | 73 25 1 -1.1128 4.46300000 21.97900000 3.93600000 103 | 74 25 2 0.5564 5.85600000 23.08400001 3.39999999 104 | 75 25 2 0.5564 3.98600000 22.18000000 5.60200000 105 | 76 26 1 -1.1128 6.25800000 25.85100001 8.52000000 106 | 77 26 2 0.5564 5.76700000 27.69300001 8.47600000 107 | 78 26 2 0.5564 7.20200001 25.50600000 10.18600000 108 | 79 27 1 -1.1128 0.60099999 29.73699999 12.74700001 109 | 80 27 2 0.5564 -0.68500000 30.84200000 12.34999999 110 | 81 27 2 0.5564 1.33600000 30.71600000 14.03099999 111 | 82 28 1 -1.1128 7.56300000 28.19100001 24.33300000 112 | 83 28 2 0.5564 9.20100000 28.82800000 24.68400000 113 | 84 28 2 0.5564 7.38100001 27.62100000 22.79900000 114 | 85 29 1 -1.1128 3.65300000 27.10900001 27.77200001 115 | 86 29 2 0.5564 5.12600000 27.01500000 26.77200001 116 | 87 29 2 0.5564 3.03099999 28.75600000 27.69800000 117 | 88 30 1 -1.1128 2.59600001 23.99100001 32.47600000 118 | 89 30 2 0.5564 2.87900000 24.79099999 30.85899999 119 | 90 30 2 0.5564 4.00300000 22.91299999 32.70099999 120 | 91 31 1 -1.1128 3.08300000 31.31700001 3.64399999 121 | 92 31 2 0.5564 4.13300000 30.58900001 2.53900001 122 | 93 31 2 0.5564 4.21800000 32.17300001 5.03700001 123 | 94 32 1 -1.1128 4.66100001 30.55500000 9.36799999 124 | 95 32 2 0.5564 3.18400001 29.84300000 10.13200000 125 | 96 32 2 0.5564 4.35800000 32.44800000 9.12600000 126 | 127 | Bonds 128 | 129 | 1 1 1 2 130 | 2 1 1 3 131 | 3 1 4 5 132 | 4 1 4 6 133 | 5 1 7 8 134 | 6 1 7 9 135 | 7 1 10 11 136 | 8 1 10 12 137 | 9 1 13 14 138 | 10 1 13 15 139 | 11 1 16 17 140 | 12 1 16 18 141 | 13 1 19 20 142 | 14 1 19 21 143 | 15 1 22 23 144 | 16 1 22 24 145 | 17 1 25 26 146 | 18 1 25 27 147 | 19 1 28 29 148 | 20 1 28 30 149 | 21 1 31 32 150 | 22 1 31 33 151 | 23 1 34 35 152 | 24 1 34 36 153 | 25 1 37 38 154 | 26 1 37 39 155 | 27 1 40 41 156 | 28 1 40 42 157 | 29 1 43 44 158 | 30 1 43 45 159 | 31 1 46 47 160 | 32 1 46 48 161 | 33 1 49 50 162 | 34 1 49 51 163 | 35 1 52 53 164 | 36 1 52 54 165 | 37 1 55 56 166 | 38 1 55 57 167 | 39 1 58 59 168 | 40 1 58 60 169 | 41 1 61 62 170 | 42 1 61 63 171 | 43 1 64 65 172 | 44 1 64 66 173 | 45 1 67 68 174 | 46 1 67 69 175 | 47 1 70 71 176 | 48 1 70 72 177 | 49 1 73 74 178 | 50 1 73 75 179 | 51 1 76 77 180 | 52 1 76 78 181 | 53 1 79 80 182 | 54 1 79 81 183 | 55 1 82 83 184 | 56 1 82 84 185 | 57 1 85 86 186 | 58 1 85 87 187 | 59 1 88 89 188 | 60 1 88 90 189 | 61 1 91 92 190 | 62 1 91 93 191 | 63 1 94 95 192 | 64 1 94 96 193 | 194 | Angles 195 | 196 | 1 1 2 1 3 197 | 2 1 5 4 6 198 | 3 1 8 7 9 199 | 4 1 11 10 12 200 | 5 1 14 13 15 201 | 6 1 17 16 18 202 | 7 1 20 19 21 203 | 8 1 23 22 24 204 | 9 1 26 25 27 205 | 10 1 29 28 30 206 | 11 1 32 31 33 207 | 12 1 35 34 36 208 | 13 1 38 37 39 209 | 14 1 41 40 42 210 | 15 1 44 43 45 211 | 16 1 47 46 48 212 | 17 1 50 49 51 213 | 18 1 53 52 54 214 | 19 1 56 55 57 215 | 20 1 59 58 60 216 | 21 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34.55700001 34.34100000 3.07800000 34 | 5 2 2 0.5564 33.72200001 34.68900000 4.84000001 35 | 6 2 2 0.5564 36.02900000 33.22000001 3.71100001 36 | 7 3 1 -1.1128 5.59100000 1.96299999 13.47700000 37 | 8 3 2 0.5564 7.26500000 1.86400000 13.85100001 38 | 9 3 2 0.5564 5.00899999 3.55500000 13.91599999 39 | 10 4 1 -1.1128 1.06000000 2.06100000 21.71800001 40 | 11 4 2 0.5564 0.75700000 0.26100000 21.82000000 41 | 12 4 2 0.5564 0.21300001 3.01299999 23.04700000 42 | 13 5 1 -1.1128 1.20000000 1.33700000 29.00599999 43 | 14 5 2 0.5564 0.81800000 1.88399999 30.73200000 44 | 15 5 2 0.5564 2.88300001 1.82500000 29.01100000 45 | 16 6 1 -1.1128 1.33100001 1.38599999 34.30600001 46 | 17 6 2 0.5564 2.39200001 2.89799999 34.84600000 47 | 18 6 2 0.5564 0.81400000 0.53200001 35.83600000 48 | 19 7 1 -1.1128 31.45100000 10.20100000 0.72599999 49 | 20 7 2 0.5564 32.28199999 10.87699999 -0.75000000 50 | 21 7 2 0.5564 30.91999999 11.59399999 1.67700000 51 | 22 8 1 -1.1128 0.83600000 10.80800001 4.29800000 52 | 23 8 2 0.5564 0.30500000 10.64300001 2.79300000 53 | 24 8 2 0.5564 -0.35600001 10.33400000 5.52400000 54 | 25 9 1 -1.1128 34.38100001 5.97900000 9.19400000 55 | 26 9 2 0.5564 33.61600000 7.67300000 8.85700000 56 | 27 9 2 0.5564 35.11500000 5.25999999 7.61800001 57 | 28 10 1 -1.1128 33.21200000 6.48000000 24.27799999 58 | 29 10 2 0.5564 31.62400000 6.90800001 23.52100001 59 | 30 10 2 0.5564 32.54400000 4.99000000 24.98200000 60 | 31 11 1 -1.1128 1.99200000 9.00199999 26.86300000 61 | 32 11 2 0.5564 1.85600000 10.17500000 25.57899999 62 | 33 11 2 0.5564 0.51900000 8.09899999 26.38599999 63 | 34 12 1 -1.1128 2.05400000 8.66000000 32.51499999 64 | 35 12 2 0.5564 2.16699999 8.72700000 30.49400000 65 | 36 12 2 0.5564 2.37400001 10.51300000 33.03799999 66 | 37 13 1 -1.1128 3.40200000 16.63900001 3.00800000 67 | 38 13 2 0.5564 4.12700001 15.87200001 4.44600001 68 | 39 13 2 0.5564 2.90500001 18.33899999 3.15999999 69 | 40 14 1 -1.1128 4.22200000 15.44400000 8.07200000 70 | 41 14 2 0.5564 5.21100000 16.75600000 8.29900001 71 | 42 14 2 0.5564 2.56000000 15.49200001 8.86000000 72 | 43 15 1 -1.1128 2.83100000 9.24599999 16.48800000 73 | 44 15 2 0.5564 2.86900001 8.02300001 18.05000000 74 | 45 15 2 0.5564 3.96000000 8.46700001 15.15400000 75 | 46 16 1 -1.1128 5.56300000 6.00300000 20.90700000 76 | 47 16 2 0.5564 4.65300000 4.63800000 21.48000000 77 | 48 16 2 0.5564 6.40500000 6.20800000 22.52899999 78 | 49 17 1 -1.1128 2.08700001 13.37000000 22.91299999 79 | 50 17 2 0.5564 2.83200000 14.80400001 23.42200000 80 | 51 17 2 0.5564 1.43400000 13.50900000 21.19599999 81 | 52 18 1 -1.1128 3.36900000 17.88600000 25.10900001 82 | 53 18 2 0.5564 3.65500000 17.20000000 26.76599999 83 | 54 18 2 0.5564 4.77200001 18.97699999 24.49999999 84 | 55 19 1 -1.1128 34.76400000 20.80300000 0.94800001 85 | 56 19 2 0.5564 35.20999999 21.26700001 2.81599999 86 | 57 19 2 0.5564 35.96200001 21.72599999 0.13099999 87 | 58 20 1 -1.1128 2.83600000 24.17799999 15.22900000 88 | 59 20 2 0.5564 2.79500000 22.34599999 14.87600001 89 | 60 20 2 0.5564 2.41399999 24.11500000 17.13000001 90 | 61 21 1 -1.1128 33.00000000 24.48100000 15.23000000 91 | 62 21 2 0.5564 34.63999999 24.80400001 15.01299999 92 | 63 21 2 0.5564 32.40100000 25.76400000 14.29500001 93 | 64 22 1 -1.1128 0.40399999 26.77900001 23.39999999 94 | 65 22 2 0.5564 1.35300001 27.24800000 24.98700001 95 | 66 22 2 0.5564 1.54600001 28.05000000 22.31700001 96 | 67 23 1 -1.1128 34.22200000 21.38000000 25.41799999 97 | 68 23 2 0.5564 35.66899999 20.15100000 25.31700001 98 | 69 23 2 0.5564 32.96000000 21.18000000 23.99200000 99 | 70 24 1 -1.1128 33.25900000 17.43800000 32.48000000 100 | 71 24 2 0.5564 33.31399999 18.78200000 33.88300001 101 | 72 24 2 0.5564 32.74300001 18.18100001 30.87100000 102 | 73 25 1 -1.1128 4.46300000 21.97900000 3.93600000 103 | 74 25 2 0.5564 5.85600000 23.08400001 3.39999999 104 | 75 25 2 0.5564 3.98600000 22.18000000 5.60200000 105 | 76 26 1 -1.1128 6.25800000 25.85100001 8.52000000 106 | 77 26 2 0.5564 5.76700000 27.69300001 8.47600000 107 | 78 26 2 0.5564 7.20200001 25.50600000 10.18600000 108 | 79 27 1 -1.1128 0.60099999 29.73699999 12.74700001 109 | 80 27 2 0.5564 -0.68500000 30.84200000 12.34999999 110 | 81 27 2 0.5564 1.33600000 30.71600000 14.03099999 111 | 82 28 1 -1.1128 7.56300000 28.19100001 24.33300000 112 | 83 28 2 0.5564 9.20100000 28.82800000 24.68400000 113 | 84 28 2 0.5564 7.38100001 27.62100000 22.79900000 114 | 85 29 1 -1.1128 3.65300000 27.10900001 27.77200001 115 | 86 29 2 0.5564 5.12600000 27.01500000 26.77200001 116 | 87 29 2 0.5564 3.03099999 28.75600000 27.69800000 117 | 88 30 1 -1.1128 2.59600001 23.99100001 32.47600000 118 | 89 30 2 0.5564 2.87900000 24.79099999 30.85899999 119 | 90 30 2 0.5564 4.00300000 22.91299999 32.70099999 120 | 91 31 1 -1.1128 3.08300000 31.31700001 3.64399999 121 | 92 31 2 0.5564 4.13300000 30.58900001 2.53900001 122 | 93 31 2 0.5564 4.21800000 32.17300001 5.03700001 123 | 94 32 1 -1.1128 4.66100001 30.55500000 9.36799999 124 | 95 32 2 0.5564 3.18400001 29.84300000 10.13200000 125 | 96 32 2 0.5564 4.35800000 32.44800000 9.12600000 126 | 127 | Bonds 128 | 129 | 1 1 1 2 130 | 2 1 1 3 131 | 3 1 4 5 132 | 4 1 4 6 133 | 5 1 7 8 134 | 6 1 7 9 135 | 7 1 10 11 136 | 8 1 10 12 137 | 9 1 13 14 138 | 10 1 13 15 139 | 11 1 16 17 140 | 12 1 16 18 141 | 13 1 19 20 142 | 14 1 19 21 143 | 15 1 22 23 144 | 16 1 22 24 145 | 17 1 25 26 146 | 18 1 25 27 147 | 19 1 28 29 148 | 20 1 28 30 149 | 21 1 31 32 150 | 22 1 31 33 151 | 23 1 34 35 152 | 24 1 34 36 153 | 25 1 37 38 154 | 26 1 37 39 155 | 27 1 40 41 156 | 28 1 40 42 157 | 29 1 43 44 158 | 30 1 43 45 159 | 31 1 46 47 160 | 32 1 46 48 161 | 33 1 49 50 162 | 34 1 49 51 163 | 35 1 52 53 164 | 36 1 52 54 165 | 37 1 55 56 166 | 38 1 55 57 167 | 39 1 58 59 168 | 40 1 58 60 169 | 41 1 61 62 170 | 42 1 61 63 171 | 43 1 64 65 172 | 44 1 64 66 173 | 45 1 67 68 174 | 46 1 67 69 175 | 47 1 70 71 176 | 48 1 70 72 177 | 49 1 73 74 178 | 50 1 73 75 179 | 51 1 76 77 180 | 52 1 76 78 181 | 53 1 79 80 182 | 54 1 79 81 183 | 55 1 82 83 184 | 56 1 82 84 185 | 57 1 85 86 186 | 58 1 85 87 187 | 59 1 88 89 188 | 60 1 88 90 189 | 61 1 91 92 190 | 62 1 91 93 191 | 63 1 94 95 192 | 64 1 94 96 193 | 194 | Angles 195 | 196 | 1 1 2 1 3 197 | 2 1 5 4 6 198 | 3 1 8 7 9 199 | 4 1 11 10 12 200 | 5 1 14 13 15 201 | 6 1 17 16 18 202 | 7 1 20 19 21 203 | 8 1 23 22 24 204 | 9 1 26 25 27 205 | 10 1 29 28 30 206 | 11 1 32 31 33 207 | 12 1 35 34 36 208 | 13 1 38 37 39 209 | 14 1 41 40 42 210 | 15 1 44 43 45 211 | 16 1 47 46 48 212 | 17 1 50 49 51 213 | 18 1 53 52 54 214 | 19 1 56 55 57 215 | 20 1 59 58 60 216 | 21 1 62 61 63 217 | 22 1 65 64 66 218 | 23 1 68 67 69 219 | 24 1 71 70 72 220 | 25 1 74 73 75 221 | 26 1 77 76 78 222 | 27 1 80 79 81 223 | 28 1 83 82 84 224 | 29 1 86 85 87 225 | 30 1 89 88 90 226 | 31 1 92 91 93 227 | 32 1 95 94 96 228 | -------------------------------------------------------------------------------- /tutorial-4/solutions/input/reactant/phonons/min.xc.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 0 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 3 | H 1.63089e+00 1.36267e+00 1.15180e+00 4 | C 8.44945e-01 7.89704e-01 6.62032e-01 5 | H 1.29316e+00 6.34755e-02 -1.44336e-02 6 | H 2.02556e-01 1.46367e+00 9.72761e-02 7 | H 2.53301e-01 2.69000e-01 1.41347e+00 8 | H 5.82909e+00 2.17935e+00 1.85263e+00 9 | 6 10 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 1 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 11 | H 1.63089e+00 1.36267e+00 1.15180e+00 12 | C 8.44945e-01 7.89704e-01 6.62032e-01 13 | H 1.29316e+00 6.34755e-02 -1.44336e-02 14 | H 2.02556e-01 1.46367e+00 9.72761e-02 15 | H 2.53301e-01 2.69000e-01 1.41347e+00 16 | H 5.82909e+00 2.17935e+00 1.85263e+00 17 | 6 18 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 2 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 19 | H 1.63089e+00 1.36267e+00 1.15180e+00 20 | C 8.44945e-01 7.89704e-01 6.62032e-01 21 | H 1.29316e+00 6.34755e-02 -1.44336e-02 22 | H 2.02556e-01 1.46367e+00 9.72761e-02 23 | H 2.53301e-01 2.69000e-01 1.41347e+00 24 | H 5.82909e+00 2.17935e+00 1.85263e+00 25 | 6 26 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 3 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 27 | H 1.63089e+00 1.36267e+00 1.15180e+00 28 | C 8.44945e-01 7.89704e-01 6.62032e-01 29 | H 1.29316e+00 6.34755e-02 -1.44336e-02 30 | H 2.02556e-01 1.46367e+00 9.72761e-02 31 | H 2.53301e-01 2.69000e-01 1.41347e+00 32 | H 5.82909e+00 2.17935e+00 1.85263e+00 33 | 6 34 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 4 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 35 | H 1.63089e+00 1.36267e+00 1.15180e+00 36 | C 8.44945e-01 7.89704e-01 6.62032e-01 37 | H 1.29316e+00 6.34755e-02 -1.44336e-02 38 | H 2.02556e-01 1.46367e+00 9.72761e-02 39 | H 2.53301e-01 2.69000e-01 1.41347e+00 40 | H 5.82909e+00 2.17935e+00 1.85263e+00 41 | 6 42 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 5 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 43 | H 1.63089e+00 1.36267e+00 1.15180e+00 44 | C 8.44945e-01 7.89704e-01 6.62032e-01 45 | H 1.29316e+00 6.34755e-02 -1.44336e-02 46 | H 2.02556e-01 1.46367e+00 9.72761e-02 47 | H 2.53301e-01 2.69000e-01 1.41347e+00 48 | H 5.82909e+00 2.17935e+00 1.85263e+00 49 | 6 50 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 6 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 51 | H 1.63089e+00 1.36267e+00 1.15180e+00 52 | C 8.44945e-01 7.89704e-01 6.62032e-01 53 | H 1.29316e+00 6.34755e-02 -1.44336e-02 54 | H 2.02556e-01 1.46367e+00 9.72761e-02 55 | H 2.53301e-01 2.69000e-01 1.41347e+00 56 | H 5.82909e+00 2.17935e+00 1.85263e+00 57 | 6 58 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 7 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 59 | H 1.63089e+00 1.36267e+00 1.15180e+00 60 | C 8.44945e-01 7.89704e-01 6.62032e-01 61 | H 1.29316e+00 6.34755e-02 -1.44336e-02 62 | H 2.02556e-01 1.46367e+00 9.72761e-02 63 | H 2.53301e-01 2.69000e-01 1.41347e+00 64 | H 5.82909e+00 2.17935e+00 1.85263e+00 65 | 6 66 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 8 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 67 | H 1.63089e+00 1.36267e+00 1.15180e+00 68 | C 8.44945e-01 7.89704e-01 6.62032e-01 69 | H 1.29316e+00 6.34755e-02 -1.44336e-02 70 | H 2.02556e-01 1.46367e+00 9.72761e-02 71 | H 2.53301e-01 2.69000e-01 1.41347e+00 72 | H 5.82909e+00 2.17935e+00 1.85263e+00 73 | 6 74 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 9 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 75 | H 1.63089e+00 1.36267e+00 1.15180e+00 76 | C 8.44945e-01 7.89704e-01 6.62032e-01 77 | H 1.29316e+00 6.34755e-02 -1.44336e-02 78 | H 2.02556e-01 1.46367e+00 9.72761e-02 79 | H 2.53301e-01 2.69000e-01 1.41347e+00 80 | H 5.82909e+00 2.17935e+00 1.85263e+00 81 | 6 82 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 10 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 83 | H 1.63089e+00 1.36267e+00 1.15180e+00 84 | C 8.44945e-01 7.89704e-01 6.62032e-01 85 | H 1.29316e+00 6.34755e-02 -1.44336e-02 86 | H 2.02556e-01 1.46367e+00 9.72761e-02 87 | H 2.53301e-01 2.69000e-01 1.41347e+00 88 | H 5.82909e+00 2.17935e+00 1.85263e+00 89 | 6 90 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 11 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 91 | H 1.63089e+00 1.36267e+00 1.15180e+00 92 | C 8.44945e-01 7.89704e-01 6.62032e-01 93 | H 1.29316e+00 6.34755e-02 -1.44336e-02 94 | H 2.02556e-01 1.46367e+00 9.72761e-02 95 | H 2.53301e-01 2.69000e-01 1.41347e+00 96 | H 5.82909e+00 2.17935e+00 1.85263e+00 97 | 6 98 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 12 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 99 | H 1.63089e+00 1.36267e+00 1.15180e+00 100 | C 8.44945e-01 7.89704e-01 6.62032e-01 101 | H 1.29316e+00 6.34755e-02 -1.44336e-02 102 | H 2.02556e-01 1.46367e+00 9.72761e-02 103 | H 2.53301e-01 2.69000e-01 1.41347e+00 104 | H 5.82909e+00 2.17935e+00 1.85263e+00 105 | 6 106 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 13 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 107 | H 1.63089e+00 1.36267e+00 1.15180e+00 108 | C 8.44945e-01 7.89704e-01 6.62032e-01 109 | H 1.29316e+00 6.34755e-02 -1.44336e-02 110 | H 2.02556e-01 1.46367e+00 9.72761e-02 111 | H 2.53301e-01 2.69000e-01 1.41347e+00 112 | H 5.82909e+00 2.17935e+00 1.85263e+00 113 | 6 114 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 14 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 115 | H 1.63089e+00 1.36267e+00 1.15180e+00 116 | C 8.44945e-01 7.89704e-01 6.62032e-01 117 | H 1.29316e+00 6.34755e-02 -1.44336e-02 118 | H 2.02556e-01 1.46367e+00 9.72761e-02 119 | H 2.53301e-01 2.69000e-01 1.41347e+00 120 | H 5.82909e+00 2.17935e+00 1.85263e+00 121 | 6 122 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 15 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 123 | H 1.63089e+00 1.36267e+00 1.15180e+00 124 | C 8.44945e-01 7.89704e-01 6.62032e-01 125 | H 1.29316e+00 6.34755e-02 -1.44336e-02 126 | H 2.02556e-01 1.46367e+00 9.72761e-02 127 | H 2.53301e-01 2.69000e-01 1.41347e+00 128 | H 5.82909e+00 2.17935e+00 1.85263e+00 129 | 6 130 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 16 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 131 | H 1.63089e+00 1.36267e+00 1.15180e+00 132 | C 8.44945e-01 7.89704e-01 6.62032e-01 133 | H 1.29316e+00 6.34755e-02 -1.44336e-02 134 | H 2.02556e-01 1.46367e+00 9.72761e-02 135 | H 2.53301e-01 2.69000e-01 1.41347e+00 136 | H 5.82909e+00 2.17935e+00 1.85263e+00 137 | 6 138 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 17 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 139 | H 1.63089e+00 1.36267e+00 1.15180e+00 140 | C 8.44945e-01 7.89704e-01 6.62032e-01 141 | H 1.29316e+00 6.34755e-02 -1.44336e-02 142 | H 2.02556e-01 1.46367e+00 9.72761e-02 143 | H 2.53301e-01 2.69000e-01 1.41347e+00 144 | H 5.82909e+00 2.17935e+00 1.85263e+00 145 | 6 146 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 18 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 147 | H 1.63089e+00 1.36267e+00 1.15180e+00 148 | C 8.44945e-01 7.89704e-01 6.62032e-01 149 | H 1.29316e+00 6.34755e-02 -1.44336e-02 150 | H 2.02556e-01 1.46367e+00 9.72761e-02 151 | H 2.53301e-01 2.69000e-01 1.41347e+00 152 | H 5.82909e+00 2.17935e+00 1.85263e+00 153 | --------------------------------------------------------------------------------