├── exercises ├── day-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-2 │ │ └── precomputed-imvacf │ │ └── conv.imvacf ├── day-1 │ ├── ex-3 │ │ ├── n.01 │ │ │ ├── boxfile │ │ │ ├── in.lmp │ │ │ ├── data.lmp │ │ │ └── input.xml │ │ ├── n.02 │ │ │ ├── boxfile │ │ │ ├── in.lmp │ │ │ ├── data.lmp │ │ │ └── input.xml │ │ ├── n.04 │ │ │ ├── boxfile │ │ │ ├── in.lmp │ │ │ ├── data.lmp │ │ │ └── input.xml │ │ ├── n.08 │ │ │ ├── boxfile │ │ │ ├── in.lmp │ │ │ ├── data.lmp │ │ │ └── input.xml │ │ ├── n.16 │ │ │ ├── boxfile │ │ │ ├── in.lmp │ │ │ ├── data.lmp │ │ │ └── input.xml │ │ ├── n.32 │ │ │ ├── boxfile │ │ │ ├── in.lmp │ │ │ ├── data.lmp │ │ │ └── input.xml │ │ ├── n.64 │ │ │ ├── boxfile │ │ │ ├── in.lmp │ │ │ ├── data.lmp │ │ │ └── input.xml │ │ ├── extract-gOH.bash │ │ ├── extract-kin.bash │ │ └── extract-pot.bash │ ├── ex-4 │ │ ├── n.001 │ │ │ ├── boxfile │ │ │ ├── input.xml │ │ │ └── in.cp2k │ │ └── n.128 │ │ │ ├── boxfile │ │ │ ├── input.xml │ │ │ └── in.cp2k │ ├── ex-2 │ │ ├── h2o.xyz │ │ ├── input.xml │ │ └── cp2k.in │ └── ex-1 │ │ ├── in.water │ │ ├── water-gas.pdb │ │ ├── data.water │ │ └── input.xml ├── day-2 │ ├── day-2.pdf │ ├── ex-4 │ │ ├── in.ice_short │ │ ├── in.ice_long │ │ ├── in.ice │ │ ├── highorder.xml │ │ └── ultimate.xml │ ├── README.md │ ├── 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 └── instanton │ ├── solutions │ ├── TS │ │ ├── INSTANTON_FINAL_12.ener │ │ ├── init.xyz │ │ ├── INSTANTON_FINAL_12.xyz │ │ ├── inst.out │ │ ├── data.out │ │ ├── input.xml │ │ ├── inst.pos_0.xyz │ │ └── INSTANTON_FINAL.hess_12 │ ├── instanton │ │ ├── 40 │ │ │ ├── init.xyz │ │ │ ├── inst.out │ │ │ ├── INSTANTON_0.ener │ │ │ ├── INSTANTON_FINAL_7.ener │ │ │ ├── input.xml │ │ │ └── hessian.dat │ │ └── 80 │ │ │ ├── inst.out │ │ │ ├── data.out │ │ │ ├── input.xml │ │ │ ├── INSTANTON_0.ener │ │ │ ├── INSTANTON_FINAL_2.ener │ │ │ └── log.ipi │ └── reactant │ │ ├── phonons │ │ ├── freq.dat │ │ ├── init.xyz │ │ ├── phonons.eigval │ │ ├── min.out │ │ ├── input.xml │ │ ├── data.out │ │ ├── log.ipi │ │ ├── phonons.eigvec │ │ ├── phonons.mode │ │ ├── phonons.hess │ │ └── phonons.dynmat │ │ └── minization │ │ ├── init.xyz │ │ ├── input.xml │ │ ├── min.out │ │ └── RESTART │ ├── input │ ├── reactant │ │ ├── minization │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ └── phonons │ │ │ └── input.xml │ ├── TS │ │ ├── init.xyz │ │ └── input.xml │ └── instanton │ │ └── 40 │ │ └── input.xml │ └── README.txt ├── handouts ├── ice.png ├── ice.tga ├── gle4md.pdf ├── ipi-logo.pdf ├── mdchart.pdf ├── ipi-scheme.pdf ├── Makefile └── style.tex ├── reset.sh └── README.md /exercises/day-3/ex-1/precomputed-trajectories/cmd/.vv: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /exercises/day-3/ex-1/precomputed-trajectories/cmd/.dpl: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.01/boxfile: -------------------------------------------------------------------------------- 1 | 18.64450 0 0 0 18.64450 0 0 0 18.64450 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.02/boxfile: -------------------------------------------------------------------------------- 1 | 18.64450 0 0 0 18.64450 0 0 0 18.64450 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.04/boxfile: -------------------------------------------------------------------------------- 1 | 18.64450 0 0 0 18.64450 0 0 0 18.64450 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.08/boxfile: -------------------------------------------------------------------------------- 1 | 18.64450 0 0 0 18.64450 0 0 0 18.64450 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.16/boxfile: -------------------------------------------------------------------------------- 1 | 18.64450 0 0 0 18.64450 0 0 0 18.64450 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.32/boxfile: -------------------------------------------------------------------------------- 1 | 18.64450 0 0 0 18.64450 0 0 0 18.64450 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.64/boxfile: -------------------------------------------------------------------------------- 1 | 18.64450 0 0 0 18.64450 0 0 0 18.64450 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-4/n.001/boxfile: -------------------------------------------------------------------------------- 1 | 25.00000 0 0 0 25.00000 0 0 0 25.00000 2 | -------------------------------------------------------------------------------- /exercises/day-1/ex-4/n.128/boxfile: -------------------------------------------------------------------------------- 1 | 25.00000 0 0 0 25.00000 0 0 0 25.00000 2 | -------------------------------------------------------------------------------- /exercises/day-3/tools/charges.tip4pf: -------------------------------------------------------------------------------- 1 | O 0.0000 2 | M -1.1128 3 | H 0.5564 4 | -------------------------------------------------------------------------------- /handouts/ice.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/pimd-tutorial/HEAD/handouts/ice.png -------------------------------------------------------------------------------- /handouts/ice.tga: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/pimd-tutorial/HEAD/handouts/ice.tga -------------------------------------------------------------------------------- /handouts/gle4md.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/pimd-tutorial/HEAD/handouts/gle4md.pdf -------------------------------------------------------------------------------- /handouts/ipi-logo.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/pimd-tutorial/HEAD/handouts/ipi-logo.pdf -------------------------------------------------------------------------------- /handouts/mdchart.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/pimd-tutorial/HEAD/handouts/mdchart.pdf -------------------------------------------------------------------------------- /handouts/ipi-scheme.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/pimd-tutorial/HEAD/handouts/ipi-scheme.pdf -------------------------------------------------------------------------------- /exercises/day-2/day-2.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/pimd-tutorial/HEAD/exercises/day-2/day-2.pdf -------------------------------------------------------------------------------- /exercises/instanton/solutions/TS/INSTANTON_FINAL_12.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.6505828184784609 3 | -------------------------------------------------------------------------------- /reset.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | git clean -dxn 4 | 5 | echo "WARNING. This command will reset the tutorial to pristine state." 6 | echo "Press CTRL+C to abort" 7 | read 8 | 9 | git clean -dfx 10 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 6.18877042e-01 4 | 1.00000000e+00 6.18887885e-01 5 | 2.00000000e+00 6.18902370e-01 6 | 3.00000000e+00 6.18907542e-01 7 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/extract-gOH.bash: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | for x in $(ls -p | grep "/" ) 4 | do 5 | #Moves to a sub directory. 6 | cd $x 7 | #Extracts number of beads from the directory. 8 | nP=$(echo $x| cut -d . -f 2| cut -d / -f 1) 9 | #Calculates gOH. 10 | cat *pos* | trajworks -box boxfile -gr -gr1 O -gr2 H -grmax 2 -hwin gauss-2 -hwinfac 5 > gOH.data 11 | cd .. 12 | done 13 | 14 | -------------------------------------------------------------------------------- /exercises/day-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 | Follow the exercise sheet (day-2.pdf) and the annotations in the input 7 | files. 8 | 9 | -------------------------------------------------------------------------------- /handouts/Makefile: -------------------------------------------------------------------------------- 1 | .PHONY: all clean 2 | 3 | all: day-1.pdf day-2.pdf day-3.pdf instanton.pdf 4 | cp day-?.pdf instanton.pdf ../ 5 | 6 | clean: 7 | rm -f *.aux *.bbl *.log *.blg 8 | 9 | %.aux : %.tex 10 | pdflatex $* 11 | 12 | %.pdf : %.tex %.bbl 13 | while (pdflatex $* ; \ 14 | grep -q "Rerun to get cross" $*.log ) do true ; \ 15 | done 16 | 17 | %.bbl : %.aux biblio.bib 18 | bibtex $* 19 | 20 | 21 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/freq.dat: -------------------------------------------------------------------------------- 1 | 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 0.000000000000000000e+00 3.976167735125746126e-05 3.976685483735975090e-05 3.976807506060556100e-05 4.995107938561502836e-05 4.995721228684269605e-05 1.860896515061276520e-04 2.081378061816762965e-04 2.081473425079697378e-04 2.081748356983191290e-04 2 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/extract-kin.bash: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | mlag=${1:-10} 4 | echo "#nbeads avg error" $mlag 5 | for x in $(ls -p | grep "/" ) 6 | do 7 | #Moves to a sub directory. 8 | cd $x 9 | #Extracts number of beads from the directory. 10 | nP=$(echo $x| cut -d . -f 2| cut -d / -f 1) 11 | #Calculates thekinetic energy energy. 12 | grep -v "#" *out| awk '{print $4+$5}'| autocorr -maxlag $mlag | head | awk -v P=$nP '/mean:/ {printf "%5d %15e %15e\n",P,$3,$5}' | sed -e "s/nan/0./g" 13 | cd .. 14 | done 15 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/extract-pot.bash: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | mlag=${1:-10} 4 | echo "#nbeads avg error" 5 | for x in $(ls -p | grep "/" ) 6 | do 7 | #Moves to a sub directory. 8 | cd $x 9 | #Extracts number of beads from the directory. 10 | nP=$(echo $x| cut -d . -f 2| cut -d / -f 1) 11 | #Calculates the potential energy. 12 | grep -v "#" *out| awk '{print $6}'| autocorr -maxlag $mlag | head | awk -v P=$nP '/mean:/ {printf "%5d %15e %15e\n",P,$3,$5}' | sed -e "s/nan/0./g" 13 | cd .. 14 | done 15 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 31 Bead: 0 x_centroid{angstrom} cell{atomic_unit} 3 | H 1.63090e+00 1.36266e+00 1.15180e+00 4 | C 8.44971e-01 7.89691e-01 6.62016e-01 5 | H 1.29316e+00 6.34936e-02 -1.44182e-02 6 | H 2.02546e-01 1.46367e+00 9.72790e-02 7 | H 2.53290e-01 2.69002e-01 1.41347e+00 8 | H 5.82907e+00 2.17934e+00 1.85263e+00 9 | -------------------------------------------------------------------------------- /exercises/instanton/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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 1.3384253229396237 1.6274017116655604 1.3889068177030293 4 | C 0.5982853194799348 0.737062005542996 0.6191260184553369 5 | H 0.018252994259674735 0.12724588160295913 1.311973074412382 6 | H 1.3129952944388439 0.14128880830488075 0.05114876404928569 7 | H -0.04034313383127954 1.3363247554566795 -0.03001935020008532 8 | H 1.8032591270731935 2.186266972917346 1.8719610621764697 9 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 1.3384253229396237 1.6274017116655604 1.3889068177030293 4 | C 0.5982853194799348 0.737062005542996 0.6191260184553369 5 | H 0.018252994259674735 0.12724588160295913 1.311973074412382 6 | H 1.3129952944388439 0.14128880830488075 0.05114876404928569 7 | H -0.04034313383127954 1.3363247554566795 -0.03001935020008532 8 | H 1.8032591270731935 2.186266972917346 1.8719610621764697 9 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/phonons.eigval: -------------------------------------------------------------------------------- 1 | # Eigenvalues (atomic units) 2 | -6.592874279288675e-09 3 | -4.230077452055857e-09 4 | -2.170997547004094e-09 5 | -1.2694904761422985e-09 6 | -1.251366658615728e-09 7 | 8.558023143177855e-15 8 | 6.255922169242788e-13 9 | 9.157513718745075e-13 10 | 1.09174724746681e-08 11 | 3.9761677379798636e-05 12 | 3.976685511127151e-05 13 | 3.976807527646292e-05 14 | 4.9951079543502376e-05 15 | 4.9957212345418074e-05 16 | 0.00018608965154706108 17 | 0.00020813780614246068 18 | 0.00020814734260215647 19 | 0.0002081748357416115 20 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 6.29204771e-01 5 | 2.00000000e+00 6.27791669e-01 6 | 3.00000000e+00 6.15349547e-01 7 | 4.00000000e+00 6.19161967e-01 8 | 5.00000000e+00 6.18799929e-01 9 | 6.00000000e+00 6.18982866e-01 10 | 7.00000000e+00 6.18881630e-01 11 | 8.00000000e+00 6.18877053e-01 12 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | Support files for a PIMD Tutorial 2 | ================================= 3 | 4 | This repository contains support files as well as the LaTeX sources 5 | for the exercise sheets for a series of three tutorials explaining 6 | how to compute static and dynamical quantum properties of matter 7 | by performing path integral simulations using atomistic models. 8 | 9 | The examples are meant to be run with a development version of i-PI 10 | and use some utilities that are available as part of the toolbox 11 | package. See http://cosmo.epfl.ch for more details of the softare 12 | needed to perform these tutorials. 13 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.02/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.02 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.04/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.04 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.08/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.08 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.16/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.16 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.32/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.32 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.64/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.64 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/TS/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 1.41494114e+00 4 | 1.00000000e+00 1.32894287e+00 5 | 2.00000000e+00 8.41733630e-01 6 | 3.00000000e+00 6.39981511e-01 7 | 4.00000000e+00 6.59012712e-01 8 | 5.00000000e+00 6.52906541e-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.02/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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.04/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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.08/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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.16/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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.32/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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.64/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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 1.95280225e-04 4 | 1.00000000e+00 1.95280225e-04 5 | 2.00000000e+00 1.95280225e-04 6 | 3.00000000e+00 1.95280225e-04 7 | 4.00000000e+00 1.95280225e-04 8 | 5.00000000e+00 1.95280225e-04 9 | 6.00000000e+00 1.95280225e-04 10 | 7.00000000e+00 1.95280225e-04 11 | 8.00000000e+00 1.95280225e-04 12 | 9.00000000e+00 1.95280225e-04 13 | 1.00000000e+01 1.95280225e-04 14 | 1.10000000e+01 1.95280225e-04 15 | 1.20000000e+01 1.95280225e-04 16 | 1.30000000e+01 1.95280225e-04 17 | 1.40000000e+01 1.95280225e-04 18 | 1.50000000e+01 1.95280225e-04 19 | 1.60000000e+01 1.95280225e-04 20 | 1.70000000e+01 1.95280225e-04 21 | 1.80000000e+01 1.95280225e-04 22 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/data.out: -------------------------------------------------------------------------------- 1 | 2 | We are ready to start 3 | Reading RESTART ... 4 | (This can take a while) 5 | fetching ffsocket 6 | # Initializing system object 7 | # Initializing simulation object 8 | # i-PI loaded input file: RESTART 9 | We have 5 atoms. 10 | We are using asr = poly 11 | 12 | Diagonalization.... 13 | Final lowest 15 frequencies (cm^-1) 14 | [ 1382.980759 1383.070797 1383.092017 1550.08755 1550.182706 15 | 2991.885031 3164.166119 3164.238605 3164.447573] 16 | 17 | We are done 18 | Nbeads 160 19 | 20 | Qtras: 9.298069 bohr^-3 21 | Qrot: 438.760518 22 | logQvib_rp: -47.336993 23 | A file with the frequencies in atomic units was generated 24 | 25 | 26 | Remember that the output obtained from this script simply gives you components that you can use in order to calculate a rate or a tunneling splitting in the instanton approximation. 27 | Use, for example, the references below in order to obtain final desired results. 28 | Instanton Rate: J. Phys. Chem. Lett. 7, 4374(2016) 29 | Tunneling Splitting: J. Chem. Phys. 134, 054109 (2011) 30 | 31 | 32 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 | -------------------------------------------------------------------------------- /exercises/instanton/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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/TS/data.out: -------------------------------------------------------------------------------- 1 | 2 | We are ready to start 3 | Reading RESTART ... 4 | (This can take a while) 5 | fetching ffsocket 6 | # Initializing system object 7 | # Initializing simulation object 8 | # i-PI loaded input file: RESTART 9 | We have 6 atoms. 10 | We are using asr = poly 11 | 12 | Diagonalization.... 13 | Final lowest 15 frequencies (cm^-1) 14 | [-1486.883818 541.881086 541.885608 1084.081704 1084.123658 15 | 1182.141391 1441.553057 1441.559025 1831.153161 3034.03602 16 | 3170.518629 3170.536208] 17 | Note: Deleted frequency for computing Qvib -1486.883818 cm^-1 18 | 19 | We are done 20 | Partition functions at 300.000000 K 21 | 22 | Qtras: 10.187982 bohr^-3 23 | Qrot: 1206.150975 24 | logQvib: -44.278404 25 | Potential energy at TS: 0.650583 eV, V/kBT 25.165639 26 | 27 | 28 | 29 | Remember that the output obtained from this script simply gives you components that you can use in order to calculate a rate or a tunneling splitting in the instanton approximation. 30 | Use, for example, the references below in order to obtain final desired results. 31 | Instanton Rate: J. Phys. Chem. Lett. 7, 4374(2016) 32 | Tunneling Splitting: J. Chem. Phys. 134, 054109 (2011) 33 | 34 | 35 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/instanton/40/INSTANTON_0.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.6444480598878105 3 | 1 0.6444807214359295 4 | 2 0.6445783816508036 5 | 3 0.6447400236339479 6 | 4 0.6449638136010644 7 | 5 0.6452469141761308 8 | 6 0.6455852639328461 9 | 7 0.6459733585079044 10 | 8 0.6464040713715444 11 | 9 0.6468685507121861 12 | 10 0.6473562229919009 13 | 11 0.6478549241495043 14 | 12 0.6483511671764202 15 | 13 0.6488305411821408 16 | 14 0.6492782235801919 17 | 15 0.6496795751328737 18 | 16 0.6500207785847085 19 | 17 0.6502894764461419 20 | 18 0.6504753626659789 21 | 19 0.6505706864544324 22 | 20 0.6505706338909607 23 | 21 0.6504735632587497 24 | 22 0.65028108208796 25 | 23 0.6499979663378482 26 | 24 0.6496319337269637 27 | 25 0.6491932928558887 28 | 26 0.6486944966944868 29 | 27 0.648149632831316 30 | 28 0.6475738835861183 31 | 29 0.6469829869712992 32 | 30 0.6463927251073185 33 | 31 0.645818460754084 34 | 32 0.6452747358722476 35 | 33 0.6447749393025503 36 | 34 0.6443310443791933 37 | 35 0.6439534120684866 38 | 36 0.6436506513823975 39 | 37 0.6434295265318153 40 | 38 0.6432948995803468 41 | 39 0.6432496981282528 42 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/instanton/40/INSTANTON_FINAL_7.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.5909187364413652 3 | 1 0.5925117082160818 4 | 2 0.5956257675656544 5 | 3 0.600117170887837 6 | 4 0.6057714202942139 7 | 5 0.6123073361175614 8 | 6 0.6193863477946148 9 | 7 0.6266289065414814 10 | 8 0.633638709290126 11 | 9 0.6400334223238303 12 | 10 0.6454782495111298 13 | 11 0.6497168045027464 14 | 12 0.6525932201246115 15 | 13 0.6540608031384583 16 | 14 0.6541755875153339 17 | 15 0.6530768168467143 18 | 16 0.6509593222246323 19 | 17 0.6480439534185575 20 | 18 0.644551484633725 21 | 19 0.6406834451341912 22 | 20 0.6366109162450821 23 | 21 0.6324704505376302 24 | 22 0.6283652708185921 25 | 23 0.6243696393817983 26 | 24 0.6205345749520013 27 | 25 0.616893625692369 28 | 26 0.6134679486534116 29 | 27 0.6102703780341281 30 | 28 0.6073084518364846 31 | 29 0.6045865239587959 32 | 30 0.6021071512313592 33 | 31 0.5998719483156144 34 | 32 0.5978820767544553 35 | 33 0.5961384974775052 36 | 34 0.5946420800191555 37 | 35 0.5933936315693743 38 | 36 0.5923938861000464 39 | 37 0.5916434776600042 40 | 38 0.5911429112441983 41 | 39 0.5908925380326207 42 | -------------------------------------------------------------------------------- /exercises/instanton/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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.02/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.02
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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.16/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.16
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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.32/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.32
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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.64/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.64
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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.04/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.04
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 | -------------------------------------------------------------------------------- /exercises/day-1/ex-3/n.08/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.08
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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/instanton/80/data.out: -------------------------------------------------------------------------------- 1 | 2 | We are ready to start 3 | Reading RESTART ... 4 | (This can take a while) 5 | fetching ffsocket 6 | # Initializing system object 7 | # Initializing simulation object 8 | # i-PI loaded input file: RESTART 9 | The instanton mode is rate 10 | The temperature is 300.000000 K 11 | The full ring polymer is made of 160 12 | We used 80 beads in the calculation. 13 | We have 6 atoms. 14 | We are using asr = poly 15 | 16 | Diagonalization.... 17 | Final lowest 15 frequencies (cm^-1) 18 | [-1606.565553 7.375401 515.863701 515.863807 594.757567 19 | 1007.474394 1007.474476 1155.575156 1308.310322 1308.310353 20 | 1308.703468 1309.120808 1309.12081 1309.120815 1309.120815] 21 | 2.97453628786e+20 1.0 6.57863879564 160 22 | Note: Deleted frequency for computing Qvib 7.375401 cm^-1 23 | 24 | 25 | We are done 26 | Nbeads 160 27 | (diff only 80) 28 | 1/(betaP*hbar): 0.152007 a.u. 29 | BN 14.278827 30 | BN*N 2284.612301 31 | Qtras: 10.187982 bohr^-3 32 | Qrot: 1251.023751 33 | log(Qvib*N): -43.477383 34 | S1/hbar 23.940388 35 | S2/hbar 1.085242 36 | S/hbar 25.025629 37 | 38 | 39 | Remember that the output obtained from this script simply gives you components that you can use in order to calculate a rate or a tunneling splitting in the instanton approximation. 40 | Use, for example, the references below in order to obtain final desired results. 41 | Instanton Rate: J. Phys. Chem. Lett. 7, 4374(2016) 42 | Tunneling Splitting: J. Chem. Phys. 134, 054109 (2011) 43 | 44 | 45 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 3.40445043e-01 6 | 3.00000000e+00 8.57102039e-02 7 | 4.00000000e+00 3.98703611e-02 8 | 5.00000000e+00 2.09751318e-02 9 | 6.00000000e+00 1.23137329e-02 10 | 7.00000000e+00 7.26009103e-03 11 | 8.00000000e+00 4.39006282e-03 12 | 9.00000000e+00 2.68807087e-03 13 | 1.00000000e+01 1.69463915e-03 14 | 1.10000000e+01 1.10008642e-03 15 | 1.20000000e+01 7.46451146e-04 16 | 1.30000000e+01 5.32407696e-04 17 | 1.40000000e+01 4.03039569e-04 18 | 1.50000000e+01 3.23841128e-04 19 | 1.60000000e+01 2.75320048e-04 20 | 1.70000000e+01 2.45306942e-04 21 | 1.80000000e+01 2.26712309e-04 22 | 1.90000000e+01 2.15106447e-04 23 | 2.00000000e+01 2.07847665e-04 24 | 2.10000000e+01 2.03279911e-04 25 | 2.20000000e+01 2.00397835e-04 26 | 2.30000000e+01 1.98567834e-04 27 | 2.40000000e+01 1.97400794e-04 28 | 2.50000000e+01 1.96649717e-04 29 | 2.60000000e+01 1.96162198e-04 30 | 2.70000000e+01 1.95840387e-04 31 | 2.80000000e+01 1.95624258e-04 32 | 2.90000000e+01 1.95474358e-04 33 | 3.00000000e+01 1.95367039e-04 34 | 3.10000000e+01 1.95286082e-04 35 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/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 | 22 | [ 0,1,2,3,4,5 ] 23 | 24 | 25 | 26 | 10 27 | 28 | 5e-6 29 | 5e-6 30 | 1e-3 31 | 32 | 0.1 33 | nichols 34 | powell 35 | poly 36 | true 37 | 0.3 38 | hessian.dat 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/instanton/80/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 | 22 | [ 0,1,2,3,4,5 ] 23 | 24 | 25 | 26 | 10 27 | 28 | 5e-6 29 | 5e-6 30 | 1e-3 31 | 32 | 0.1 33 | nichols 34 | powell 35 | poly 36 | true 37 | 0.3 38 | hessian.dat 39 | 40 | 41 | 42 | 43 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/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 | -------------------------------------------------------------------------------- /handouts/style.tex: -------------------------------------------------------------------------------- 1 | \usepackage{exercise} 2 | \usepackage[obeyspaces]{url} 3 | \usepackage[dvipsnames]{xcolor} 4 | \usepackage{graphicx} 5 | \usepackage{listings} 6 | \usepackage[scaled]{helvet} 7 | \usepackage{amsmath,amssymb,amsfonts,mathtools,cancel} 8 | 9 | % typeset in helvetica 10 | \renewcommand*\familydefault{\sfdefault} 11 | 12 | \newcommand{\ipi}{i-PI} 13 | \newcommand{\hints}[1]{\emph{Hints: #1}} 14 | \newcommand{\lstinxml}{\lstinline[language=XML]} 15 | \newcommand{\lstinbash}{\lstinline[language=Bash]} 16 | \usepackage[space=true]{accsupp} 17 | 18 | \newcommand{\pdfactualhex}[3]{\newcommand{#1}{% 19 | \BeginAccSupp{method=hex,ActualText=#2}#3\EndAccSupp{}}} 20 | 21 | % PASTABLE lstlisting code 22 | \pdfactualhex{\pdfactualdspace}{2020}{\textperiodcentered\textperiodcentered} 23 | \pdfactualhex{\pdfactualsquote}{27}{'} 24 | \pdfactualhex{\pdfactualbtick}{60}{`} 25 | 26 | \lstset{tabsize=4,basicstyle=\ttfamily,breaklines=true,columns=flexible,emptylines=10000} 27 | \lstset{literate={'}{\pdfactualsquote}1 28 | {`}{\pdfactualbtick}1 29 | {\ \ }{\pdfactualdspace}2 30 | } 31 | 32 | \lstset{ 33 | basicstyle=\ttfamily, 34 | keywordstyle=\color{BrickRed}, 35 | commentstyle=\color{Gray}, 36 | stringstyle=\color{black}, 37 | emphstyle=\color{RedOrange}, 38 | columns=flexible, 39 | showstringspaces=false, 40 | xleftmargin=1em, 41 | deletekeywords={bin,all} 42 | } 43 | 44 | 45 | \lstdefinelanguage{Bash} 46 | { 47 | alsodigit={-,.}, 48 | morekeywords={ cp2k.popt, lmp_serial, i-pi, vmd, for, done, python, mpirun, touch, tail, trajworks, autocorr, awk, i-pi-mergebeadspdb, grep, head, cp, cd, cat, ls, pwd, bash, sed, mkdir, vi, sh} 49 | %morecomment=[s][\color{orange}]{#}{\} 50 | } 51 | 52 | %\lstdefinelanguage{Python} 53 | %{ 54 | % morecomment=[s][\color{orange}]{#}{\} 55 | %} 56 | 57 | 58 | \lstdefinelanguage{XML} 59 | { 60 | morestring=[b][\color{RedOrange}]", 61 | % morestring=[s]{>}{<}, 62 | morecomment=[s]{}, 63 | morecomment=[s][\color{orange}]{}, 64 | identifierstyle=\color{BlueViolet}, 65 | keywordstyle=\color{ForestGreen}, 66 | stringstyle=\color{RedOrange}, 67 | % tagstyle=\color{Blue}, 68 | morekeywords={xmlns,version,type, mode, units, forcefield, filename, stride, overwrite, nbeads,prefix}% list your attributes here 69 | } 70 | 71 | \lstdefinestyle{XML} 72 | { 73 | \tagstyle=\color{Blue} 74 | } 75 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/instanton/80/INSTANTON_0.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.590845384274853 3 | 1 0.591242878023949 4 | 2 0.5920465167631477 5 | 3 0.5932302733417801 6 | 4 0.5947927383832639 7 | 5 0.596704738198927 8 | 6 0.5989586953621399 9 | 7 0.6015089109314109 10 | 8 0.6043384221569917 11 | 9 0.6074094578317605 12 | 10 0.6106815993976776 13 | 11 0.6141189693158223 14 | 12 0.6176636532241883 15 | 13 0.6212698506485267 16 | 14 0.6248938352663804 17 | 15 0.6284811013087915 18 | 16 0.6319962756387749 19 | 17 0.6353671923221473 20 | 18 0.6385668876069553 21 | 19 0.6415447448042165 22 | 20 0.6442652841403074 23 | 21 0.6466996040283071 24 | 22 0.6488154413253805 25 | 23 0.6505982219654104 26 | 24 0.6520316800357104 27 | 25 0.6531107802908561 28 | 26 0.6538381213048159 29 | 27 0.6542208646576319 30 | 28 0.65427156295482 31 | 29 0.6540077160001745 32 | 30 0.6534495302404495 33 | 31 0.6526241541776602 34 | 32 0.6515590385058542 35 | 33 0.6502791360475968 36 | 34 0.6488144252892992 37 | 35 0.64719013379002 38 | 36 0.645438278950997 39 | 37 0.6435826036566887 40 | 38 0.641645338682833 41 | 39 0.63964203463148 42 | 40 0.6376033744305633 43 | 41 0.635540131304789 44 | 42 0.6334676432393297 45 | 43 0.6314001604282646 46 | 44 0.6293424314172467 47 | 45 0.6273113611879823 48 | 46 0.6253095052115923 49 | 47 0.6233522689812194 50 | 48 0.6214338165676301 51 | 49 0.6195592635836437 52 | 50 0.6177398620206086 53 | 51 0.615970530400753 54 | 52 0.6142590885665288 55 | 53 0.6126015626783062 56 | 54 0.6110008000372756 57 | 55 0.6094597579205214 58 | 56 0.6079809339569522 59 | 57 0.6065581449873043 60 | 58 0.6051969604474841 61 | 59 0.6038976118398143 62 | 60 0.60265895039394 63 | 61 0.6014796078059611 64 | 62 0.6003621820801959 65 | 63 0.5993029242412603 66 | 64 0.5983106880728137 67 | 65 0.5973768798539372 68 | 66 0.5965037156080772 69 | 67 0.595693742375792 70 | 68 0.5949454448315705 71 | 69 0.5942602553869778 72 | 70 0.5936367265093118 73 | 71 0.59307149975755 74 | 72 0.5925735972406267 75 | 73 0.5921368323244492 76 | 74 0.5917598429829227 77 | 75 0.5914474133288978 78 | 76 0.5911967975588857 79 | 77 0.5910086515175303 80 | 78 0.5908849269927755 81 | 79 0.5908213582836059 82 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/instanton/80/INSTANTON_FINAL_2.ener: -------------------------------------------------------------------------------- 1 | #Bead Energy (eV) 2 | 0 0.5908861587292017 3 | 1 0.5912866117214162 4 | 2 0.5920830287842944 5 | 3 0.5932664280254888 6 | 4 0.5948233308449534 7 | 5 0.5967357671120589 8 | 6 0.5989813015750958 9 | 7 0.6015330969427957 10 | 8 0.6043600312871046 11 | 9 0.6074268884336524 12 | 10 0.6106946396363514 13 | 11 0.6141208327861432 14 | 12 0.6176601015496278 15 | 13 0.6212648011548094 16 | 14 0.6248857700836682 17 | 15 0.6284732080959523 18 | 16 0.6319776512858769 19 | 17 0.6353510149986752 20 | 18 0.6385476664167224 21 | 19 0.6415254813824823 22 | 20 0.6442468356839398 23 | 21 0.6466794802707704 24 | 22 0.648797253295623 25 | 23 0.6505805894836403 26 | 24 0.652016798667876 27 | 25 0.6531000994752149 28 | 26 0.6538314097149377 29 | 27 0.6542179105084308 30 | 28 0.6542724150209256 31 | 29 0.65401258349924 32 | 30 0.6534600332630562 33 | 31 0.652639394927992 34 | 32 0.6515773645805766 35 | 33 0.6503017964496322 36 | 34 0.6488408727525561 37 | 35 0.6472223778834837 38 | 36 0.645473094092686 39 | 37 0.6436183261839807 40 | 38 0.6416815542991549 41 | 39 0.6396842070367831 42 | 40 0.6376455421698595 43 | 41 0.6355826191027315 44 | 42 0.6335103457689139 45 | 43 0.6314415826041729 46 | 44 0.6293872872400611 47 | 45 0.6273566853255746 48 | 46 0.6253574550131582 49 | 47 0.6233959150187629 50 | 48 0.621477208436566 51 | 49 0.6196054766396307 52 | 50 0.6177840194448873 53 | 51 0.6160154393089895 54 | 52 0.6143017685790175 55 | 53 0.6126445797698351 56 | 54 0.6110450795599619 57 | 55 0.6095041876471624 58 | 56 0.6080226019028258 59 | 57 0.6066008513975532 60 | 58 0.6052393389000932 61 | 59 0.6039383743947978 62 | 60 0.6026982010697383 63 | 61 0.6015190150848306 64 | 62 0.6004009802793954 65 | 63 0.5993442388329198 66 | 64 0.5983489187321224 67 | 65 0.59741513876765 68 | 66 0.5965430116541995 69 | 67 0.5957326457548217 70 | 68 0.5949841457941407 71 | 69 0.5942976128687654 72 | 70 0.5936731439862071 73 | 71 0.5931108313172495 74 | 72 0.5926107612908781 75 | 73 0.5921730136319605 76 | 74 0.5917976604130958 77 | 75 0.5914847651684919 78 | 76 0.5912343820998804 79 | 77 0.5910465553994497 80 | 78 0.5909213186980911 81 | 79 0.5908586946490869 82 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/minization/RESTART: -------------------------------------------------------------------------------- 1 | 2 | 31 3 | 400 4 | 5 | [ step, potential{electronvolt} ] 6 | x_centroid{angstrom} 7 | 8 | 9 | 10 | 11 | 12 | [ 2.00000000e+02, 1.22464680e-14, 1.22464680e-14, 0.00000000e+00, 2.00000000e+02, 13 | 1.22464680e-14, 0.00000000e+00, 0.00000000e+00, 2.00000000e+02 ] 14 | 15 | 16 | 17 | 18 | 5.00000000e-05 19 | 5.00000000e-05 20 | 5.00000000e-05 21 | 22 | 23 | 1.24608856e-05 24 | 25 | 26 | 27 | 28 | 29 | [ 3.08196068e+00, 2.57505733e+00, 2.17657809e+00, 1.59676287e+00, 1.49230032e+00, 30 | 1.25102910e+00, 2.44371982e+00, 1.19985561e-01, -2.72464898e-02, 3.82755752e-01, 31 | 2.76593242e+00, 1.83830640e-01, 4.78648338e-01, 5.08340234e-01, 2.67108041e+00, 32 | 1.10153418e+01, 4.11835544e+00, 3.50095780e+00 ] 33 | 34 |

35 | [ 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 36 | 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 37 | 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 0.00000000e+00, 38 | 0.00000000e+00, 0.00000000e+00, 0.00000000e+00 ] 39 |

40 | 41 | [ 1.83736223e+03, 2.18941669e+04, 1.83736223e+03, 1.83736223e+03, 1.83736223e+03, 42 | 1.83736223e+03 ] 43 | 44 | 45 | [ H, C, H, H, H, 46 | H ] 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | [ -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, 56 | -1.00000000e+00, -1.00000000e+00, -1.00000000e+00, -1.00000000e+00 ] 57 | 58 | 1.00000000e+00 59 | [ 1.00000000e+00 ] 60 | 61 | 62 | 63 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/log.ipi: -------------------------------------------------------------------------------- 1 | 2 | ____ ____ ____ ____ 3 | / \ / \ / \ / | ################################# | 4 | \__#_/ \____/ \____/ \_#__/ 5 | # _ _______ _____ # 6 | # (_) |_ __ \|_ _| # -*- Development version -*- 7 | # __ ______ | |__) | | | # 8 | Y [ ||______|| ___/ | | # A Python interface for (ab initio) 9 | 0 0 | | _| |_ _| |_ # (path integral) molecular dynamics. 10 | # [___] |_____| |_____| # 11 | __#_ ____ ____ _#__ 12 | / # \ / \ / \ / # \ 13 | | ################################# | 14 | \____/ \____/ \____/ \____/ 15 | 16 | 17 | fetching ffsocket 18 | # Initializing system object 19 | # Initializing simulation object 20 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 21 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 22 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 23 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 24 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 25 | !W! Overwriting previous cell parameters 26 | !W! Momenta not specified in initialize. Will start with zero velocity if they are not specified in beads. 27 | Import of PyFFTW unsuccessful, using NumPy library instead 28 | # i-PI loaded input file: input.xml 29 | --- begin input file content --- 30 | 31 | 32 | [ step, potential{electronvolt}] 33 | x_centroid{angstrom} 34 | 35 | 400 36 | 37 |
localhost
38 | 39 | 40 | 41 | init.xyz 42 | [200.0, 200.0, 200.0 ] 43 | 44 | 45 | 46 | 47 | 48 | 49 | 0.01 50 | phonons 51 | none 52 | 53 | 54 | 55 | 56 | --- end input file content --- 57 | Created unix socket with address localhost 58 | @ForceField: Starting the polling thread main loop. 59 | @SOCKET: Client asked for connection from . Now hand-shaking. 60 | @SOCKET: Handshaking was successful. Added to the client list. 61 | # Average timings at MD step 0. t/step: 7.23970e-02 62 | SOFTEXIT CALLED FROM THREAD Dynamic matrix is calculated. Exiting simulation 63 | !W! Soft exit has been requested with message: 'Dynamic matrix is calculated. Exiting simulation'. Cleaning up. 64 | @SOCKET: Shutting down the driver interface. 65 | SOFTEXIT CALLED FROM THREAD <_MainThread(MainThread, started 140621738768128)> @ SIMULATION: Exiting cleanly. 66 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/instanton/README.txt: -------------------------------------------------------------------------------- 1 | 2 | 3 | Inside the 'input' folder you can find all the required files to perform an instanton rate calculation with i-PI 4 | Inside the 'solution' folder you can find all the expected results. 5 | 6 | 7 | Here I show how to do the simulation with the provided inputs and how to use the post proc. scripts. 8 | Not all features are shown in this example 9 | 10 | 11 | Work flow: 12 | 13 | (Adjust your python path and compile the driver first) 14 | 15 | A TS optimization 16 | A.1 Go to the folder input/TS 17 | A.2 Run i-pi typing: i-pi input.xml & 18 | A.3 Run the driver typing: i-pi-driver -m ch4hcbe -u 19 | 20 | The simulation takes 12 steps. 21 | TS geometry: INSTANTON_FINAL_12.xyz 22 | Hessian at transition state: INSTANTON_FINAL.hess_12 23 | 24 | B Reactant minimization 25 | B.1 Go to the folder input/reactant/minimization 26 | B.2 Run i-pi typing: i-pi input.xml & 27 | B.3 Run the driver typing: i-pi-driver -m ch4hcbe -u 28 | 29 | The simulation takes 31 steps. 30 | Final geometry: last frame in min.xc.xyz 31 | 32 | 33 | C Calculation the Reactant hessian 34 | C.1 Go to the folder input/reactant/phononos 35 | C.2 Copy the optimized geometry obtained in B and named it init.xyz 36 | C.3 Run i-pi typing: i-pi input.xml & 37 | C.4 Run the driver typing: i-pi-driver -m ch4hcbe -u 38 | 39 | Hessian file: phonons.hess 40 | 41 | 42 | D. First Instanton calculation 43 | D.1 Go to the folder input/instanton/40 44 | D.2 Copy the optimized transition state geometry obtained in A and name it init.xyz 45 | D.3 Copy the transition state hessian obtained in A and name it hessian.dat 46 | D.4 Run i-pi typing: i-pi input.xml & 47 | D.5 Run the 4 instances of driver typing: 48 | i-pi-driver -m ch4hcbe -u & 49 | i-pi-driver -m ch4hcbe -u & 50 | i-pi-driver -m ch4hcbe -u & 51 | i-pi-driver -m ch4hcbe -u & 52 | 53 | The program first generate the initial instanton guess and then performs a optimization which takes 8 steps 54 | Finally a hessian is also computed 55 | instanton geometry: INSTANTON_FINAL_7.xyz 56 | Last physical Hessian (it does not contain the spring terms) : INSTANTON_FINAL.hess_7 57 | (In this case it is the exact hessian but could also be an approximation to it) 58 | 59 | E Second and sucesive instanton calculations 60 | E.1 Go to folder input/instanton/80 61 | E.2 Copy the optimized instanton geometry obtained in D and name it init0 62 | E.3 Copy the last hessian obtained in D and name it hess0 63 | E.4 Interpolate the instanton and the hessian to 80 beads by typing: 64 | ' python (ipi-path)/tools/py/Instanton_interpolation.py -m -xyz init0 -hess hess0 -n 80' 65 | E.5 Rename the new hessian and instanton geometry to hessian.dat and init.xyz respectively 66 | E.6 Copy the 'input.xml' file from input/instanton/40 67 | E.7 Change the number of beads from 40 to 80 (input.xml) 68 | E.8 Change the hessian shape from (18,18) to (18,1440) (input.xml) 69 | E.9 Run i-pi typing: i-pi input.xml & 70 | E.10 Run the 4 instances of driver typing: 71 | i-pi-driver -m ch4hcbe -u & 72 | i-pi-driver -m ch4hcbe -u & 73 | i-pi-driver -m ch4hcbe -u & 74 | i-pi-driver -m ch4hcbe -u & 75 | 76 | The program performs a optimization which takes 2 steps 77 | Finally a hessian is computed 78 | instanton geometry: INSTANTON_FINAL_2.xyz 79 | Last physical Hessian (it does not contain the spring terms) : INSTANTON_FINAL.hess_2 80 | 81 | F Post proc. 82 | F.1. CH4 partition function 83 | F.1.1 Go the input/reactant/phonons folder 84 | F.1.2 type ' python (ipi-path)/tools/py/Instanton_postproc.py RESTART -c reactant -t 300 -n 80 -f 5 ' 85 | (computes the ring polymer parittion function for CH4 witn n=80) 86 | (check data.out file in the corresponding inside 'solution') 87 | 88 | F.2. TS partition function 89 | F.2.1 Go the input/TS folder 90 | F.2.2 type python '~/Codes/i-pi/ipi-dev/tools/py/Instanton_postproc.py RESTART -c TS -t 300 -n 80' 91 | (computes the ring polymer parittion function for TS witn n=80) 92 | (check data.out file in the corresponding inside 'solution') 93 | 94 | F.3. instanton partition function ,BN and action 95 | F.3.1 Go the input/instanton/80 96 | F.3.2 python ~/Codes/i-pi/ipi-dev/tools/py/Instanton_postproc.py RESTART -c instanton -t 300 97 | (check data.out file in the corresponding inside 'solution') 98 | 99 | DONE 100 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/phonons.eigvec: -------------------------------------------------------------------------------- 1 | # Eigenvector matrix (normalized) 2 | 0.010917231612685442 -0.41605861362564234 -0.03297943578502848 0.005263013556903166 -0.012643431535357092 -0.03932719535813807 -0.06512266020621249 0.23664152650477524 0.07885708172431623 -0.12671412342970054 -0.04959608493204044 -0.366513239527034 -0.03210615866827259 0.3445493632665978 0.36086920498128644 0.00455428348478513 -0.5453452006835146 -0.23927730256912308 3 | -0.29671698241228056 0.34963655493748436 -0.251377005021117 0.005299950903887623 0.04039053187031748 0.19163596117938042 -0.1481028305971741 -0.014667649234499425 -0.001794701677418284 0.1562073361631789 -0.3297729994437497 0.3068050304150066 0.3489528878208541 -0.2429107349775233 0.26307646842940996 -0.011284680641987765 -0.40585322127752843 -0.15452778189925537 4 | 0.3292416445480512 0.27116127793980427 0.3498098208004153 -0.02001891878831095 0.029504886735029587 0.14518616059364325 0.1741593371281876 0.0705619602504271 -0.0016573770980120028 0.18073155850758854 0.44210024575646156 0.14797375743156443 -0.3567113521660261 -0.26869076827357674 0.22487969958683132 0.018018581457839012 -0.3472041194080708 -0.130936390463908 5 | -0.0004428379268383194 0.019900731831258595 -0.000820964116188299 0.006005979188242361 -0.06843878924442223 -0.13475877671673978 -0.22489398557973922 0.7969928160294726 0.1990645721148351 0.38316194984363083 -0.006981600727405023 0.11409482286284484 -1.653576521978145e-05 5.448773677774188e-05 0.00015824193817115528 0.007437308439694553 0.2813489355863754 -0.11058774454600362 6 | -0.00869023692284425 0.003913179828595452 -0.018197527766954467 -0.14714727724243035 0.1395141421317584 0.6546542042798127 -0.5239658740969636 -0.037057468523934205 0.051503753207351295 0.1013846900492793 0.20521313232546884 -0.32787586531876123 -1.9414314393007004e-05 -3.727861762470308e-05 -0.00012858588864710085 -0.20437831251951724 0.08616590564007102 0.2055098499569807 7 | 0.009656204400205572 0.006802159560982367 0.03232753311423426 0.14395448549630668 0.14151946628959594 0.5076046924383961 0.6162228084360974 0.2595994475233226 0.044234935500570685 0.052841426650429804 -0.34312226430092485 -0.19841177929336912 2.3272800509951258e-05 -2.7629785746347913e-05 -0.00012064710755401082 0.22271674386505702 0.0696784343862043 0.19228339176020304 8 | -0.013792717243511117 0.5588398655319595 0.0662515295234455 -0.006613681372658598 -0.02970963585050615 -0.03882320975651761 -0.06530472019262877 0.22331028509599554 0.029754951046589984 -0.497343828498261 0.05807983365831118 0.09662109404271174 -0.009273267568325586 0.45556733421763 0.20552457439924987 -0.0006486825157349767 0.002235159289691417 0.3401972443392586 9 | 0.36647017339318644 0.21538466221054645 -0.16603986887775626 -0.026722363557446706 0.039502178107736416 0.19122585264434222 -0.15413557573394854 -0.014251430672626759 0.005361034131639145 -0.20268112517728554 -0.3648695738199991 0.042832496933663866 -0.34373283744012423 0.14357318912182152 -0.3330384524701504 -0.012339982470331554 0.03410896268908378 -0.5494255812841337 10 | -0.4023907405802586 0.1383950342801829 0.22601267653973678 0.019092811325158856 0.03542938618937848 0.14549705584333633 0.1809317061738875 0.07396186660825402 0.00458358620951382 -0.1306879933742881 0.4061210979337304 -0.10947881132322075 0.362883789521641 0.14765440593378154 -0.3102136762536026 0.017266715526682616 0.031034939620490722 -0.5117131510408636 11 | 0.019706245422256338 -0.11313969073501493 0.47322789385171793 -0.07377754890367533 -0.027281967741283237 -0.04246717536604902 -0.0675733678184573 0.2320279638347741 0.06163155222536455 -0.3550002796201551 -0.28194740982665956 -0.0013259829477483415 0.1151519345204482 -0.3870034214778738 -0.2951279590239239 -0.4061462542995571 -0.22586962991078732 0.14508156426537158 12 | 0.330284458190822 -0.2810201654201606 0.1923960530773546 -0.08377473192114984 0.04028305340921397 0.18810138109735441 -0.1555672505308582 -0.007741214112975188 0.028593574730877445 -0.33036369409114824 0.019555685670659628 0.29212701748984055 0.37228304262191764 -0.12510239746690177 0.30964346589924063 0.412416534434243 0.26351079230764396 -0.14598417480670556 13 | 0.3774034457157303 -0.1995017211262405 -0.29331592310386145 0.07849924608112127 0.049319588849310904 0.14910361555951404 0.1767615521557912 0.07747317907623946 0.0246245005008679 0.0844458326367469 0.22269665931608595 0.4158544157929069 0.31331331637230614 0.2909276162402528 -0.2594790083086418 -0.34199123462586717 -0.2109258062858477 0.14768534177743686 14 | -0.017348751077578328 -0.006568706398425522 -0.5074448274052976 0.08208724234609117 -0.009672496079747694 -0.03553494152509465 -0.06259963529266037 0.2315536824868228 0.06041810475192069 -0.34358017957411535 0.297561762171188 -0.12264303973836631 -0.07371680286932142 -0.41328567991074383 -0.27180676586370117 0.37656753374256763 -0.2022305668504453 0.13573776453954292 15 | -0.4100386304627865 -0.2793637277221362 0.20392140906950706 -0.06531647724978432 0.04148735772927845 0.18763307305670396 -0.14935148186359554 -0.006283669552153093 0.027540515577454305 0.02686869950186778 -0.03328850852433024 0.49003133938736004 -0.37743870672573454 0.22457472355337904 -0.2392367819506452 0.31671230025246017 -0.18920780173391846 0.14052681202294143 16 | -0.2931435266485981 -0.20210213930166537 -0.24503884965151407 0.08924319832685022 0.049733862351469454 0.1484112331818077 0.18221104395654963 0.07881723901158982 0.023724292470832575 -0.31688979628990105 0.11350856398272849 0.2305478132274559 -0.3195640382464897 -0.16979016703834418 0.3452298756370707 -0.46210159346723456 0.28656779462770654 -0.16878933484601605 17 | 0.0009940742541071912 -0.03760307188408146 -0.0021112263022001337 -0.02529683469436022 0.31287744389826566 -0.03907284394402256 -0.06516039512662977 0.23198027202103622 -0.9167665608774325 -6.362004287507189e-06 3.4978354105930087e-06 1.98878222519034e-05 1.3684396713564695e-06 -1.5669812327021027e-05 -5.6880514826969105e-06 -1.0756407877246521e-07 7.532060569490594e-06 4.14999209894071e-06 18 | 0.016219811782677757 -0.024384459236849967 0.09398937289874368 0.6790566914739709 -0.6432489496032243 0.1900665402047785 -0.150815519362826 -0.01072418711161613 -0.23756155703771437 2.5545498806740785e-07 -1.4559771652489228e-06 5.349630327923516e-06 2.6333745131194505e-06 -6.097304570719169e-06 -7.136575957365302e-07 -2.973859235255727e-07 8.162066122763468e-07 8.207119186443048e-07 19 | -0.017958745820583513 -0.017399661985249115 -0.11822063307211905 -0.675765873752257 -0.6547632305349173 0.1464486822129326 0.17736302352487296 0.07486945442124875 -0.2037496479363227 5.143582087622015e-07 3.166646410091012e-06 3.849863748573747e-06 -2.055094454382622e-06 -5.7097452674333875e-06 -6.176212600344321e-07 2.794273992415969e-07 6.992804782757109e-07 7.202045712628971e-07 20 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/phonons.mode: -------------------------------------------------------------------------------- 1 | # Phonon modes (mass-scaled) 2 | 0.010918076592991098 -0.4161458506446023 -0.033000254693080204 0.005368332209648324 -0.012907298715302164 -0.06603149909660304 -0.10940691973116146 0.3971065649379622 0.08050513661784654 -0.13715598871410278 -0.05368333106086526 -0.3967164294869187 -0.03210615868580157 0.34454936407494063 0.3608692142592483 0.004757890624520316 -0.5697281716317409 -0.2499756457517119 3 | -0.29673994794194836 0.3497098649226001 -0.2515356916277638 0.005406008713311425 0.04123347832131048 0.3217623245761 -0.24881468981448443 -0.024613684205208427 -0.0018322096198531384 0.16907958683661042 -0.35694981021851824 0.3320878568314018 0.3489528880113717 -0.24291073554741305 0.2630764751931166 -0.01178918185628768 -0.42399935567323027 -0.1614368836997694 4 | 0.32926712744658393 0.27121813363457936 0.35003064502986253 -0.02041951923013087 0.030120650836381296 0.24377176518117982 0.29258996111768476 0.11840955416491833 -0.001692015057939976 0.19562472538983652 0.47853401911773835 0.1601678039837458 -0.35671135236077955 -0.2686907689039487 0.22487970536849747 0.018824133383838444 -0.3627279893275653 -0.1367906960132932 5 | -0.00012829555269565154 0.005766247496937538 -0.0002379750494005371 0.0017746875324784008 -0.020239785159504732 -0.0655463363200745 -0.10945199446024206 0.38743932192675307 0.05887217021284868 0.1201448907235337 -0.0021891738396728317 0.035775823418730916 -4.7902422638795234e-06 1.578454075614768e-05 4.584107412904452e-05 0.0022508334854005117 0.08514804014933666 -0.033468509826776335 6 | -0.002517667709792886 0.001133845909940988 -0.0052749657188614135 -0.043480077132386157 0.04125929600207724 0.3184221888365142 -0.25500508517904696 -0.018014617181573347 0.01523193048974368 0.031790350038622114 0.06434730921818489 -0.10280947694715693 -5.624128553686362e-06 -1.0799234727443142e-05 -3.7250019315646126e-05 -0.06185323000096967 0.02607743291316726 0.062195937361967824 7 | 0.002797520278607169 0.0019709293042518084 0.009370867907815926 0.04253664933684233 0.04185234170872824 0.24689766929356582 0.29990493183424133 0.12619816878911044 0.013082220630608654 0.016569044585931347 -0.10759055324782041 -0.06221443359203786 6.741892565591161e-06 -8.004066694416501e-06 -3.495023547333135e-05 0.06740318879008701 0.021087629552584503 0.058193053968789 8 | -0.013793784782869599 0.5589570401855982 0.06629335208555437 -0.006746028364419721 -0.03032967304587873 -0.06518529268663549 -0.10971278288627566 0.3747354977783173 0.030376807595257654 -0.5383273993634993 0.06286623112512742 0.10458333099019496 -0.009273267573388507 0.4555673352864307 0.20552457968329496 -0.000677682992333823 0.0023350956675249365 0.35540782566324775 9 | 0.36649853773408464 0.21542982295291688 -0.16614468476319527 -0.02725710725468555 0.040326584702562174 0.3210737404776338 -0.25894978043958566 -0.023915230616736758 0.005473075794123169 -0.21938304401245323 -0.3949387164784416 0.04636218672880756 -0.3437328376277919 0.14357318945865674 -0.33303846103258244 -0.012891662782626627 0.03563401112680667 -0.5739909845161137 10 | -0.40242188512889787 0.13842405223542786 0.22615535142241447 0.01947487934458201 0.03616879401508093 0.24429376730241673 0.3039676295702092 0.12411491431370074 0.004679379783373377 -0.1414573250333612 0.43958980595046687 -0.11850061184329097 0.3628837897197645 0.14765440628019164 -0.3102136842292087 0.018038653982589876 0.03242254517784767 -0.5345923913285945 11 | 0.019707770661426025 -0.11316341328040286 0.4735266281318866 -0.07525391828204855 -0.027851339740578962 -0.07130361639781349 -0.11352414052908942 0.38936457623855614 0.06291960624689145 -0.38425404388405193 -0.3051828821613261 -0.0014352529836850845 0.11515193458331764 -0.38700342238581753 -0.2951279666116756 -0.4243037268039271 -0.2359685041968334 0.15156831560915762 12 | 0.33031002180184865 -0.2810790882754892 0.19251750681490917 -0.08545115585671992 0.04112375679523233 0.31582766233111287 -0.26135501279788664 -0.012990479694149615 0.029191159370434507 -0.3575872828686932 0.021167282647788808 0.3162002755610798 0.37228304282517277 -0.12510239776040288 0.30964347386018665 0.4308543306839017 0.2752926434825114 -0.15251128282965729 13 | 0.3774326562784654 -0.19954355161564383 -0.29350108446541445 0.08007010177993101 0.05034888384642662 0.25034928543616414 0.2969617163522949 0.13000722431178302 0.02513913441406635 0.0914045834401748 0.24104923815248247 0.4501236551034929 0.31331331654336564 0.29092761692279434 -0.2594790149798576 -0.3572805457390868 -0.22035652613164997 0.1542885107884905 14 | -0.017350093849583935 -0.006570083690821006 -0.5077651617879698 0.08372989777115958 -0.009874360127214196 -0.059664195166833266 -0.10516820492248133 0.38856868787660676 0.06168079861551476 -0.3718928715803384 0.32208402359942373 -0.1327496624384239 -0.07371680290956853 -0.413285680880348 -0.2718067728518641 0.3934026382587009 -0.2112725131812784 0.14180674464041126 15 | -0.41007036694870075 -0.27942230326417256 0.20405013841141784 -0.0666235313380232 0.04235319482870701 0.3150413595784875 -0.25091244025104525 -0.01054458390256549 0.028116092056767204 0.029082812127768077 -0.036031836506505766 0.5304132629678355 -0.37743870693180454 0.22457472408025092 -0.23923678810143253 0.33087147277406204 -0.19766748621830302 0.1468099155402183 16 | -0.29316621559718287 -0.20214451503330683 -0.24519353517473674 0.0910290522511907 0.050771803196070074 0.24918675538713134 0.30611693375485927 0.13226268231140403 0.02422011269962052 -0.3430030698011728 0.12286287973895371 0.24954652499767907 -0.31956403842096187 -0.16979016743668673 0.34522988451294473 -0.48276064642853134 0.2993805491955417 -0.17633608587653604 17 | 0.0009941511942323877 -0.0376109563017752 -0.002112559054723506 -0.025803052001217137 0.3194071655611691 -0.06560443571162375 -0.10947031489032852 0.3892845449244887 -0.9359263063795682 -6.886264645475847e-06 3.7860943379015367e-06 2.152671440798977e-05 1.3684396721035955e-06 -1.566981236378377e-05 -5.688051628936943e-06 -1.1237291741640948e-07 7.868827105284776e-06 4.335542668103759e-06 18 | 0.016221067176169807 -0.024389572044187943 0.09404870551210229 0.6926453579500086 -0.6566734922884739 0.3191272213422465 -0.2533720423719432 -0.017996186757863533 -0.24252641850645879 2.765057320526141e-07 -1.5759652054435333e-06 5.7904763427030626e-06 2.6333745145571924e-06 -6.097304585023977e-06 -7.136576140846957e-07 -3.106810768661218e-07 8.527000885001049e-07 8.574068231146577e-07 19 | -0.017960135805432327 -0.017403310256412827 -0.11829526213811606 -0.6892886873694464 -0.668428075137415 0.2458915755160985 0.297972196108333 0.12563793136029092 -0.20800786542286953 5.567438480141751e-07 3.4276118330419684e-06 4.167118771251502e-06 -2.055094455504641e-06 -5.709745280828947e-06 -6.176212759134996e-07 2.919196856162356e-07 7.305460611855596e-07 7.524056851266489e-07 20 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/instanton/80/log.ipi: -------------------------------------------------------------------------------- 1 | 2 | ____ ____ ____ ____ 3 | / \ / \ / \ / | ################################# | 4 | \__#_/ \____/ \____/ \_#__/ 5 | # _ _______ _____ # 6 | # (_) |_ __ \|_ _| # -*- Development version -*- 7 | # __ ______ | |__) | | | # 8 | Y [ ||______|| ___/ | | # A Python interface for (ab initio) 9 | 0 0 | | _| |_ _| |_ # (path integral) molecular dynamics. 10 | # [___] |_____| |_____| # 11 | __#_ ____ ____ _#__ 12 | / # \ / \ / \ / # \ 13 | | ################################# | 14 | \____/ \____/ \____/ \____/ 15 | 16 | 17 | fetching ffsocket 18 | # Initializing system object 19 | # Initializing simulation object 20 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 21 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 22 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 23 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 24 | Initializing from file init.xyz. Dimension: length, units: automatic, cell_units: automatic 25 | !W! Overwriting previous cell parameters 26 | !W! Momenta not specified in initialize. Will start with zero velocity if they are not specified in beads. 27 | Import of PyFFTW unsuccessful, using NumPy library instead 28 | # i-PI loaded input file: input.xml 29 | --- begin input file content --- 30 | 31 | 32 | [ step, potential{electronvolt}] 33 | 34 | 20 35 | 36 |
localhost
37 | 38 | 39 | 40 | init.xyz 41 | [200.0, 200.0, 200.0 ] 42 | 43 | 44 | 45 | 46 | 47 | 300 48 | 49 | 50 | 51 | [ 0,1,2,3,4,5 ] 52 | 53 | 54 | 55 | 10 56 | 57 | 5e-6 58 | 5e-6 59 | 1e-3 60 | 61 | 0.1 62 | nichols 63 | powell 64 | poly 65 | true 66 | 0.3 67 | hessian.dat 68 | 69 | 70 | 71 | 72 | --- end input file content --- 73 | Created unix socket with address localhost 74 | @ForceField: Starting the polling thread main loop. 75 | @SOCKET: Client asked for connection from . Now hand-shaking. 76 | @SOCKET: Handshaking was successful. Added to the client list. 77 | 78 | Instanton optimization STEP 0 79 | @GEOP: Initializing INSTANTON 80 | @GEOP: Starting from the provided geometry in the extended phase space 81 | @SOCKET: Client asked for connection from . Now hand-shaking. 82 | @SOCKET: Handshaking was successful. Added to the client list. 83 | @Clean hessian: We have 1 'neg' frequencies 84 | @Instanton: Current step norm = 0.000106757 85 | @Exit step: Energy difference: 5.3e-06, (condition: 5.0e-06) 86 | @Exit step: Maximum force component: 2.7e-06, (condition: 5.0e-06) 87 | @Exit step: Maximum component step component: 1.1e-04, (condition: 1.0e-03) 88 | # Average timings at MD step 0. t/step: 1.64239e+00 89 | 90 | Instanton optimization STEP 1 91 | @SOCKET: Client asked for connection from . Now hand-shaking. 92 | @SOCKET: Handshaking was successful. Added to the client list. 93 | @Clean hessian: We have 1 'neg' frequencies 94 | @Instanton: Current step norm = 4.41746e-05 95 | @Exit step: Energy difference: 7.1e-06, (condition: 5.0e-06) 96 | @Exit step: Maximum force component: 1.0e-06, (condition: 5.0e-06) 97 | @Exit step: Maximum component step component: 4.4e-05, (condition: 1.0e-03) 98 | 99 | Instanton optimization STEP 2 100 | @Clean hessian: We have 1 'neg' frequencies 101 | @Instanton: Current step norm = 1.98795e-05 102 | @Exit step: Energy difference: 2.5e-06, (condition: 5.0e-06) 103 | @Exit step: Maximum force component: 7.8e-07, (condition: 5.0e-06) 104 | @Exit step: Maximum component step component: 2.0e-05, (condition: 1.0e-03) 105 | We are going to compute the final hessian 106 | @Instanton: Computing hessian 107 | @Instanton: Computing hessian: 1 of 18 108 | @SOCKET: Client asked for connection from . Now hand-shaking. 109 | @SOCKET: Handshaking was successful. Added to the client list. 110 | @Instanton: Computing hessian: 2 of 18 111 | @Instanton: Computing hessian: 3 of 18 112 | @Instanton: Computing hessian: 4 of 18 113 | @Instanton: Computing hessian: 5 of 18 114 | @Instanton: Computing hessian: 6 of 18 115 | @Instanton: Computing hessian: 7 of 18 116 | @Instanton: Computing hessian: 8 of 18 117 | @Instanton: Computing hessian: 9 of 18 118 | @Instanton: Computing hessian: 10 of 18 119 | @Instanton: Computing hessian: 11 of 18 120 | @Instanton: Computing hessian: 12 of 18 121 | @Instanton: Computing hessian: 13 of 18 122 | @Instanton: Computing hessian: 14 of 18 123 | @Instanton: Computing hessian: 15 of 18 124 | @Instanton: Computing hessian: 16 of 18 125 | @Instanton: Computing hessian: 17 of 18 126 | @Instanton: Computing hessian: 18 of 18 127 | 128 | Instanton optimization STEP 3 129 | SOFTEXIT CALLED FROM THREAD Geometry optimization converged. Exiting simulation 130 | !W! Soft exit has been requested with message: 'Geometry optimization converged. Exiting simulation'. Cleaning up. 131 | @SOCKET: Shutting down the driver interface. 132 | SOFTEXIT CALLED FROM THREAD <_MainThread(MainThread, started 140391644092160)> @ SIMULATION: Exiting cleanly. 133 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/TS/inst.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 -3.22639e-02 1.37801e+00 -1.85139e-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 4.85441e-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 5.01252e-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 2.26187e-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 -4.13158e-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 -3.05887e-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 -3.00194e-02 112 | H 1.80326e+00 2.18627e+00 1.87196e+00 113 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/phonons.hess: -------------------------------------------------------------------------------- 1 | # Hessian matrix (atomic units) 2 | 0.20233039965678046 0.11405214092596871 0.09749227786182146 -0.19020488406518155 -0.10374547956826241 -0.0886827496160425 0.009999144706673844 0.009662243227737122 0.008385119126819163 -0.011527520327181406 -0.012564066870224265 -0.006585485073928866 -0.010593110971734985 -0.0074040461262026005 -0.010608452866156524 -5.201394870368858e-06 -1.1463052729254741e-06 -9.837963776959668e-07 3 | 0.11405214092596871 0.12903638879624424 0.0710753632338079 -0.10374670178503465 -0.12354043565920847 -0.06464888555046677 -0.01733010693283354 -0.00949373094027983 -0.007953256386805663 0.016719623324723543 0.010821945284344988 0.010615154588666796 -0.009694253316760992 -0.006825632697937679 -0.009088255842337743 -1.1354805984353789e-06 4.1883163603984036e-07 -1.898481372109018e-07 4 | 0.09749227786182146 0.0710753632338079 0.1066459773269024 -0.08868374687387436 -0.06464876911582706 -0.10317355428335341 -0.016115610790290447 -0.008993560757231121 -0.00753780649009883 -0.010799680733031279 -0.01070428801153156 -0.006324537699109457 0.018107443183756896 0.0132714732259398 0.010388357812862736 -9.740819262304965e-07 -1.8929302569858922e-07 4.772571227107392e-07 5 | -0.19020488406518155 -0.10374670178503465 -0.08868374687387436 0.5559229576679313 -3.086406130670127e-05 -2.7183255646434642e-05 -0.0941832636880413 0.07500449580866153 0.06986323297653028 -0.14297314332445407 0.09974491524400442 -0.08357558589633383 -0.12854717471033617 -0.07096823836927334 0.10242652684344655 -1.0303702335789922e-05 -3.2809865935234943e-06 -2.811639809863209e-06 6 | -0.10374547956826241 -0.12354043565920847 -0.06464876911582706 -3.086406130670127e-05 0.5558945131989289 4.097638894862143e-05 0.0750032633223263 -0.16943352137976928 -0.11320329493247351 0.09974173861837521 -0.15254916649332095 0.08767919820740211 -0.07096573981235642 -0.11036767583183503 0.0901327878999325 -3.2554514639571157e-06 5.866140906363171e-07 -7.785438960183911e-07 7 | -0.0886827496160425 -0.06464888555046677 -0.10317355428335341 -2.7183255646434642e-05 4.097638894862143e-05 0.5558934892957444 0.06986201200875894 -0.1132037488749127 -0.1533472269998892 -0.08357314021378846 0.0876778832870073 -0.12138004115702652 0.10242344278266204 0.09013438079241709 -0.17798924598078078 -2.789574127248784e-06 -7.786826738964693e-07 8.278100427361323e-07 8 | 0.009999144706673844 -0.01733010693283354 -0.016115610790290447 -0.0941832636880413 0.0750032633223263 0.06986201200875894 0.09676692863669345 -0.08245014240793046 -0.07679885019595821 -0.006540878116911841 0.011488232032341728 0.013600308934602623 -0.006042540495743154 0.01328916546250447 0.009452337523807584 -4.853062396392717e-07 -2.689515277154442e-07 -2.371713936355491e-07 9 | 0.009662243227737122 -0.00949373094027983 -0.008993560757231121 0.07500449580866153 -0.16943352137976928 -0.1132037488749127 -0.08245014240793046 0.17948514813292954 0.12444975799885681 0.00612414785550186 -0.011198677263291046 -0.014564412731399301 -0.00834019658890739 0.010639751163443732 0.012311618668991997 -3.835820550079916e-07 -8.451572774959004e-08 -1.376676550535194e-07 10 | 0.008385119126819163 -0.007953256386805663 -0.00753780649009883 0.06986323297653028 -0.11320329493247351 -0.1533472269998892 -0.07679885019595821 0.12444975799885681 0.16180072948124288 -0.008832461151353499 0.013683757321691914 0.010709857167778834 0.007383516298364868 -0.0169772512714772 -0.011626522106178427 -3.4305891460917337e-07 -1.3974932322469158e-07 -5.037636974236648e-08 11 | -0.011527520327181406 0.016719623324723543 -0.010799680733031279 -0.14297314332445407 0.09974173861837521 -0.08357314021378846 -0.006540878116911841 0.00612414785550186 -0.008832461151353499 0.15040463652304936 -0.10965130151086024 0.09187630128915102 0.010636263120256116 -0.012934016774268642 0.0113286910408128 -3.1488700535931e-07 -5.939693181744588e-08 -9.645062526431047e-08 12 | -0.012564066870224265 0.010821945284344988 -0.01070428801153156 0.09974491524400442 -0.15254916649332095 0.0876778832870073 0.011488232032341728 -0.011198677263291046 0.013683757321691914 -0.10965130151086024 0.16092675830803313 -0.09639342296585694 0.010982649789603727 -0.00800195687489236 0.005736077723916821 7.369105325949477e-08 4.565792188770956e-08 1.484923295436147e-08 13 | -0.006585485073928866 0.010615154588666796 -0.006324537699109457 -0.08357558589633383 0.08767919820740211 -0.12138004115702652 0.013600308934602623 -0.014564412731399301 0.010709857167778834 0.09187630128915102 -0.09639342296585694 0.12666240417624763 -0.015315337886789852 0.01266394003551774 -0.009668676276275432 -1.6056600493641326e-07 -3.469446951953615e-08 -2.3175905639050143e-08 14 | -0.010593110971734985 -0.009694253316760992 0.018107443183756896 -0.12854717471033617 -0.07096573981235642 0.10242344278266204 -0.006042540495743154 -0.00834019658890739 0.007383516298364868 0.010636263120256116 0.010982649789603727 -0.015315337886789852 0.13454591912820388 0.07801740808943691 -0.11259875448699219 -3.1641356201816967e-07 -1.0935696792557792e-07 -4.315992008230296e-08 15 | -0.0074040461262026005 -0.006825632697937679 0.0132714732259398 -0.07096823836927334 -0.11036767583183503 0.09013438079241709 0.01328916546250447 0.010639751163443732 -0.0169772512714772 -0.012934016774268642 -0.00800195687489236 0.01266394003551774 0.07801740808943691 0.11455445619867888 -0.09909210701986025 -1.6417422976644502e-07 -2.914335439641036e-08 -2.6784130469081905e-08 16 | -0.010608452866156524 -0.009088255842337743 0.010388357812862736 0.10242652684344655 0.0901327878999325 -0.17798924598078078 0.009452337523807584 0.012311618668991997 -0.011626522106178427 0.0113286910408128 0.005736077723916821 -0.009668676276275432 -0.11259875448699219 -0.09909210701986025 0.18889491137930034 9.617306950815419e-08 2.4980018054066022e-08 4.829470157119431e-08 17 | -5.201394870368858e-06 -1.1354805984353789e-06 -9.740819262304965e-07 -1.0303702335789922e-05 -3.2554514639571157e-06 -2.789574127248784e-06 -4.853062396392717e-07 -3.835820550079916e-07 -3.4305891460917337e-07 -3.1488700535931e-07 7.369105325949477e-08 -1.6056600493641326e-07 -3.1641356201816967e-07 -1.6417422976644502e-07 9.617306950815419e-08 1.662170401317553e-05 4.864997293907436e-06 4.172218126541338e-06 18 | -1.1463052729254741e-06 4.1883163603984036e-07 -1.8929302569858922e-07 -3.2809865935234943e-06 5.866140906363171e-07 -7.786826738964693e-07 -2.689515277154442e-07 -8.451572774959004e-08 -1.3974932322469158e-07 -5.939693181744588e-08 4.565792188770956e-08 -3.469446951953615e-08 -1.0935696792557792e-07 -2.914335439641036e-08 2.4980018054066022e-08 4.864997293907436e-06 -9.37860900052101e-07 1.11743947428522e-06 19 | -9.837963776959668e-07 -1.898481372109018e-07 4.772571227107392e-07 -2.811639809863209e-06 -7.785438960183911e-07 8.278100427361323e-07 -2.371713936355491e-07 -1.376676550535194e-07 -5.037636974236648e-08 -9.645062526431047e-08 1.484923295436147e-08 -2.3175905639050143e-08 -4.315992008230296e-08 -2.6784130469081905e-08 4.829470157119431e-08 4.172218126541338e-06 1.11743947428522e-06 -1.2800871473928055e-06 20 | -------------------------------------------------------------------------------- /exercises/instanton/solutions/reactant/phonons/phonons.dynmat: -------------------------------------------------------------------------------- 1 | # Dynamical matrix (atomic units) 2 | 0.0001101200383009492 6.207384628497688e-05 5.306100017793734e-05 -2.9988867091478857e-05 -1.6357147785165036e-05 -1.398226551654168e-05 5.442119424186869e-06 5.258757933145031e-06 4.56367229526403e-06 -6.273950835354101e-06 -6.83810009426044e-06 -3.5842061786145115e-06 -5.765390608195587e-06 -4.029714982931392e-06 -5.7737405645253075e-06 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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 | -------------------------------------------------------------------------------- /exercises/day-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 | -------------------------------------------------------------------------------- /exercises/day-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 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 | -------------------------------------------------------------------------------- /exercises/day-2/ex-3/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 | --------------------------------------------------------------------------------