├── .gitignore ├── MANIFEST.in ├── README.rst ├── bin ├── i-pi ├── i-pi-contract-trajectory ├── i-pi-getacf ├── i-pi-getproperty ├── i-pi-gleacf ├── i-pi-kinetic2tag ├── i-pi-mergebeadspdb ├── i-pi-mux-positions ├── i-pi-paraweights ├── i-pi-pepper ├── i-pi-posforce2kinetic ├── i-pi-regtest ├── i-pi-remdsort └── i-pi-trimsim ├── doc ├── Makefile ├── README ├── create_man.py ├── elsarticle-num-names.bst ├── etoolbox.sty ├── figures │ ├── README │ ├── ipi-depend.pdf │ ├── ipi-depend.svg │ ├── ipi-forces.pdf │ ├── ipi-forces.svg │ ├── ipi-logo.pdf │ ├── ipi-logo.svg │ ├── ipi-network.pdf │ ├── ipi-network.svg │ ├── ipi-running.pdf │ ├── ipi-running.svg │ ├── ipi-scheme.pdf │ └── ipi-scheme.svg ├── help.py ├── help_list.py ├── manual.tex └── mybib.bib ├── drivers ├── LJ.f90 ├── LJPolymer.f90 ├── Makefile ├── README ├── SG.f90 ├── distance.f90 ├── driver.f90 ├── fsockets.f90 ├── fsockets_pure.f90 ├── pes │ ├── LEPS.f90 │ ├── README.md │ ├── ch52008.f │ ├── eckart.f90 │ ├── efield.f90 │ ├── h5o2.dms4B.coeff.com.dat │ ├── h5o2.pes4B.coeff.dat │ ├── morse.f │ ├── pswater.f90 │ ├── qtip4pf.f90 │ ├── utility.f │ └── zundel.f └── sockets.c ├── env.sh ├── examples ├── ASE │ └── W2-PIMD-MP2 │ │ ├── init.xyz │ │ ├── input.xml │ │ └── run-ase.py ├── MBPOL │ └── splitting │ │ ├── TS │ │ ├── TS.xyz │ │ └── input.xml │ │ ├── instanton │ │ ├── 32 │ │ │ ├── hessian.dat │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ └── 32-lbfgs │ │ │ ├── hessian.dat │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ ├── min-freq │ │ ├── init.xyz │ │ └── input.xml │ │ └── min │ │ ├── input.xml │ │ └── trimer.xyz ├── cp2k │ ├── .gitignore │ ├── Makefile │ ├── README │ ├── basis │ │ ├── GTH_BASIS_SETS │ │ ├── GTH_POTENTIALS │ │ └── dftd3.dat │ ├── npt-classical │ │ ├── in.cp2k │ │ ├── init.xyz │ │ └── input.xml │ ├── npt-piglet │ │ ├── in.cp2k │ │ ├── init.xyz │ │ └── input.xml │ ├── nvt-cl │ │ ├── idtau_plot.py │ │ ├── in.cp2k │ │ ├── init.xyz │ │ └── input.xml │ ├── nvt-classical │ │ ├── in.cp2k │ │ ├── init.xyz │ │ └── input.xml │ └── nvt-piglet │ │ ├── in.cp2k │ │ ├── init.xyz │ │ └── input.xml ├── dftb │ ├── Makefile │ ├── README.md │ ├── c18s4 │ │ ├── c6.gen │ │ ├── c6.xyz │ │ ├── dftb_in.hsd │ │ ├── init.gen │ │ ├── init.xyz │ │ ├── input-md.xml │ │ └── input.xml │ ├── dftb-param │ │ ├── C-C.skf │ │ ├── C-H.skf │ │ ├── C-S.skf │ │ ├── H-C.skf │ │ ├── H-H.skf │ │ ├── H-O.skf │ │ ├── H-S.skf │ │ ├── LICENSE │ │ ├── O-H.skf │ │ ├── O-O.skf │ │ ├── README │ │ ├── S-C.skf │ │ ├── S-H.skf │ │ └── S-S.skf │ └── zundel │ │ ├── dftb_in.hsd │ │ ├── init.xyz │ │ └── input.xml ├── ffdebye │ ├── Makefile │ ├── README │ └── single_particle │ │ ├── data.hessian │ │ ├── data.ref │ │ ├── init.xyz │ │ └── input.xml ├── fhi-aims │ ├── Makefile │ ├── h2o-npt │ │ ├── aims_control.in │ │ ├── aims_geometry.in │ │ ├── init.pdb │ │ └── input.xml │ └── zundel │ │ ├── aims_control.in │ │ ├── aims_geometry.in │ │ ├── init.pdb │ │ └── input.xml ├── harmonic │ ├── Makefile │ ├── README │ ├── init.pdb │ └── input.xml ├── hswfqmc │ ├── FixWF_1Bead │ │ ├── HswfQMC_Example_FixWF │ │ │ ├── dati_DFT.d │ │ │ ├── dati_SR.d │ │ │ ├── dati_conduttivita.d │ │ │ ├── dati_fisici.d │ │ │ ├── dati_funzione_onda.d │ │ │ ├── dati_mc.d │ │ │ ├── dati_ottimizzazione.d │ │ │ ├── estimatori │ │ │ │ ├── .gitkeep │ │ │ │ └── gradiente │ │ │ │ │ └── .gitkeep │ │ │ ├── ottimizzazione │ │ │ │ ├── .gitkeep │ │ │ │ └── splines │ │ │ │ │ └── .gitkeep │ │ │ ├── posizioni │ │ │ │ └── .gitkeep │ │ │ ├── randomseed.d │ │ │ ├── reticolo │ │ │ │ └── .gitkeep │ │ │ └── wf_now.d │ │ ├── init.xyz │ │ ├── input.xml │ │ └── intau_plot.py │ ├── README │ └── WFOpt_2Bead │ │ ├── HswfQMC_Example_WFOpt │ │ ├── 0 │ │ │ ├── dati_DFT.d │ │ │ ├── dati_SR.d │ │ │ ├── dati_conduttivita.d │ │ │ ├── dati_fisici.d │ │ │ ├── dati_funzione_onda.d │ │ │ ├── dati_mc.d │ │ │ ├── dati_ottimizzazione.d │ │ │ ├── estimatori │ │ │ │ ├── .gitkeep │ │ │ │ └── gradiente │ │ │ │ │ └── .gitkeep │ │ │ ├── ottimizzazione │ │ │ │ ├── .gitkeep │ │ │ │ └── splines │ │ │ │ │ └── .gitkeep │ │ │ ├── posizioni │ │ │ │ └── .gitkeep │ │ │ ├── randomseed.d │ │ │ ├── reticolo │ │ │ │ └── .gitkeep │ │ │ └── wf_now.d │ │ ├── 1 │ │ │ ├── dati_DFT.d │ │ │ ├── dati_SR.d │ │ │ ├── dati_conduttivita.d │ │ │ ├── dati_fisici.d │ │ │ ├── dati_funzione_onda.d │ │ │ ├── dati_mc.d │ │ │ ├── dati_ottimizzazione.d │ │ │ ├── estimatori │ │ │ │ ├── .gitkeep │ │ │ │ └── gradiente │ │ │ │ │ └── .gitkeep │ │ │ ├── ottimizzazione │ │ │ │ ├── .gitkeep │ │ │ │ └── splines │ │ │ │ │ └── .gitkeep │ │ │ ├── posizioni │ │ │ │ └── .gitkeep │ │ │ ├── randomseed.d │ │ │ ├── reticolo │ │ │ │ └── .gitkeep │ │ │ └── wf_now.d │ │ └── SR_wf.dir │ │ │ ├── 0 │ │ │ └── 1 │ │ ├── init.xyz │ │ ├── input.xml │ │ └── intau_plot.py ├── lammps │ ├── .gitignore │ ├── Makefile │ ├── NaCl-cellopt │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml │ ├── README │ ├── benz-graph-slc │ │ ├── CH.airebo │ │ ├── data.full │ │ ├── data.part │ │ ├── in.full │ │ ├── in.partbeads │ │ ├── in.partcontr │ │ ├── init.chk │ │ └── input.xml │ ├── graphene │ │ ├── C.opt.tersoff │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml │ ├── h2o-alchemical │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-bias │ │ ├── data.water_longrange │ │ ├── data.water_shortrange │ │ ├── in.water_longrange │ │ ├── in.water_shortrange │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── h2o-enmfdphonons │ │ ├── data.dynmat │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml │ ├── h2o-extreme-rem │ │ ├── data_h2o.longrange │ │ ├── data_h2o.shortrange │ │ ├── h2o-32.xyz │ │ ├── in.water_longrange │ │ ├── in.water_shortrange │ │ ├── input.xml │ │ └── input_template.xml │ ├── h2o-fdphonons │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml │ ├── h2o-fixatoms │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-geop │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml │ ├── h2o-multi │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-open-all │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.chk │ │ └── input.xml │ ├── h2o-open-one │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.chk │ │ └── input.xml │ ├── h2o-piglet.2 │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-piglet.4 │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-piglet.8 │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd+mts.4 │ │ ├── data_long.lmp │ │ ├── data_short.lmp │ │ ├── in_long.lmp │ │ ├── in_short.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd+rpc │ │ ├── data_long.lmp │ │ ├── data_short.lmp │ │ ├── in_long.lmp │ │ ├── in_short.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd+sc+gle.4 │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd+sc+mts │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd+sc+rpc │ │ ├── data_long.lmp │ │ ├── data_short.lmp │ │ ├── in_long.lmp │ │ ├── in_short.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd+sc │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd.1 │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-pimd.4 │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── h2o-remd-bias │ │ ├── data.water_longrange │ │ ├── data.water_shortrange │ │ ├── in.water_longrange │ │ ├── in.water_shortrange │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── h2o-repimd │ │ ├── 0_init.xyz │ │ ├── 10_init.xyz │ │ ├── 11_init.xyz │ │ ├── 12_init.xyz │ │ ├── 13_init.xyz │ │ ├── 14_init.xyz │ │ ├── 15_init.xyz │ │ ├── 16_init.xyz │ │ ├── 17_init.xyz │ │ ├── 18_init.xyz │ │ ├── 19_init.xyz │ │ ├── 1_init.xyz │ │ ├── 2_init.xyz │ │ ├── 3_init.xyz │ │ ├── 4_init.xyz │ │ ├── 5_init.xyz │ │ ├── 6_init.xyz │ │ ├── 7_init.xyz │ │ ├── 8_init.xyz │ │ ├── 9_init.xyz │ │ ├── data.lmp │ │ ├── in.lmp │ │ └── input.xml │ ├── h2o-trpmd │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ └── input.xml │ ├── ice-npt │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml │ ├── ice-nst │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── in.xyz │ │ └── input.xml │ ├── isof-vapor │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ ├── input.xml │ │ └── process_out.py │ ├── isof-water │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ ├── input.xml │ │ └── process_out.py │ ├── isofsc-vapor │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ ├── input.xml │ │ ├── process_dif.py │ │ └── process_out.py │ ├── isofsc-water │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.pdb │ │ ├── input.xml │ │ └── process_out.py │ ├── paracetamol-geop │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml │ └── paracetamol-phonons │ │ ├── data.lmp │ │ ├── in.lmp │ │ ├── init.xyz │ │ └── input.xml ├── lj │ ├── Makefile │ ├── README.md │ ├── high_density │ │ ├── init.pdb │ │ └── input.xml │ ├── low_density │ │ ├── init.pdb │ │ └── input.xml │ ├── mid_density │ │ ├── init.pdb │ │ └── input.xml │ └── nst │ │ ├── init.pdb │ │ └── input.xml ├── lm │ ├── h2o-bulk │ │ ├── init.xyz │ │ └── input.xml │ ├── iron-piglet │ │ ├── init.xyz │ │ ├── input.xml │ │ └── load.vmd │ └── iron-pimd │ │ ├── init.xyz │ │ ├── input.xml │ │ └── load.vmd ├── pes-regtest │ ├── io-units │ │ ├── h2o-angstrom.xyz │ │ ├── h2o-nocomment.xyz │ │ ├── h2o-velocities.xyz │ │ └── input.xml │ ├── split-baoab-npt │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-baoab-nve │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-baoab-nvt-mts │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-baoab-nvt │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-obabo-npt-mts │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-obabo-npt │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-obabo-nst │ │ ├── input.xml │ │ └── start.pdb │ ├── split-obabo-nve-mts │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-obabo-nve │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-obabo-nvt-mts │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-obabo-nvt │ │ ├── input.xml │ │ └── water_298K.pdb │ ├── split-obabo-sc-mts │ │ ├── input.xml │ │ └── water_298K.pdb │ └── zundel │ │ └── input.xml ├── pes │ ├── CH4H-CBE │ │ └── instanton-rate │ │ │ ├── TS │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ ├── instanton │ │ │ ├── 40 │ │ │ │ ├── hessian.dat │ │ │ │ ├── init.xyz │ │ │ │ └── input.xml │ │ │ └── 80 │ │ │ │ ├── hessian.dat │ │ │ │ ├── init.xyz │ │ │ │ └── input.xml │ │ │ └── reactant │ │ │ ├── minization │ │ │ ├── init.xyz │ │ │ ├── input.xml │ │ │ └── run_all │ │ │ └── phonons │ │ │ ├── init.xyz │ │ │ ├── input.xml │ │ │ └── run_all │ ├── README.md │ ├── geop │ │ ├── README.md │ │ ├── waterbox │ │ │ ├── bfgs │ │ │ │ ├── init.pdb │ │ │ │ └── input.xml │ │ │ ├── cg │ │ │ │ ├── init.pdb │ │ │ │ └── input.xml │ │ │ ├── lbfgs │ │ │ │ ├── init.pdb │ │ │ │ └── input.xml │ │ │ └── sd │ │ │ │ ├── init.pdb │ │ │ │ └── input.xml │ │ └── waterhexamers │ │ │ ├── book │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ ├── cage │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ ├── prism │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ └── ring │ │ │ ├── bfgs │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ ├── cg │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ ├── lbfgs │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ └── sd │ │ │ ├── init.xyz │ │ │ └── input.xml │ ├── neb │ │ ├── README.md │ │ ├── h5o2.dms4B.coeff.com.dat │ │ ├── h5o2.pes4B.coeff.dat │ │ ├── init.xyz │ │ └── input.xml │ ├── pswater │ │ ├── README.md │ │ ├── init.xyz │ │ ├── input.xml │ │ └── phonon │ │ │ ├── init.xyz │ │ │ └── input.xml │ ├── qtip4pf │ │ ├── h2o-piglet │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── init.pdb │ │ ├── input.xml │ │ └── tun-splitting │ │ │ ├── TS │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ ├── instanton │ │ │ ├── 32 │ │ │ │ ├── hessian.dat │ │ │ │ ├── init.xyz │ │ │ │ └── input.xml │ │ │ └── 32-lbfgs │ │ │ │ ├── hessian.dat │ │ │ │ ├── init.xyz │ │ │ │ └── input.xml │ │ │ ├── min-freq │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ │ └── min │ │ │ ├── init.xyz │ │ │ └── input.xml │ ├── zundel-systempart │ │ ├── double.xyz │ │ ├── h5o2+.xyz │ │ ├── h5o2.dms4B.coeff.com.dat │ │ ├── h5o2.pes4B.coeff.dat │ │ └── input.xml │ └── zundel │ │ ├── h5o2.dms4B.coeff.com.dat │ │ ├── h5o2.pes4B.coeff.dat │ │ ├── init.xyz │ │ └── input.xml ├── ph2 │ ├── Makefile │ ├── README │ ├── mht-14K │ │ └── init.pdb │ ├── mht-17K │ │ └── init.pdb │ ├── mht-20K │ │ └── init.pdb │ ├── mht-25K │ │ └── init.pdb │ ├── nst-cubic │ │ ├── init.pdb │ │ └── input.xml │ ├── nvt │ │ ├── init.pdb │ │ └── input.xml │ ├── remd │ │ ├── our_ref.pdb │ │ ├── our_ref.xyz │ │ ├── remd.xml │ │ └── remd_npt.xml │ └── rpmd │ │ ├── Makefile │ │ ├── README │ │ ├── consolidate.f │ │ ├── start-1.chk │ │ ├── start-2.chk │ │ ├── start-3.chk │ │ ├── start-4.chk │ │ └── vel_est.f ├── plumed │ └── zundel │ │ ├── h5o2+.xyz │ │ ├── h5o2.dms4B.coeff.com.dat │ │ ├── h5o2.pes4B.coeff.dat │ │ ├── input.xml │ │ └── plumed │ │ └── plumed.dat ├── ppi │ ├── LJ │ │ ├── Makefile │ │ ├── init.pdb │ │ ├── input.xml │ │ └── ppi.sh │ ├── harmonic │ │ ├── Makefile │ │ ├── README │ │ ├── init.pdb │ │ ├── input.xml │ │ └── ppi.sh │ └── qtip4pf │ │ ├── Makefile │ │ ├── init.pdb │ │ ├── input.xml │ │ └── ppi.sh ├── qespresso │ ├── Makefile │ ├── README │ ├── dia-npt-classical │ │ ├── C.pbe-rrkjus.UPF │ │ ├── init.xyz │ │ ├── input.xml │ │ └── pw.in │ ├── dia-npt-pimd.4 │ │ ├── C.pbe-rrkjus.UPF │ │ ├── init.xyz │ │ ├── input.xml │ │ └── pw.in │ ├── dia_big-npt-classical │ │ ├── C.pbe-rrkjus.UPF │ │ ├── init.xyz │ │ ├── input.xml │ │ └── pw.in │ ├── dia_big-npt-pimd.4 │ │ ├── C.pbe-rrkjus.UPF │ │ ├── init.xyz │ │ ├── input.xml │ │ └── pw.in │ ├── h2o │ │ ├── H.pbe-rrkjus.UPF │ │ ├── O.pbe-rrkjus.UPF │ │ ├── init.pdb │ │ ├── input.xml │ │ └── pw.in │ └── li4 │ │ ├── Li.pbe-tm.UPF │ │ ├── init.pdb │ │ ├── input.xml │ │ └── pw.in ├── regtest │ ├── README.rst │ ├── integrators │ │ ├── h2o-md_npt │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-md_nst │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-md_nvt │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-md_nvt_mts │ │ │ ├── data_long.lmp │ │ │ ├── data_short.lmp │ │ │ ├── in_long.lmp │ │ │ ├── in_short.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd_npt │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd_nst │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd_nvt │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd_nvt_mts │ │ │ ├── data_long.lmp │ │ │ ├── data_short.lmp │ │ │ ├── in_long.lmp │ │ │ ├── in_short.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-repimd_npt │ │ │ ├── 0_init.xyz │ │ │ ├── 1_init.xyz │ │ │ ├── 2_init.xyz │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ └── input.xml │ │ ├── h2o-rescpimd_nvt │ │ │ ├── 0_init.xyz │ │ │ ├── 1_init.xyz │ │ │ ├── 2_init.xyz │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ └── input.xml │ │ └── h2o-scpimd_nvt │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ ├── lammps │ │ ├── benz-graph-slc │ │ │ ├── CH.airebo │ │ │ ├── data.full │ │ │ ├── data.part │ │ │ ├── in.full │ │ │ ├── in.partbeads │ │ │ ├── in.partcontr │ │ │ ├── init.chk │ │ │ └── input.xml │ │ ├── h2o-alchemical │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-fixatoms │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-fixcom │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ ├── h2o-piglet.2 │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-piglet.8 │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd+mts.4 │ │ │ ├── data_long.lmp │ │ │ ├── data_short.lmp │ │ │ ├── in_long.lmp │ │ │ ├── in_short.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd+rpc │ │ │ ├── data_long.lmp │ │ │ ├── data_short.lmp │ │ │ ├── in_long.lmp │ │ │ ├── in_short.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd+sc+mts │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd+sc+rpc │ │ │ ├── data_long.lmp │ │ │ ├── data_short.lmp │ │ │ ├── in_long.lmp │ │ │ ├── in_short.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd+sc │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── h2o-pimd.1 │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── ice-npt │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ └── ice-nst │ │ │ ├── data.lmp │ │ │ ├── in.lmp │ │ │ ├── init.xyz │ │ │ └── input.xml │ ├── pes │ │ ├── CH4_H │ │ │ └── instanton_rate │ │ │ │ ├── hessian.dat │ │ │ │ ├── init.xyz │ │ │ │ └── input.xml │ │ ├── io-units │ │ │ ├── init-angstrom.xyz │ │ │ ├── init-nocomment.xyz │ │ │ ├── init-velocities.xyz │ │ │ └── input.xml │ │ ├── neb │ │ │ ├── README.md │ │ │ ├── h5o2.dms4B.coeff.com.dat │ │ │ ├── h5o2.pes4B.coeff.dat │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ ├── pswater │ │ │ ├── init.xyz │ │ │ └── input.xml │ │ ├── qtip4pf │ │ │ ├── h2o-piglet │ │ │ │ ├── init.pdb │ │ │ │ └── input.xml │ │ │ ├── init.pdb │ │ │ ├── input.xml │ │ │ └── tun-splitting │ │ │ │ ├── hessian.dat │ │ │ │ ├── init.xyz │ │ │ │ └── input.xml │ │ └── zundel │ │ │ ├── h5o2.dms4B.coeff.com.dat │ │ │ ├── h5o2.pes4B.coeff.dat │ │ │ ├── init.xyz │ │ │ └── input.xml │ ├── ph2 │ │ ├── mht-14K │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── mht-17K │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── mht-20K │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── mht-25K │ │ │ ├── init.pdb │ │ │ └── input.xml │ │ ├── remd-npt │ │ │ ├── our_ref.pdb │ │ │ ├── our_ref.xyz │ │ │ └── remd_npt.xml │ │ ├── remd-nvt │ │ │ ├── our_ref.pdb │ │ │ ├── our_ref.xyz │ │ │ └── remd_nvt.xml │ │ └── remd-template │ │ │ ├── our_ref.pdb │ │ │ ├── our_ref.xyz │ │ │ └── remd.xml │ └── qespresso │ │ ├── dia-npt-classical │ │ ├── C.pbe-rrkjus.UPF │ │ ├── init.xyz │ │ ├── input.xml │ │ └── pw.in │ │ ├── dia-npt-pimd.4 │ │ ├── C.pbe-rrkjus.UPF │ │ ├── init.xyz │ │ ├── input.xml │ │ └── pw.in │ │ ├── dia_big-npt-pimd.4 │ │ ├── C.pbe-rrkjus.UPF │ │ ├── init.xyz │ │ ├── input.xml │ │ └── pw.in │ │ ├── h2o │ │ ├── H.pbe-rrkjus.UPF │ │ ├── O.pbe-rrkjus.UPF │ │ ├── init.pdb │ │ ├── input.xml │ │ └── pw.in │ │ └── li4 │ │ ├── Li.pbe-tm.UPF │ │ ├── init.pdb │ │ ├── input.xml │ │ └── pw.in ├── tools │ ├── getacf │ │ ├── init.chk │ │ └── input.xml │ └── gleacf │ │ ├── h2o-gle │ │ ├── README │ │ ├── init.xyz │ │ ├── input.xml │ │ ├── simulation-gle01.vvac │ │ └── simulation-svr.vvac │ │ ├── h2o-qt │ │ ├── README │ │ ├── init.xyz │ │ ├── input.xml │ │ └── simulation-svr.vvac │ │ └── h2o-wn │ │ ├── README │ │ ├── init.xyz │ │ ├── input.xml │ │ ├── simulation-svr.vvac │ │ └── simulation-wle1e1.vvac ├── tutorial │ ├── README.md │ ├── tutorial-1 │ │ ├── our_ref.pdb │ │ ├── our_ref.xyz │ │ └── tutorial-1.xml │ ├── tutorial-2 │ │ ├── tutorial-1_RESTART │ │ ├── tutorial-2a.xml │ │ └── tutorial-2b.xml │ └── tutorial-3 │ │ ├── our_ref.pdb │ │ ├── tutorial-3_npt.xml │ │ └── tutorial-3_nvt.xml └── yaff │ ├── Makefile │ ├── README │ ├── mil53_ffsocket │ ├── init.chk │ ├── init.xyz │ ├── input.xml │ ├── pars.txt │ ├── run.py │ └── yaffdriver.py │ └── mil53_ffyaff │ ├── init.chk │ ├── init.xyz │ ├── input.xml │ └── pars.txt ├── ipi ├── __init__.py ├── engine │ ├── __init__.py │ ├── atoms.py │ ├── barostats.py │ ├── beads.py │ ├── cell.py │ ├── ensembles.py │ ├── forcefields.py │ ├── forces.py │ ├── initializer.py │ ├── motion │ │ ├── __init__.py │ │ ├── alchemy.py │ │ ├── dynamics.py │ │ ├── geop.py │ │ ├── instanton.py │ │ ├── motion.py │ │ ├── multi.py │ │ ├── neb.py │ │ ├── phonons.py │ │ └── replay.py │ ├── normalmodes.py │ ├── outputs.py │ ├── properties.py │ ├── simulation.py │ ├── smotion │ │ ├── __init__.py │ │ ├── metad.py │ │ ├── remd.py │ │ └── smotion.py │ ├── system.py │ └── thermostats.py ├── external │ ├── __init__.py │ └── importlib │ │ ├── __init__.py │ │ └── bundledimportlib.py ├── inputs │ ├── __init__.py │ ├── atoms.py │ ├── barostats.py │ ├── beads.py │ ├── cell.py │ ├── ensembles.py │ ├── forcefields.py │ ├── forces.py │ ├── initializer.py │ ├── interface.py │ ├── motion │ │ ├── __init__.py │ │ ├── alchemy.py │ │ ├── dynamics.py │ │ ├── geop.py │ │ ├── instanton.py │ │ ├── motion.py │ │ ├── neb.py │ │ └── phonons.py │ ├── normalmodes.py │ ├── outputs.py │ ├── prng.py │ ├── simulation.py │ ├── smotion │ │ ├── __init__.py │ │ ├── metad.py │ │ ├── remd.py │ │ └── smotion.py │ ├── system.py │ └── thermostats.py ├── interfaces │ ├── __init__.py │ ├── clients.py │ └── sockets.py ├── tests │ ├── __init__.py │ ├── common.py │ ├── test.pos_0.pdb │ ├── test.pos_0.xyz │ ├── test_atoms.py │ ├── test_contraction.py │ ├── test_depend.py │ ├── test_interface.py │ ├── test_io.py │ ├── test_runs.py │ └── test_units.py └── utils │ ├── __init__.py │ ├── decorators.py │ ├── depend.py │ ├── inputvalue.py │ ├── instools.py │ ├── io │ ├── __init__.py │ ├── backends │ │ ├── __init__.py │ │ ├── io_binary.py │ │ ├── io_json.py │ │ ├── io_pdb.py │ │ ├── io_units.py.bak │ │ └── io_xyz.py │ ├── inputs │ │ ├── __init__.py │ │ └── io_xml.py │ └── io_units.py │ ├── mathtools.py │ ├── messages.py │ ├── mintools.py │ ├── nmtransform.py │ ├── prng.py │ ├── softexit.py │ └── units.py ├── ipi_tests ├── __init__.py ├── engine │ ├── __init__.py │ ├── test_initializer.py │ └── test_properties.py ├── pdb_generator.py ├── utils │ ├── __init__.py │ ├── io │ │ ├── __init__.py │ │ └── backends │ │ │ ├── __init__.py │ │ │ ├── test__init__.py │ │ │ ├── test_io_units.py │ │ │ └── test_io_xyz.py │ └── test_depend.py └── xyz_generator.py ├── licenses ├── license_GPL.txt └── license_MIT.txt ├── setup.py ├── tests ├── README └── test_docs.py └── tools ├── bash └── update-tool-links.sh ├── f90 ├── compile.sh └── fortran.f90 └── py ├── Instanton_interpolation.py ├── Instanton_postproc.py ├── a2b.py ├── bin2xyz.py ├── contract-trajectory.py ├── effective_temperatures.py ├── energies_ppi.py ├── energy_ppi.py ├── fixcom.py ├── get_np.py ├── get_np_rad.py ├── get_np_vec.py ├── get_np_xyz.py ├── getacf.py ├── getproperty.py ├── gleacf.py ├── heat_capacity_ppi.py ├── kinetic2tag.py ├── kinetic_energy_ppi.py ├── mergebeadspdb.py ├── mux-positions.py ├── paraweights.py ├── pepper.py ├── posforce2kinetic.py ├── potential_energy_ppi.py ├── rdf_ppi.py ├── regtest-parallel.py ├── regtest.py ├── remdsort.py ├── total_energy_ppi.py ├── trimsim.py ├── xyz2bin.py └── xyz2pdb.py /.gitignore: -------------------------------------------------------------------------------- 1 | #ignored patterns 2 | 3 | bin/i-pi-driver 4 | doc/manual.pdf 5 | doc/manual.xml 6 | *.pyc 7 | *.pyo 8 | *.x 9 | *.mod 10 | *.out 11 | *.o 12 | *~ 13 | \#* 14 | *.orig 15 | regtest-ref 16 | -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | include README.rst 2 | -------------------------------------------------------------------------------- /bin/i-pi-contract-trajectory: -------------------------------------------------------------------------------- 1 | ../tools/py/contract-trajectory.py -------------------------------------------------------------------------------- /bin/i-pi-getacf: -------------------------------------------------------------------------------- 1 | ../tools/py/getacf.py -------------------------------------------------------------------------------- /bin/i-pi-getproperty: -------------------------------------------------------------------------------- 1 | ../tools/py/getproperty.py -------------------------------------------------------------------------------- /bin/i-pi-gleacf: -------------------------------------------------------------------------------- 1 | ../tools/py/gleacf.py -------------------------------------------------------------------------------- /bin/i-pi-kinetic2tag: -------------------------------------------------------------------------------- 1 | ../tools/py/kinetic2tag.py -------------------------------------------------------------------------------- /bin/i-pi-mergebeadspdb: -------------------------------------------------------------------------------- 1 | ../tools/py/mergebeadspdb.py -------------------------------------------------------------------------------- /bin/i-pi-mux-positions: -------------------------------------------------------------------------------- 1 | ../tools/py/mux-positions.py -------------------------------------------------------------------------------- /bin/i-pi-paraweights: -------------------------------------------------------------------------------- 1 | ../tools/py/paraweights.py -------------------------------------------------------------------------------- /bin/i-pi-pepper: -------------------------------------------------------------------------------- 1 | ../tools/py/pepper.py -------------------------------------------------------------------------------- /bin/i-pi-posforce2kinetic: -------------------------------------------------------------------------------- 1 | ../tools/py/posforce2kinetic.py -------------------------------------------------------------------------------- /bin/i-pi-regtest: -------------------------------------------------------------------------------- 1 | ../tools/py/regtest.py -------------------------------------------------------------------------------- /bin/i-pi-remdsort: -------------------------------------------------------------------------------- 1 | ../tools/py/remdsort.py -------------------------------------------------------------------------------- /bin/i-pi-trimsim: -------------------------------------------------------------------------------- 1 | ../tools/py/trimsim.py -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the help files 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | .PHONY: all distclean clean aux 9 | all: manual.pdf 10 | 11 | aux: 12 | PYTHONPATH=..:$(PYTHONPATH) python create_man.py 13 | rm -f *.pyc 14 | 15 | manual.pdf: aux 16 | pdflatex manual 17 | bibtex manual 18 | pdflatex manual 19 | pdflatex manual 20 | 21 | clean: 22 | bash -c "rm -rf input_docs manual.{aux,bbl,blg,brf,idx,log,lof,out,toc}" 23 | 24 | distclean: clean 25 | rm -f manual.pdf manual.xml 26 | -------------------------------------------------------------------------------- /doc/figures/README: -------------------------------------------------------------------------------- 1 | -- Figures directory -- 2 | 3 | * This gives the figures used in the user manual. 4 | 5 | * Files: 6 | ipi-depend.pdf: Figure to show how the dependency mechanism works. 7 | ipi-logo.pdf: ipi logo, used on the front of the manual. 8 | ipi-network.pdf: Figure to show how the internet network addresses are 9 | named, and how they are used to connect between computers. 10 | ipi-running.pdf: Figure to show the different modes of running ipi. 11 | ipi-scheme.pdf: Figure to show how an ipi simulation is run. 12 | -------------------------------------------------------------------------------- /doc/figures/ipi-depend.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/doc/figures/ipi-depend.pdf -------------------------------------------------------------------------------- /doc/figures/ipi-forces.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/doc/figures/ipi-forces.pdf -------------------------------------------------------------------------------- /doc/figures/ipi-logo.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/doc/figures/ipi-logo.pdf -------------------------------------------------------------------------------- /doc/figures/ipi-network.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/doc/figures/ipi-network.pdf -------------------------------------------------------------------------------- /doc/figures/ipi-running.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/doc/figures/ipi-running.pdf -------------------------------------------------------------------------------- /doc/figures/ipi-scheme.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/doc/figures/ipi-scheme.pdf -------------------------------------------------------------------------------- /drivers/README: -------------------------------------------------------------------------------- 1 | -- Driver code directory -- 2 | 3 | * This gives simple test driver codes. 4 | 5 | * Files: 6 | - LJ.f90: Calculates the Lennard-Jones potential/forces/virial. 7 | - SG.f90: Calculates the Silvera-Goldman potential/forces/virial. 8 | - distance.f90: Deals with calculating the separation between atoms and 9 | the neighbour list calculation. 10 | - sockets.c: Contains the functions to create the client socket and read from 11 | and write to it. 12 | - driver.f90: Socket interface for the driver codes. 13 | - Makefile: A makefile that which compiles all the fortran code as 14 | necessary. 15 | -------------------------------------------------------------------------------- /drivers/pes/README.md: -------------------------------------------------------------------------------- 1 | Potential energy surfaces for driver.x 2 | ====================================== 3 | 4 | This is meant to contain routines that provide a quick&dirty implementation of 5 | simple potential energy surfaces to use as tests with `driver.x`. 6 | They are typically quickly put together and do not necessarily implement 7 | all of the possible features (e.g. they might not have the virial, etc.), 8 | or simply they are not implemented in clean, standard-compliant F90. 9 | 10 | -------------------------------------------------------------------------------- /drivers/pes/morse.f: -------------------------------------------------------------------------------- 1 | 2 | SUBROUTINE getmorse(r0,D,a,q,pot,force) 3 | IMPLICIT NONE 4 | DOUBLE PRECISION r0, D, a, q(1,3), pot, force(1,3) 5 | DOUBLE PRECISION nq, dr 6 | nq=dsqrt(sum(q*q)) 7 | dr=nq-r0 8 | pot=D*(dexp(-2.*a*dr)-2.*dexp(-a*dr)) 9 | force=-2*a*D*(dexp(-a*dr)-dexp(-2.0*a*dr))*q/nq 10 | END SUBROUTINE 11 | -------------------------------------------------------------------------------- /env.sh: -------------------------------------------------------------------------------- 1 | ENV_BASE_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" 2 | 3 | export PATH=$ENV_BASE_DIR/bin:$PATH 4 | export PYTHONPATH=$ENV_BASE_DIR:$PYTHONPATH 5 | export IPI_ROOT=$ENV_BASE_DIR 6 | 7 | unset ENV_BASE_DIR 8 | -------------------------------------------------------------------------------- /examples/ASE/W2-PIMD-MP2/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | positions{angstrom} 3 | O -1.609897056834251 -0.103087275528143 0.000000000000000 4 | H -1.912995977596714 0.806433754963565 0.000000000000000 5 | H -0.647962494659909 -0.019318873282295 -0.000000000000000 6 | O 1.301879273880096 0.048939209162592 -0.000000000000000 7 | H 1.747649062946381 -0.340161166119908 -0.756895540576383 8 | H 1.747649062946381 -0.340161166119908 0.756895540576383 9 | -------------------------------------------------------------------------------- /examples/MBPOL/splitting/TS/TS.xyz: -------------------------------------------------------------------------------- 1 | 9 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 | O -0.0090103919768718329641465913937282 -1.0286525912377360025828920697677 0.31011666010936911330730936242617 4 | H -0.84539070490470680230288280654349 -1.0428108783717564556070556136547 -0.15564037438587852157922952756053 5 | H 0.66576175467037157496008603629889 -1.1604546828304098671225119687733 -0.36964113171469809016045360294811 6 | O 1.5271535148424255634580504192854 1.2644398418324058752659766469151 0.84178442871556791171627764924779 7 | H 1.8535379602504398199869228847092 1.3427458222870713999697045437642 1.7381018638977077106488877689117 8 | H 0.82697352731269535563995987104136 0.59459192810402072826292396712233 0.87992587361103935528205965965753 9 | O 2.2991676449915612323593450128101 -0.50278767615649910815989187540254 -1.1703649292635247558536093492876 10 | H 3.0555753363614504003464844572591 -0.45718726635640694055950916663278 -1.7520453850133628215246517356718 11 | H 2.3566553513966512767296990205068 0.25629858570878755186228659113112 -0.57197771233107363997305583325215 12 | -------------------------------------------------------------------------------- /examples/MBPOL/splitting/instanton/32-lbfgs/init.xyz: -------------------------------------------------------------------------------- 1 | 9 2 | CELL(abcABC): 130.180340 170.292060 240.217580 90.000000 90.000000 90.000000 cell{atomic_unit} Traj: positions{angstrom} Bead: 0 3 | O -0.00901040550037 -1.02865262628 0.310116666747 4 | H -0.845390723964 -1.04281020903 -0.155640417375 5 | H 0.665761699218 -1.16045461591 -0.369641207675 6 | O 1.52715348877 1.26443984146 0.841784439603 7 | H 1.85353788919 1.34274622373 1.7381018658 8 | H 0.826973683785 0.594591720787 0.879926062767 9 | O 2.29916770662 -0.502787725405 -1.17036491004 10 | H 3.05557493171 -0.457186895101 -1.7520459632 11 | H 2.35665539543 0.256298627892 -0.571977789499 12 | -------------------------------------------------------------------------------- /examples/MBPOL/splitting/instanton/32/init.xyz: -------------------------------------------------------------------------------- 1 | 9 2 | CELL(abcABC): 130.180340 170.292060 240.217580 90.000000 90.000000 90.000000 cell{atomic_unit} Traj: positions{angstrom} Bead: 0 3 | O -0.00901040550037 -1.02865262628 0.310116666747 4 | H -0.845390723964 -1.04281020903 -0.155640417375 5 | H 0.665761699218 -1.16045461591 -0.369641207675 6 | O 1.52715348877 1.26443984146 0.841784439603 7 | H 1.85353788919 1.34274622373 1.7381018658 8 | H 0.826973683785 0.594591720787 0.879926062767 9 | O 2.29916770662 -0.502787725405 -1.17036491004 10 | H 3.05557493171 -0.457186895101 -1.7520459632 11 | H 2.35665539543 0.256298627892 -0.571977789499 12 | -------------------------------------------------------------------------------- /examples/MBPOL/splitting/min-freq/init.xyz: -------------------------------------------------------------------------------- 1 | 9 2 | # CELL(abcABC): 130.18034 170.29206 240.21758 90.00000 90.00000 90.00000 cell{atomic_unit} Traj: x_centroid{angstrom} Step: 146 Bead: 0 3 | O -1.79023e+00 -5.25499e-01 1.53684e+00 4 | H -1.28859e+00 2.91196e-01 1.39258e+00 5 | H -1.23712e+00 -1.07110e+00 2.09602e+00 6 | O -1.79240e+00 -4.18553e-01 -1.26201e+00 7 | H -1.95096e+00 -7.35119e-01 -3.59669e-01 8 | H -2.62460e+00 -5.19922e-01 -1.72285e+00 9 | O -5.12435e-01 1.58699e+00 2.20463e-01 10 | H -7.39028e-01 2.51139e+00 1.23220e-01 11 | H -9.01481e-01 1.13679e+00 -5.43819e-01 12 | -------------------------------------------------------------------------------- /examples/MBPOL/splitting/min-freq/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | positions{angstrom} 6 | 7 | 400 8 | 9 |
localhost
10 | 11 | 12 | 13 | init.xyz 14 | [200.0, 200.0, 200.0 ] 15 | 16 | 17 | 18 | 19 | 20 | 35 21 | 22 | 23 | 24 | 0.01 25 | simulation-fd 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /examples/MBPOL/splitting/min/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | positions{angstrom} 6 | 7 | 400 8 | 9 |
localhost
10 | 11 | 12 | 13 | trimer.xyz 14 | [200.0, 200.0, 200.0 ] 15 | 16 | 17 | 18 | 19 | 20 | 35 21 | 22 | 23 | 24 | 25 | 1e-5 26 | 1e-5 27 | 1e-5 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /examples/MBPOL/splitting/min/trimer.xyz: -------------------------------------------------------------------------------- 1 | 9 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 | O -1.516074336e+00 -2.023167650e-01 1.454672917e+00 4 | H -6.218989773e-01 -6.009430735e-01 1.572437625e+00 5 | H -2.017613812e+00 -4.190350349e-01 2.239642849e+00 6 | O -1.763651687e+00 -3.816594649e-01 -1.300353949e+00 7 | H -1.903851736e+00 -4.935677617e-01 -3.457810126e-01 8 | H -2.527904158e+00 -7.613550077e-01 -1.733803676e+00 9 | O -5.588472140e-01 2.006699172e+00 -1.392786582e-01 10 | H -9.411558180e-01 1.541226676e+00 6.163293071e-01 11 | H -9.858551734e-01 1.567124294e+00 -8.830970941e-01 12 | -------------------------------------------------------------------------------- /examples/cp2k/.gitignore: -------------------------------------------------------------------------------- 1 | make.in 2 | -------------------------------------------------------------------------------- /examples/cp2k/nvt-cl/idtau_plot.py: -------------------------------------------------------------------------------- 1 | from pylab import * 2 | 3 | idtdata = [] 4 | # output is a standard output from i-pi 5 | for line in open("output"): 6 | llist = line.split() 7 | if llist: 8 | if llist[0] == "ThermoCL": 9 | idtdata.append(float(llist[5])) 10 | 11 | nsteps = len(idtdata) 12 | maxt = nsteps * 0.1 13 | print("Mean IDTAU for " + str(maxt * 0.5) + " dftb.log; \ 18 | wait 19 | 20 | c18s4: 21 | cd c18s4; $(IPI) input.xml & sleep 5; \ 22 | $(DFTB) > dftb.log; \ 23 | wait 24 | 25 | clean: 26 | rm -f */*simulation* */*output* */*.log* */*tmp* */*charges* */*dftb_pin.hsd* */*RESTART* */EXIT 27 | -------------------------------------------------------------------------------- /examples/dftb/README.md: -------------------------------------------------------------------------------- 1 | Examples of usage of the DFTB+ i-PI interface 2 | ============================================= 3 | 4 | This folder contains examples for running DFTB+ as the backend of i-PI. 5 | 6 | Examples exploit fairly advanced features of i-PI, including replica exchange, 7 | threaded execution, and the evaluation of isotope fractionation estimators. 8 | 9 | Running the examples 10 | -------------------- 11 | 12 | Compile DFTB+ and create make.in file containing the path to dftb+ executable, e.g. 13 | 14 | DFTB:=~/bin/dftb+ 15 | 16 | * Run an example automatically, type for instance: 17 | 18 | $ make zundel 19 | 20 | or 21 | 22 | To clean up output files: 23 | 24 | $ make clean 25 | 26 | * Run an example manually: 27 | 28 | In the example directory run 29 | 30 | $ python path/src/i-pi input.xml 31 | 32 | In another terminal launch dftb+: 33 | 34 | $ path/dftb+ 35 | -------------------------------------------------------------------------------- /examples/dftb/dftb-param/README: -------------------------------------------------------------------------------- 1 | MICHAEL GAUS (mgaus@wisc.edu) Nov 13th, 2012 2 | 3 | GENERAL PURPOSE PARAMETER SET 4 | 5 | name requires elements 6 | 3ob - C-H-N-O 7 | 8 | short description: 9 | DFTB3 files for bio and organic molecules 10 | 11 | detailed description: 12 | This set has been specifically designed for DFTB3 and supersedes the MIO 13 | parameter set. Main improvements over MIO are improved geometries for 14 | non-covalent bonds as e.g. the hydrogen bond in the water dimer, a 15 | great reduction of the consistent overbinding and an overall improved 16 | performance. Comprehensive benchmark tests can be found in [JCTC2012]. 17 | 18 | The following zeta and Hubbard derivative parameters should be used 19 | for DFTB3 calculations (atomic units): 20 | zeta: 4.00 (also called DampXHExponent) 21 | C -0.1492 22 | H -0.1857 23 | N -0.1535 24 | O -0.1575 25 | 26 | RELEVANT PUBLICATIONS 27 | [JCTC2012] J. Chem. Theory Comput., 2013, 9 (1), pp 338–354. 28 | DOI: http://dx.doi.org/10.1021/ct300849w 29 | 30 | PUBLICATIONS TO BE CITED 31 | [JCTC2012] J. Chem. Theory Comput., 2013, 9 (1), pp 338–354. 32 | DOI: http://dx.doi.org/10.1021/ct300849w 33 | 34 | -------------------------------------------------------------------------------- /examples/dftb/zundel/init.xyz: -------------------------------------------------------------------------------- 1 | 7 2 | #CELL{H}: 25.29166 0.0 0.0 0.0 25.29166 0.0 0.0 0.0 25.29166 positions{angstrom} 3 | O 0.54044984 -0.97485007 -0.21657970 4 | O 2.92484146 -0.83925223 0.15239669 5 | H 0.18385954 -1.25804198 -1.07875142 6 | H 1.74328720 -0.90927800 -0.10039502 7 | H 3.29706729 -1.59324218 0.64725255 8 | H 3.53032937 -0.60813812 -0.57607828 9 | H 0.04233158 -0.19485993 0.09228101 10 | -------------------------------------------------------------------------------- /examples/dftb/zundel/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 1.00000000e-01 4 | 6.00000000e+02 5 |
zundel
6 | 7 | 20 8 | 9 | [ step, time, conserved, temperature{kelvin}, kinetic_cv, 10 | potential, kinetic_cv(H), kinetic_cv(O) ] 11 | 12 | 13 | 18885 14 | 15 | 16 | 17 | 18 | 19 | 20 | init.xyz 21 | 22 | 23 | 300.0 24 | 25 | 26 | 27 | 0.25 28 | 29 | 100 30 | 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /examples/ffdebye/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the CP2K example 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | .PHONY: all single_particle 8 | all: single_particle 9 | 10 | IPI:=i-pi 11 | 12 | single_particle: 13 | cd single_particle; $(IPI) input.xml; 14 | wait 15 | 16 | clean: 17 | rm -rf */*simulation* */*RESTART* */*EXIT* 18 | -------------------------------------------------------------------------------- /examples/ffdebye/README: -------------------------------------------------------------------------------- 1 | -- Running the ffdebye example -- 2 | 3 | ** Run the examples automatically: 4 | 5 | #TODO description of the example goes here 6 | * You can run debye crystal simulation... 7 | To run the single_particle example, just type: 8 | 9 | $ make single_particle 10 | 11 | * To clean up output files: 12 | 13 | $ make clean 14 | 15 | 16 | ** Run the examples manually: 17 | 18 | * Go to example directory and run 19 | 20 | $ python path/src/i-pi input.xml 21 | -------------------------------------------------------------------------------- /examples/ffdebye/single_particle/data.hessian: -------------------------------------------------------------------------------- 1 | # Hessian matrix (atomic units) 2 | 10 0 0 3 | 0 1 0 4 | 0 0 0.01 5 | -------------------------------------------------------------------------------- /examples/ffdebye/single_particle/data.ref: -------------------------------------------------------------------------------- 1 | 0 0. 0. 2 | -------------------------------------------------------------------------------- /examples/ffdebye/single_particle/init.xyz: -------------------------------------------------------------------------------- 1 | 1 2 | # CELL(abcABC): 13.17884 17.29009 24.21482 90.00000 66.14000 90.00000 cell{atomic_unit} Traj: positions{atomic_unit} Step: 133 Bead: 0 3 | C 1.60668e-1 0e+01 0e+01 4 | -------------------------------------------------------------------------------- /examples/fhi-aims/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the FHI-AIMS examples 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | .PHONY: all zundel h2o-npt clean 8 | all: zundel h2o-npt 9 | 10 | AIMS:=aims.x 11 | IPI:=i-pi 12 | 13 | define run_aims 14 | for i in `seq 1 $1`; do \ 15 | mkdir -p run_$$i; cp $2_control.in run_$$i/control.in; cp $2_geometry.in run_$$i/geometry.in; cd run_$$i; \ 16 | $(AIMS) > aims.out & cd ..; \ 17 | done; 18 | endef 19 | 20 | zundel: 21 | cd zundel; $(IPI) input.xml & sleep 3; \ 22 | $(call run_aims,3,aims) \ 23 | wait 24 | 25 | h2o-npt: 26 | cd h2o-npt; $(IPI) input.xml & sleep 3; \ 27 | $(call run_aims,1,aims) \ 28 | wait 29 | 30 | clean: 31 | rm -rf */*simulation* */*.log */run_* */*RESTART* */EXIT 32 | -------------------------------------------------------------------------------- /examples/fhi-aims/zundel/aims_geometry.in: -------------------------------------------------------------------------------- 1 | atom 0.13653169 -1.42167286 -0.89038905 H 2 | atom 1.60777812 -0.97592555 -0.28273782 H 3 | atom 0.41131003 -0.93977977 -0.11788910 O 4 | atom 3.41185678 -1.68527470 0.53487569 H 5 | atom 3.58513613 -0.37429751 -0.32374851 H 6 | atom 2.94337023 -0.95785919 0.08987083 O 7 | atom 0.16618329 -0.02285293 -0.08985620 H 8 | 9 | -------------------------------------------------------------------------------- /examples/fhi-aims/zundel/init.pdb: -------------------------------------------------------------------------------- 1 | TITLE cell{angstrom} Traj: positions{angstrom} Step: 163 Bead: 0 2 | CRYST 35.218 35.218 35.218 90.00 90.00 90.00 P 1 1 3 | ATOM 1 H 1 1 0.258 -2.687 -1.683 0.00 0.00 0 4 | ATOM 2 H 1 1 3.038 -1.844 -0.534 0.00 0.00 0 5 | ATOM 3 O 1 1 0.777 -1.776 -0.223 0.00 0.00 0 6 | ATOM 4 H 1 1 6.447 -3.185 1.011 0.00 0.00 0 7 | ATOM 5 H 1 1 6.775 -0.707 -0.612 0.00 0.00 0 8 | ATOM 6 O 1 1 5.562 -1.810 0.170 0.00 0.00 0 9 | ATOM 7 H 1 1 0.314 -0.043 -0.170 0.00 0.00 0 10 | -------------------------------------------------------------------------------- /examples/harmonic/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the harmonic oscillator example 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | .PHONY: all clean harmonic 8 | all: harmonic 9 | 10 | driver:=i-pi-driver 11 | IPI:=i-pi 12 | 13 | define run_driver 14 | for i in `seq 1 $1`; do \ 15 | $(driver) -u -h harmonic -m harm -o 1 & \ 16 | done; 17 | endef 18 | -include make.in 19 | 20 | harmonic: 21 | $(IPI) input.xml & sleep 5; \ 22 | $(call run_driver,4) \ 23 | wait 24 | 25 | clean: 26 | rm -f *simulation.* RESTART EXIT 27 | -------------------------------------------------------------------------------- /examples/harmonic/init.pdb: -------------------------------------------------------------------------------- 1 | TITLE cell{atomic_unit} positions{atomic_unit} 2 | CRYST1 71.230 71.230 71.230 90.00 90.00 90.00 P 1 1 3 | ATOM 1 H 1 1 0.108 0.000 0.000 0.00 0.00 0 4 | END 5 | -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/dati_DFT.d: -------------------------------------------------------------------------------- 1 | !name of the folder where the DFT orbitals will be stored inside orbitals/ . If nothing is provided it will be used the default name "qespresso" 2 | ORBITALS_FOLDER="simple" 3 | !want to overwrite a previous orbitals' folder? If so set equal to T, otherwise it will be assumed false 4 | OVERWRITE=T 5 | !specify the path to the folder where the pseudo potential that is to be used is stored 6 | PSEUDO_DIR="/storage/Codes/espresso-5.1.2/pseudo" 7 | !pseudo potential to be used 8 | PSEUDO="H.coulomb-ae.UPF" 9 | !Energy cutoff for the plane waves basis set [Rydberg] 10 | ECUTWFC=3.0 11 | !type of K-points to use (gamma if no TABC are used, automatic otherwise) 12 | K_POINTS="automatic" 13 | !if K_points=="gamma" then the K-points' grid must be specified (example: 3 3 3) - offset is automatically set to zero 14 | K_GRID=3 3 3 15 | !Input wave function to be set for using the generated orbitals 16 | WF="dati_funzione_onda.d" 17 | -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/dati_conduttivita.d: -------------------------------------------------------------------------------- 1 | !DEPRECATED 2 | &dati_conduttivita 3 | cutoff=0.5d0 4 | N_exc=10 !-1 fa considerare tutti quelli entro il cutoff 5 | / 6 | -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/dati_fisici.d: -------------------------------------------------------------------------------- 1 | &dati_fisici 2 | r_s=1.33 !Density in r_s=a/a_0 units 3 | crystal_cell='datex' !Crystal cell that specifies the initial protonic positions: 'bcc', 'fcc', 'hcp', 'hcp_w', 'mhcpo', 'sc_', 'mol', 'dat', 'datex', 'grp__', 'quadr' 4 | file_reticolo='reticolo/rp_now.d' !Path to the file containing the protonic initial position, for the cases 'dat__' and 'datex' 5 | flag_molecular=T !Molecule in the crystal cell (implemented only for 'hcp__' and 'mhcpo') 6 | strecthing_cov_bond=1. !Distance between H atoms in the H2 molecule, in 0.74 Angstrom units (the equilibrium distance) 7 | N_cell_side=8 !Number of replica of the crystal cell on each direction (x,y,z). In the cases 'dat__' and 'datex', then N_cell_side specifies the number of atoms 8 | / 9 | 10 | !Distances are in a_0 units, where a_0 is the Bohr radius 11 | !In order to express them in Angstrom, multiply for 0.53 12 | !Energies are in Rydberg units per atom (multiply for 2 in order to have them in Hartree units) 13 | !'.datex' files contain non-normalized positions, and the first line contains the L(1:3) (i.e. the x,y,z lengths of the simulation box) 14 | !'.dat' files contain normalized positions 15 | -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/dati_ottimizzazione.d: -------------------------------------------------------------------------------- 1 | &dati_ottimizzazione 2 | opt_SDe=F 3 | opt_orbital=F 4 | opt_dynamic_backflow=T 5 | opt_A_Jee=F 6 | opt_F_Jee=F 7 | opt_A_Jep=F 8 | opt_F_Jep=F 9 | opt_Jse=F 10 | opt_Kse=F 11 | opt_Jsesp=F 12 | opt_SDse=F 13 | opt_rp=T 14 | costri_rp='none__' !ring__ or h2ring 15 | costri_rp_param=0.d0 !radius of rings 16 | / 17 | 18 | !It specifies which part of the wave function is optimized with Stochastic Reconfiguration 19 | -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/estimatori/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/estimatori/.gitkeep -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/estimatori/gradiente/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/estimatori/gradiente/.gitkeep -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/ottimizzazione/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/ottimizzazione/.gitkeep -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/ottimizzazione/splines/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/ottimizzazione/splines/.gitkeep -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/posizioni/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/posizioni/.gitkeep -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/reticolo/.gitkeep: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/examples/hswfqmc/FixWF_1Bead/HswfQMC_Example_FixWF/reticolo/.gitkeep -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/init.xyz: -------------------------------------------------------------------------------- 1 | 8 2 | # CELL(abcABC): 4.2879 4.2879 4.2879 90.0 90.0 90.0 Traj: positions{atomic_unit} Step: 0 Bead: 0 cell{atomic_unit} 3 | H 1.0844189333099281 1.0997891342724069 0.09741645926582456 4 | H 0.75544822047597715 -0.90642400336781914 -2.0458639602589437 5 | H -1.1976602615819170 1.1396815781971990 -1.9735788319702261 6 | H -1.1984578304368108 -1.0242788849081876 0.21991064568270161 7 | H 0.90319073386049098 1.2668935050186461 1.1798728839733514 8 | H 0.81224726935132552 -1.0887362294162308 -0.90224074280975874 9 | H -1.2099856391545645 -1.9863861947310959 2.0788980296595865 10 | H -1.1008014258244603 0.34786109493507666 0.19398551645747622 11 | -------------------------------------------------------------------------------- /examples/hswfqmc/FixWF_1Bead/intau_plot.py: -------------------------------------------------------------------------------- 1 | from pylab import * 2 | 3 | invdata = [] 4 | for line in open("output"): 5 | llist = line.split() 6 | if llist: 7 | if llist[0] == "ThermoCL": 8 | invdata.append(float(llist[5])) 9 | 10 | nsteps = len(invdata) 11 | maxt = nsteps * 0.1 12 | print("Mean INTAU for " + str(maxt * 0.5) + " 2 | 3 | [ step, potential{electronvolt}] 4 | positions{angstrom} 5 | 6 | 1000 7 | 8 |
NaCl-cellopt
9 | 1e-4 10 | 11 | 12 | 13 | init.xyz 14 | [1, 2, 3, 90, 90, 90] 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 1e-8 23 | 1e-7 24 | 1e-7 25 | 26 | 27 | 100.0 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/benz-graph-slc/data.part: -------------------------------------------------------------------------------- 1 | LAMMPS Description 2 | 3 | 12 atoms 4 | 0 bonds 5 | 0 angles 6 | 0 dihedrals 7 | 8 | 2 atom types 9 | 0 bond types 10 | 0 angle types 11 | 0 dihedral types 12 | 13 | 0 17.1404 xlo xhi 14 | 0 19.792 ylo yhi 15 | 0 30.00000 zlo zhi 16 | 17 | Masses 18 | 19 | 1 12.0110 20 | 2 1.0080 21 | 22 | Atoms 23 | 24 | 1 2 8.43090 -7.64856 3.08149 25 | 2 1 7.88729 -8.59708 3.13791 26 | 3 1 6.49669 -8.60046 3.17688 27 | 4 2 5.94591 -7.65476 3.15118 28 | 5 1 5.80584 -9.80579 3.24864 29 | 6 2 4.71157 -9.80845 3.27940 30 | 7 1 6.50544 -11.00776 3.28138 31 | 8 2 5.96179 -11.95622 3.33785 32 | 9 1 7.89602 -11.00436 3.24246 33 | 10 2 8.44654 -11.95016 3.26834 34 | 11 1 8.58690 -9.79905 3.17069 35 | 12 2 9.68114 -9.79632 3.14005 36 | -------------------------------------------------------------------------------- /examples/lammps/benz-graph-slc/in.full: -------------------------------------------------------------------------------- 1 | dimension 3 2 | boundary p p p 3 | 4 | atom_style atomic 5 | 6 | units metal 7 | 8 | 9 | read_data data.full 10 | mass 1 12 11 | mass 2 1 12 | 13 | group C type 1 14 | group H type 2 15 | 16 | neighbor 0.5 bin 17 | neigh_modify delay 1 18 | 19 | 20 | pair_style airebo 3 1 1 21 | 22 | pair_coeff * * ./CH.airebo C H 23 | 24 | timestep 0.00025 25 | 26 | fix 1 all ipi fullcent3 13234 unix 27 | 28 | run 1000000000 29 | 30 | -------------------------------------------------------------------------------- /examples/lammps/benz-graph-slc/in.partbeads: -------------------------------------------------------------------------------- 1 | dimension 3 2 | boundary p p p 3 | 4 | atom_style atomic 5 | 6 | units metal 7 | 8 | 9 | read_data data.part 10 | mass 1 12 11 | mass 2 1 12 | 13 | group C type 1 14 | group H type 2 15 | 16 | neighbor 0.5 bin 17 | neigh_modify delay 1 18 | 19 | 20 | pair_style airebo 3 1 1 21 | 22 | pair_coeff * * ./CH.airebo C H 23 | 24 | timestep 0.00025 25 | 26 | fix 1 all ipi benzenebeads3 13234 unix 27 | 28 | run 1000000000 29 | 30 | -------------------------------------------------------------------------------- /examples/lammps/benz-graph-slc/in.partcontr: -------------------------------------------------------------------------------- 1 | dimension 3 2 | boundary p p p 3 | 4 | atom_style atomic 5 | 6 | units metal 7 | 8 | 9 | read_data data.part 10 | mass 1 12 11 | mass 2 1 12 | 13 | group C type 1 14 | group H type 2 15 | 16 | neighbor 0.5 bin 17 | neigh_modify delay 1 18 | 19 | 20 | pair_style airebo 3 1 1 21 | 22 | pair_coeff * * ./CH.airebo C H 23 | 24 | timestep 0.00025 25 | 26 | fix 1 all ipi benzenecent3 13234 unix 27 | 28 | run 1000000000 29 | 30 | -------------------------------------------------------------------------------- /examples/lammps/graphene/in.lmp: -------------------------------------------------------------------------------- 1 | atom_style atomic 2 | units metal 3 | dimension 3 4 | boundary p p p 5 | processors * * 1 6 | 7 | read_data ./data.lmp 8 | mass 1 12.01 ##Carbon 9 | 10 | ### Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010) 11 | pair_style tersoff 12 | pair_coeff * * C.opt.tersoff C(O) 13 | 14 | variable T equal 300 15 | variable V equal vol 16 | 17 | variable Lx equal xhi-xlo 18 | variable Ly equal yhi-ylo 19 | print "Lx = ${Lx} A" 20 | print "Ly = ${Ly} A" 21 | 22 | print "Volume simulation box = $V A^(3)" 23 | variable Volume equal v_Lx*v_Ly*3.35 24 | print "Volume = Lx*Ly*3.35A = ${Volume} A^(3)" 25 | 26 | velocity all create $T 345352 mom yes rot yes dist gaussian 27 | timestep 0.001 # 0.001 picosecond = 1 femtosecond 28 | thermo 1000 29 | thermo_style custom step temp pe etotal press pxx pyy pzz 30 | 31 | fix 1 all ipi graphene 31415 unix 32 | run 5000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-alchemical/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 h2o-alchemical 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-bias/in.water_longrange: -------------------------------------------------------------------------------- 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_longrange 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi mts_long 32347 unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-bias/in.water_shortrange: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_shortrange 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi mts_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/h2o-enmfdphonons/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 | -------------------------------------------------------------------------------- /examples/lammps/h2o-enmfdphonons/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 h2o-enmfdphonons 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-enmfdphonons/init.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 35.23300 35.23300 35.23300 90.00000 90.00000 90.00000 Traj: positions{angstrom} Step: 11 Bead: 0 3 | O 1.91256e-15 -1.90815e-02 -2.45668e-19 4 | H 7.59037e-01 5.38718e-01 7.25346e-20 5 | H -7.59037e-01 5.38718e-01 -1.29482e-20 6 | -------------------------------------------------------------------------------- /examples/lammps/h2o-enmfdphonons/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential ] 4 | 5 | 5000 6 | 7 | 32342 8 | 9 | 10 |
h2o-enmfdphonons
11 | 12 | 13 | 14 | init.xyz 15 | 16 | 17 | 18 | 19 | 20 | 21 | data.dynmat 22 | 0.001 23 | 0.001 24 | simulation 25 | crystal 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /examples/lammps/h2o-extreme-rem/in.water_longrange: -------------------------------------------------------------------------------- 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_h2o.longrange 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | # thermo_style multi 24 | # thermo 1 25 | 26 | # fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi remd_long 32347 unix 29 | 30 | #dump 1 all xyz 1 dump.xyz 31 | 32 | run 100000000 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-extreme-rem/in.water_shortrange: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_h2o.shortrange 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | #neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi remd_short 32346 unix 30 | 31 | #dump 1 all xyz 1 dump.xyz 32 | 33 | run 100000000 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-fdphonons/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 | -------------------------------------------------------------------------------- /examples/lammps/h2o-fdphonons/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 h2o-fdphonons 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-fdphonons/init.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 35.23300 35.23300 35.23300 90.00000 90.00000 90.00000 Traj: positions{angstrom} Step: 11 Bead: 0 3 | O 1.91256e-15 -1.90815e-02 -2.45668e-19 4 | H 7.59037e-01 5.38718e-01 7.25346e-20 5 | H -7.59037e-01 5.38718e-01 -1.29482e-20 6 | -------------------------------------------------------------------------------- /examples/lammps/h2o-fdphonons/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential ] 4 | 5 | 5000 6 | 7 | 32342 8 | 9 | 10 |
h2o-fdphonons
11 | 12 | 13 | 14 | init.xyz 15 | 16 | 17 | 18 | 19 | 20 | 21 | 0.001 22 | 0.001 23 | simulation 24 | poly 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /examples/lammps/h2o-fixatoms/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 9.695398182254587 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data data.lmp 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 fixatoms 32345 unix 18 | run 100000000 19 | 20 | -------------------------------------------------------------------------------- /examples/lammps/h2o-geop/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 | -------------------------------------------------------------------------------- /examples/lammps/h2o-geop/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 h2o-geop 32346 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-geop/init.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 35.23300 35.23300 35.23300 90.00000 90.00000 90.00000 Traj: positions{angstrom} Step: 11 Bead: 0 3 | O 0.00000e+00 -2.00000e-02 0.00000e+00 4 | H 7.50000e-01 5.00000e-01 0.00000e+00 5 | H -7.50000e-01 5.00000e-01 0.00000e+00 6 | -------------------------------------------------------------------------------- /examples/lammps/h2o-geop/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential ] 4 | positions 5 | 6 | 1000 7 | 8 | 32342 9 | 10 | 11 |
h2o-geop
12 | 13 | 14 | 15 | init.xyz 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 1e-5 24 | 1e-5 25 | 1e-5 26 | 27 | 28 | 29 | 30 | 31 | -------------------------------------------------------------------------------- /examples/lammps/h2o-multi/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 h2o-multi 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-open-all/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 11.7 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data data.lmp 10 | pair_coeff * * 0 0 11 | pair_coeff 1 1 0.000295147 5.96946 12 | neighbor 2.0 bin 13 | timestep 0.00025 14 | fix 1 all ipi qtip4pf 32345 unix 15 | 16 | run 100000000 17 | -------------------------------------------------------------------------------- /examples/lammps/h2o-open-one/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 11.7 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data data.lmp 10 | pair_coeff * * 0 0 11 | pair_coeff 1 1 0.000295147 5.96946 12 | neighbor 2.0 bin 13 | timestep 0.00025 14 | fix 1 all ipi qtip4pf 32345 unix 15 | 16 | run 100000000 17 | -------------------------------------------------------------------------------- /examples/lammps/h2o-piglet.2/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 h2o-piglet.2 32344 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-piglet.4/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 h2o-piglet.4 32344 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-piglet.8/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 h2o-piglet.8 32342 unix 28 | 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+mts.4/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+mts.4_long 32347 unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+mts.4/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+mts.4_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+rpc/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+rpc_long 32347 unix reset 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+rpc/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+rpc_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+sc+gle.4/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 h2o-pimd+sc+gle.4 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+sc+mts/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 h2o-pimd+sc+mts 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+sc+rpc/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+sc+rpc_long 32347 unix reset 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+sc+rpc/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+sc+rpc_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd+sc/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 h2o-pimd+sc 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd.1/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd.1/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal} ] 4 | positions 5 | 6 | 7 | 10000 8 | 9 | 31415 10 | 11 | 12 |
h2o-pimd.1
13 | 14 | 15 | 16 | init.pdb 17 | 300 18 | 19 | 20 | 21 | 22 | 23 | 24 | 0.5 25 | 26 | 100 27 | 28 | 29 | 30 | 31 | 300 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd.4/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 h2o-pimd.4 32345 unix 28 | 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-pimd.4/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv{megapascal} ] 4 | positions 5 | 6 | 7 | 10000 8 | 9 | 32415 10 | 11 | 12 |
h2o-pimd.4
13 | 14 | 15 | 16 | init.pdb 17 | 300 18 | 19 | 20 | 21 | 22 | 23 | 24 | 0.25 25 | 26 | 100 27 | 28 | 29 | 30 | 31 | 300 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/h2o-remd-bias/in.water_longrange: -------------------------------------------------------------------------------- 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_longrange 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi mts_long 32347 unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/h2o-remd-bias/in.water_shortrange: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_shortrange 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi mts_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/h2o-repimd/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | #pair_style lj/long/tip4p/long cut long 1 2 1 1 0.278072379 11.7 5 | #bond_style class2 6 | #angle_style harmonic 7 | #kspace_style pppm/disp/tip4p 1e-4 8 | 9 | pair_style lj/long/tip4p/long long long 1 2 1 1 0.278072379 11.707 10 | bond_style class2 11 | angle_style harmonic 12 | kspace_style pppm/disp/tip4p 0.0001 13 | kspace_modify force/disp/real 0.0001 14 | kspace_modify force/disp/kspace 0.0001 15 | 16 | read_data data.lmp 17 | pair_coeff * * 0 0 18 | pair_coeff 1 1 0.000295147 5.96946 19 | neighbor 2.0 bin 20 | timestep 0.00025 21 | fix 1 all ipi f1 32345 unix 22 | 23 | run 100000000 24 | -------------------------------------------------------------------------------- /examples/lammps/h2o-trpmd/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 h2o-trpmd 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/lammps/ice-npt/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. 6 | #bond_style harmonic 7 | bond_style class2 8 | angle_style harmonic 9 | kspace_style ewald 0.0001 10 | 11 | read_data data.lmp 12 | pair_coeff * * 0 0 13 | pair_coeff 1 1 0.000295147 5.96946 14 | 15 | neighbor 2.0 bin 16 | 17 | timestep 0.00025 18 | 19 | #velocity all create 298.0 2345187 20 | 21 | #thermo_style multi 22 | #thermo 1 23 | 24 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 25 | #fix 1 all nve 26 | fix 1 all ipi ice-npt 32345 unix 27 | 28 | #dump 1 all xyz 25 dump.xyz 29 | 30 | run 100000000 31 | 32 | -------------------------------------------------------------------------------- /examples/lammps/ice-nst/in.lmp: -------------------------------------------------------------------------------- 1 | units real 2 | atom_style full 3 | 4 | read_data data.lmp 5 | 6 | # TIP4PF in current LAMMPS does not give the correct stress with triclinic boxes... 7 | # pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 7 8 | pair_style lj/cut/coul/long 8 9 | 10 | pair_coeff * * 0 0 11 | pair_coeff 1 1 0.18508368 3.1589022 12 | 13 | bond_style class2 14 | angle_style harmonic 15 | kspace_style ewald 0.0001 16 | 17 | #qtip4pf bond parameters 18 | bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577 19 | angle_coeff 1 43.93 107.4 20 | 21 | neighbor 2.0 bin 22 | 23 | timestep 0.0001 24 | 25 | fix 1 all ipi ice-nst 32345 unix 26 | 27 | run 100000000 28 | 29 | -------------------------------------------------------------------------------- /examples/lammps/isof-vapor/in.lmp: -------------------------------------------------------------------------------- 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.lmp 9 | pair_coeff * * 0 0.1 10 | 11 | #atom_modify sort 1 3.00 12 | neighbor 2.0 bin 13 | neigh_modify delay 0 every 1 check yes 14 | 15 | timestep 0.00025 16 | 17 | #velocity all create 298.0 2345187 18 | 19 | #thermo_style multi 20 | #thermo 1 21 | 22 | fix 1 all ipi isof-vapor 32346 unix 23 | 24 | #dump 1 all xyz 25 dump.xyz 25 | 26 | run 100000000 27 | 28 | -------------------------------------------------------------------------------- /examples/lammps/isof-vapor/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, 4 | pressure_cv{megapascal},isotope_zetasc(1.998;H), isotope_zetasc(1.1253;O)] 5 | positions 6 | 7 | 500000 8 | 9 | 32346 10 | 11 | 12 |
isof-vapor
13 | 14 | 15 | 16 | init.pdb 17 | 298 18 | 19 | 20 | 21 | 22 | 23 | 298 24 | 25 | 26 | 27 | 28 | 100 29 | 30 | 0.25 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/isof-water/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 isof-water 32345 unix 28 | #fix 1 all driver no_rpc unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/isof-water/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, 4 | pressure_cv{megapascal}, isotope_zetasc(1.998;H), isotope_zetasc(1.1253;O)] 5 | positions 6 | 7 | 500000 8 | 9 | 32345 10 | 11 | 12 |
isof-water
13 | 14 | 15 | 16 | init.pdb 17 | 298 18 | 19 | 20 | 21 | 22 | 23 | 298 24 | 25 | 26 | 27 | 28 | 25 29 | 30 | 0.25 31 | 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /examples/lammps/isofsc-vapor/in.lmp: -------------------------------------------------------------------------------- 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.lmp 9 | pair_coeff * * 0 0.1 10 | 11 | #atom_modify sort 1 3.00 12 | neighbor 2.0 bin 13 | neigh_modify delay 0 every 1 check yes 14 | 15 | timestep 0.00025 16 | 17 | #velocity all create 298.0 2345187 18 | 19 | #thermo_style multi 20 | #thermo 1 21 | 22 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 23 | #fix 1 all nve 24 | fix 1 all ipi isofsc-vapor 32346 unix 25 | 26 | #dump 1 all xyz 25 dump.xyz 27 | 28 | run 100000000 29 | 30 | -------------------------------------------------------------------------------- /examples/lammps/isofsc-vapor/process_dif.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | 3 | table1 = np.loadtxt('accumulated.out.w') 4 | table2 = np.loadtxt('accumulated.out.v') 5 | 6 | 7 | (asize1, bsize) = np.shape(table1) 8 | (asize2, bsize) = np.shape(table2) 9 | 10 | if asize1 > asize2: 11 | asize = asize2 12 | else: 13 | asize = asize1 14 | 15 | out = np.zeros((asize, 3)) 16 | 17 | count = 0 18 | 19 | for a in range(asize): 20 | out[a][0] = table1[a][0] 21 | out[a][1] = table1[a][3] - table2[a][3] 22 | out[a][2] = table1[a][6] - table2[a][6] 23 | 24 | 25 | np.savetxt('1000loga.out', out) 26 | -------------------------------------------------------------------------------- /examples/lammps/isofsc-water/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 isofsc-water 32345 unix 28 | #fix 1 all driver no_rpc unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/lammps/paracetamol-geop/in.lmp: -------------------------------------------------------------------------------- 1 | # Created by charmm2lammps v1.8.1 on Wed Oct 8 17:52:44 CEST 2014 2 | 3 | units real 4 | neigh_modify delay 2 every 1 5 | 6 | atom_style full 7 | bond_style harmonic 8 | angle_style charmm 9 | dihedral_style charmm 10 | improper_style harmonic 11 | 12 | pair_style lj/charmm/coul/long 8 10 13 | pair_modify mix arithmetic 14 | kspace_style pppm 1e-6 15 | 16 | read_data data.lmp 17 | 18 | special_bonds charmm 19 | fix 1 all ipi paracetamol-geop 1234 unix reset 20 | 21 | thermo 100 22 | thermo_style one 23 | #timestep 0.5 24 | 25 | #restart 10 gammabox.restart1 gammabox.restart2 26 | #dump_modify 1 image yes scale yes 27 | #dump 1 all xyz 100 alphalmp.xyz 28 | 29 | run 19999999 30 | -------------------------------------------------------------------------------- /examples/lammps/paracetamol-geop/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential ] 4 | positions 5 | 6 | 2000000 7 | 8 |
paracetamol-geop
9 | 1e-4 10 | 11 | 12 | 13 | init.xyz 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 1e-7 22 | 1e-4 23 | 1e-4 24 | 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /examples/lammps/paracetamol-phonons/in.lmp: -------------------------------------------------------------------------------- 1 | # Created by charmm2lammps v1.8.1 on Wed Oct 8 17:52:44 CEST 2014 2 | 3 | units real 4 | neigh_modify delay 2 every 1 5 | 6 | atom_style full 7 | bond_style harmonic 8 | angle_style charmm 9 | dihedral_style charmm 10 | improper_style harmonic 11 | 12 | pair_style lj/charmm/coul/long 8 10 13 | pair_modify mix arithmetic 14 | 15 | box tilt large 16 | read_data data.lmp 17 | 18 | kspace_style pppm 1e-4 19 | 20 | special_bonds charmm 21 | fix 1 all ipi paracetamol-phonons 1234 unix 22 | 23 | thermo 100 24 | thermo_style one 25 | timestep 0.5 26 | 27 | #restart 10 gammabox.restart1 gammabox.restart2 28 | #dump_modify 1 image yes scale yes 29 | #dump 1 all xyz 100 alphalmp.xyz 30 | 31 | 32 | run 1999999999 33 | -------------------------------------------------------------------------------- /examples/lammps/paracetamol-phonons/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential] 4 | 5 | 100000 6 | 7 | 32342 8 | 9 | 10 |
paracetamol-phonons
11 | 12 | 13 | 14 | init.xyz 15 | 16 | 17 | 18 | 19 | 20 | 21 | 0.01 22 | 0.0009500 23 | simulation-fd 24 | crystal 25 | 26 | 27 | 28 | 29 | -------------------------------------------------------------------------------- /examples/lj/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the Lennard-Jones Neon examples 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | .PHONY: all clean high_density mid_density low_density nst 8 | all: high_density mid_density low_density nst 9 | 10 | driver:=i-pi-driver 11 | IPI:=i-pi 12 | 13 | define run_driver 14 | for i in `seq 1 $1`; do \ 15 | $(driver) -u -h $2 -m lj -o 5.270446,1.1663e-4,13.176115 & \ 16 | done; 17 | endef 18 | 19 | high_density: 20 | cd high_density; $(IPI) input.xml & sleep 5; \ 21 | $(call run_driver,1,high_density) \ 22 | wait 23 | 24 | mid_density: 25 | cd mid_density; $(IPI) input.xml & sleep 5; \ 26 | $(call run_driver,1,mid_density) \ 27 | wait 28 | 29 | low_density: 30 | cd low_density; $(IPI) input.xml & sleep 5; \ 31 | $(call run_driver,1,low_density) \ 32 | wait 33 | 34 | nst: 35 | cd nst; $(IPI) input.xml & sleep 5; \ 36 | $(call run_driver,1,nst) \ 37 | wait 38 | 39 | clean: 40 | rm -f */*simulation* */*RESTART* */EXIT 41 | -------------------------------------------------------------------------------- /examples/lj/high_density/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_md{kelvin}, potential{kelvin}, pressure_md{megapascal}] 4 | positions 5 | 6 | 7 | 100000 8 | 9 | 3848 10 | 11 | 12 |
high_density
13 | 14 | 15 | 16 | init.pdb 17 | 80 18 | 19 | 20 | 21 | 22 | 23 | 40.32753474 24 | 25 | 26 | 27 | 28 | 25 29 | 30 | 1.0 31 | 32 | False 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /examples/lj/low_density/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_md{kelvin}, potential{kelvin}, pressure_md{megapascal}] 4 | positions 5 | 6 | 7 | 100000 8 | 9 | 3848 10 | 11 | 12 |
low_density
13 | 14 | 15 | 16 | init.pdb 17 | 120 18 | 19 | 20 | 21 | 22 | 23 | 59.6646 24 | 25 | 26 | 27 | 28 | 25 29 | 30 | 1.0 31 | 32 | False 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /examples/lj/mid_density/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_md{kelvin}, potential{kelvin}, pressure_md{megapascal}] 4 | positions 5 | 6 | 7 | 100000 8 | 9 | 3848 10 | 11 | 12 |
mid_density
13 | 14 | 15 | 16 | init.pdb 17 | 80 18 | 19 | 20 | 21 | 22 | 23 | 39.36998597 24 | 25 | 26 | 27 | 28 | 25 29 | 30 | 1.0 31 | 32 | False 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /examples/lm/iron-piglet/init.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | # H interstitial in a-Fe positions{angstrom} cell{angstrom} CELL{abcABC}: 5.74 5.74 5.74 90 90 90 3 | Fe -0.00000 -0.01541 -0.00885 4 | Fe 1.35315 1.39055 1.43500 5 | Fe 2.87000 0.00636 0.00583 6 | Fe 4.38685 1.39055 1.43500 7 | Fe -0.00000 2.87379 -0.00113 8 | Fe 1.44083 4.29864 1.43500 9 | Fe 2.87000 2.91445 -0.08185 10 | Fe 4.29917 4.29864 1.43500 11 | Fe 0.00000 -0.01541 2.87885 12 | Fe 1.43387 1.43121 4.30500 13 | Fe 2.87000 0.00636 2.86417 14 | Fe 4.30613 1.43121 4.30500 15 | Fe -0.00000 2.87379 2.87113 16 | Fe 1.42615 4.32041 4.30500 17 | Fe 2.87000 2.91445 2.95185 18 | Fe 4.31385 4.32041 4.30500 19 | H 2.87000 2.15250 1.43500 20 | -------------------------------------------------------------------------------- /examples/lm/iron-pimd/init.xyz: -------------------------------------------------------------------------------- 1 | 17 2 | # H interstitial in a-Fe positions{angstrom} cell{angstrom} CELL{abcABC}: 5.74 5.74 5.74 90 90 90 3 | Fe -0.00000 -0.01541 -0.00885 4 | Fe 1.35315 1.39055 1.43500 5 | Fe 2.87000 0.00636 0.00583 6 | Fe 4.38685 1.39055 1.43500 7 | Fe -0.00000 2.87379 -0.00113 8 | Fe 1.44083 4.29864 1.43500 9 | Fe 2.87000 2.91445 -0.08185 10 | Fe 4.29917 4.29864 1.43500 11 | Fe 0.00000 -0.01541 2.87885 12 | Fe 1.43387 1.43121 4.30500 13 | Fe 2.87000 0.00636 2.86417 14 | Fe 4.30613 1.43121 4.30500 15 | Fe -0.00000 2.87379 2.87113 16 | Fe 1.42615 4.32041 4.30500 17 | Fe 2.87000 2.91445 2.95185 18 | Fe 4.31385 4.32041 4.30500 19 | H 2.87000 2.15250 1.43500 20 | -------------------------------------------------------------------------------- /examples/pes-regtest/io-units/h2o-angstrom.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 18.89726 18.89726 18.89726 90.00000 90.00000 90.00000 Step: 40 Bead: 2 positions{angstrom} cell{atomic_unit} 3 | O 4.97336e+00 4.92337e+00 4.96921e+00 4 | H 5.71284e+00 5.57553e+00 4.90940e+00 5 | H 5.01842e+00 4.53605e+00 4.05255e+00 6 | -------------------------------------------------------------------------------- /examples/pes-regtest/io-units/h2o-nocomment.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | 3 | O 5.00000 5.00000 5.00000 4 | H 5.98343 5.00000 5.00000 5 | H 4.84583 4.376419 4.10217 6 | -------------------------------------------------------------------------------- /examples/pes-regtest/io-units/h2o-velocities.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 18.89726 18.89726 18.89726 90.00000 90.00000 90.00000 Step: 40 Bead: 2 velocities{atomic_unit} cell{atomic_unit} 3 | O -1.57474e-04 -6.43328e-04 -3.02692e-04 4 | H 4.75131e-04 1.92827e-03 -9.58797e-04 5 | H 1.42102e-03 2.09636e-03 2.30678e-03 6 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/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 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/instanton/40/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: 9 Bead: 0 3 | H 1.33370e+00 1.59787e+00 1.35300e+00 4 | C 5.77568e-01 7.10503e-01 5.95431e-01 5 | H 1.00494e-04 1.08773e-01 1.29743e+00 6 | H 1.28079e+00 1.06096e-01 2.22598e-02 7 | H -6.31180e-02 1.31234e+00 -4.92875e-02 8 | H 1.80833e+00 2.15490e+00 1.82860e+00 9 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/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 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/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 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/reactant/minization/run_all: -------------------------------------------------------------------------------- 1 | 2 | rm /tmp/ipi_localhost 3 | 4 | ipi=/home/litman/Yair/Instanton/I-PI-mc/i-pi-mc/bin/i-pi 5 | driver=/home/litman/Yair/Instanton/I-PI-mc/i-pi-mc/drivers/driver.x 6 | 7 | file='input.xml' 8 | 9 | echo "1" >>LIST 10 | a=$(cat LIST | wc -l) 11 | b=$((a+40050)) 12 | sed -e "s:.*:$b:" $file > tmp 13 | 14 | mv tmp $file 15 | 16 | python $ipi $file & 17 | sleep 2 18 | $driver -u -m ch4hcbe >driver.log & 19 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/reactant/phonons/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 130.18034 170.29206 240.21758 90.00000 90.00000 90.00000 cell{atomic_unit} Traj: x_centroid{angstrom} Step: 31 Bead: 0 3 | H 1.63090e+00 1.36266e+00 1.15180e+00 4 | C 8.44971e-01 7.89691e-01 6.62016e-01 5 | H 1.29316e+00 6.34936e-02 -1.44182e-02 6 | H 2.02546e-01 1.46367e+00 9.72790e-02 7 | H 2.53290e-01 2.69002e-01 1.41347e+00 8 | H 5.82907e+00 2.17934e+00 1.85263e+00 9 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/reactant/phonons/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | 6 | 400 7 | 8 |
localhost
9 | 10 | 11 | 12 | init.xyz 13 | [200.0, 200.0, 200.0 ] 14 | 15 | 16 | 17 | 18 | 19 | 20 | 0.01 21 | phonons 22 | none 23 | 24 | 25 | 26 | 27 | -------------------------------------------------------------------------------- /examples/pes/CH4H-CBE/instanton-rate/reactant/phonons/run_all: -------------------------------------------------------------------------------- 1 | 2 | rm /tmp/ipi_localhost 3 | 4 | ipi=/home/litman/Yair/Instanton/I-PI-mc/i-pi-mc/bin/i-pi 5 | driver=/home/litman/Yair/Instanton/I-PI-mc/i-pi-mc/drivers/driver.x 6 | 7 | file='input.xml' 8 | 9 | echo "1" >>LIST 10 | a=$(cat LIST | wc -l) 11 | b=$((a+40050)) 12 | sed -e "s:.*:$b:" $file > tmp 13 | 14 | mv tmp $file 15 | 16 | python $ipi $file & 17 | sleep 2 18 | $driver -u -m ch4hcbe >driver.log & 19 | -------------------------------------------------------------------------------- /examples/pes/geop/README.md: -------------------------------------------------------------------------------- 1 | example with qTIP4P/f water model 2 | --------------------------------- 3 | 4 | One runs i-PI as usual, followed by one or more instances of the driver: 5 | 6 | ```bash 7 | i-pi input.xml & 8 | i-pi-driver -u -h driver -m qtip4pf 9 | ``` 10 | 11 | Remember that the `/env.sh` file must be sourced before running 12 | `i-pi` or `i-pi-driver`: 13 | 14 | ```bash 15 | source /env.sh 16 | ``` 17 | -------------------------------------------------------------------------------- /examples/pes/geop/waterbox/sd/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] 4 | positions{angstrom} 5 | 6 | 5000 7 | 8 | 32342 9 | 10 | 11 |
driver
12 | 13 | 14 | 15 | init.pdb 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 1.0e-3 24 | 1.0e-5 25 | 150 26 | 1.0 27 | 28 | 29 | 1.0e-7 30 | 1.0e-3 31 | 1.0e-7 32 | 33 | 34 | 35 | 36 | 37 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/book/init.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | 3 | O 4.290374 5.710696 4.899163 4 | H 3.598667 5.431455 4.292665 5 | H 4.102539 5.249263 5.753222 6 | O 7.086550 4.864191 4.983082 7 | H 6.179056 5.094748 4.732142 8 | H 7.549984 5.724283 4.992154 9 | O 8.030289 7.492524 5.021932 10 | H 7.140990 7.896945 4.978048 11 | H 8.510682 7.859666 4.275061 12 | O 5.375238 8.263526 4.900409 13 | H 4.961644 8.819977 5.565552 14 | H 4.889641 7.416305 4.931906 15 | O 4.026124 4.356559 7.195224 16 | H 3.795243 4.775253 8.028687 17 | H 4.936378 3.997578 7.326148 18 | O 6.598471 3.592587 7.296936 19 | H 6.905593 4.037489 6.469770 20 | H 6.898937 2.682856 7.225999 21 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/book/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] 4 | positions{angstrom} 5 | 6 | 5000 7 | 8 | 32342 9 | 10 | 11 |
driver
12 | 13 | 14 | 15 | init.xyz 16 | [45.0, 45.0, 45.0] 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/cage/init.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | config="cage" Lattice="50 0 0 0 50 0 0 0 50" Properties=species:S:1:pos:R:3 E_BLYP_AV5Z=-0.0256 E_CCSDt=0.0106 E_DMC=0.0144 3 | O 0.795403 0.512402 -1.576241 4 | H 0.348365 -0.346589 -1.512112 5 | H 1.659238 0.356916 -1.148623 6 | O 0.638863 -0.555826 1.663468 7 | H 0.200925 0.296803 1.517640 8 | H 0.185508 -1.142184 1.036614 9 | O 2.882899 0.096173 0.205166 10 | H 2.222577 -0.219539 0.857220 11 | H 3.649689 -0.473141 0.305787 12 | O -0.781556 -1.711613 -0.598538 13 | H -1.624410 -1.231456 -0.440213 14 | H -1.027171 -2.577446 -0.935940 15 | O -2.789349 0.029507 -0.044619 16 | H -3.322563 -0.042852 0.751943 17 | H -2.171278 0.770168 0.124159 18 | O -0.649976 1.711042 0.309216 19 | H -0.082320 1.399426 -0.445913 20 | H -0.584941 2.670109 0.31418618 21 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/cage/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] 4 | positions{angstrom} 5 | 6 | 5000 7 | 8 | 32342 9 | 10 | 11 |
driver
12 | 13 | 14 | 15 | init.xyz 16 | [15.0, 15.0, 15.0] 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/prism/init.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | config="prism" Lattice="50 0 0 0 50 0 0 0 50" Properties=species:S:1:pos:R:3 E_BLYP_AV5Z=0.0 E_CCSDt=0.0 E_DMC=0.0 3 | O 1.519957 -0.391505 1.369232 4 | H 0.589965 -0.720789 1.503428 5 | H 2.026756 -0.696488 2.126741 6 | O 0.729439 1.955476 -0.060179 7 | H 1.095772 1.403156 0.649540 8 | H 1.092258 1.529889 -0.849408 9 | O 1.659463 -0.484158 -1.388254 10 | H 2.380676 -0.919251 -1.851586 11 | H 1.821572 -0.631544 -0.436121 12 | O -1.906281 1.232137 -0.003704 13 | H -1.005916 1.625724 -0.031994 14 | H -2.516801 1.971719 -0.066999 15 | O -1.144366 -1.246745 -1.352774 16 | H -0.220096 -1.038480 -1.562838 17 | H -1.559178 -0.378664 -1.235377 18 | O -1.020955 -1.144143 1.425992 19 | H -1.097352 -1.450732 0.498715 20 | H -1.529916 -0.320705 1.388689 21 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/prism/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] 4 | positions{angstrom} 5 | 6 | 5000 7 | 8 | 32342 9 | 10 | 11 |
driver
12 | 13 | 14 | 15 | init.xyz 16 | [15.0, 15.0, 15.0] 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/ring/bfgs/init.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | config="ring" Lattice="50 0 0 0 50 0 0 0 50" Properties=species:S:1:pos:R:3 E_BLYP_AV5Z=-0.1060 E_CCSDt=0.0735 E_DMC=0.0667 3 | O 4.461673 5.294623 8.790681 4 | H 4.566428 5.800524 7.980776 5 | H 5.313898 4.817401 8.906505 6 | O 6.817017 3.994841 9.090651 7 | H 7.338665 4.178157 9.876230 8 | H 6.825512 3.015434 9.000464 9 | O 6.857846 1.298087 8.860614 10 | H 7.246565 0.916849 8.069152 11 | H 6.018156 0.804312 8.996819 12 | O 2.198450 1.222690 8.917519 13 | H 1.676782 1.039354 8.131958 14 | H 2.189957 2.202099 9.007682 15 | O 2.157622 3.919450 9.147487 16 | H 1.768883 4.300707 9.938930 17 | H 2.997314 4.413222 9.011289 18 | O 4.553801 -0.077092 9.217447 19 | H 3.701575 0.400132 9.101638 20 | H 4.449060 -0.582990 10.027356 21 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/ring/cg/init.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | config="ring" Lattice="50 0 0 0 50 0 0 0 50" Properties=species:S:1:pos:R:3 E_BLYP_AV5Z=-0.1060 E_CCSDt=0.0735 E_DMC=0.0667 3 | O 4.461673 5.294623 8.790681 4 | H 4.566428 5.800524 7.980776 5 | H 5.313898 4.817401 8.906505 6 | O 6.817017 3.994841 9.090651 7 | H 7.338665 4.178157 9.876230 8 | H 6.825512 3.015434 9.000464 9 | O 6.857846 1.298087 8.860614 10 | H 7.246565 0.916849 8.069152 11 | H 6.018156 0.804312 8.996819 12 | O 2.198450 1.222690 8.917519 13 | H 1.676782 1.039354 8.131958 14 | H 2.189957 2.202099 9.007682 15 | O 2.157622 3.919450 9.147487 16 | H 1.768883 4.300707 9.938930 17 | H 2.997314 4.413222 9.011289 18 | O 4.553801 -0.077092 9.217447 19 | H 3.701575 0.400132 9.101638 20 | H 4.449060 -0.582990 10.027356 21 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/ring/lbfgs/init.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | config="ring" Lattice="50 0 0 0 50 0 0 0 50" Properties=species:S:1:pos:R:3 E_BLYP_AV5Z=-0.1060 E_CCSDt=0.0735 E_DMC=0.0667 3 | O 4.461673 5.294623 8.790681 4 | H 4.566428 5.800524 7.980776 5 | H 5.313898 4.817401 8.906505 6 | O 6.817017 3.994841 9.090651 7 | H 7.338665 4.178157 9.876230 8 | H 6.825512 3.015434 9.000464 9 | O 6.857846 1.298087 8.860614 10 | H 7.246565 0.916849 8.069152 11 | H 6.018156 0.804312 8.996819 12 | O 2.198450 1.222690 8.917519 13 | H 1.676782 1.039354 8.131958 14 | H 2.189957 2.202099 9.007682 15 | O 2.157622 3.919450 9.147487 16 | H 1.768883 4.300707 9.938930 17 | H 2.997314 4.413222 9.011289 18 | O 4.553801 -0.077092 9.217447 19 | H 3.701575 0.400132 9.101638 20 | H 4.449060 -0.582990 10.027356 21 | -------------------------------------------------------------------------------- /examples/pes/geop/waterhexamers/ring/sd/init.xyz: -------------------------------------------------------------------------------- 1 | 18 2 | config="ring" Lattice="50 0 0 0 50 0 0 0 50" Properties=species:S:1:pos:R:3 E_BLYP_AV5Z=-0.1060 E_CCSDt=0.0735 E_DMC=0.0667 3 | O 4.461673 5.294623 8.790681 4 | H 4.566428 5.800524 7.980776 5 | H 5.313898 4.817401 8.906505 6 | O 6.817017 3.994841 9.090651 7 | H 7.338665 4.178157 9.876230 8 | H 6.825512 3.015434 9.000464 9 | O 6.857846 1.298087 8.860614 10 | H 7.246565 0.916849 8.069152 11 | H 6.018156 0.804312 8.996819 12 | O 2.198450 1.222690 8.917519 13 | H 1.676782 1.039354 8.131958 14 | H 2.189957 2.202099 9.007682 15 | O 2.157622 3.919450 9.147487 16 | H 1.768883 4.300707 9.938930 17 | H 2.997314 4.413222 9.011289 18 | O 4.553801 -0.077092 9.217447 19 | H 3.701575 0.400132 9.101638 20 | H 4.449060 -0.582990 10.027356 21 | -------------------------------------------------------------------------------- /examples/pes/neb/README.md: -------------------------------------------------------------------------------- 1 | Neb example 2 | ------------- 3 | 4 | Once the env.sh file in the i-pi root directory has been sourced with 5 | 6 | ```bash 7 | source /env.sh 8 | ``` 9 | 10 | Run i-pi with: 11 | 12 | ```bash 13 | i-pi input.xml 14 | ``` 15 | 16 | And the driver: 17 | 18 | ```bash 19 | i-pi-driver -u -h driver -p 20614 -m zundel 20 | ``` 21 | -------------------------------------------------------------------------------- /examples/pes/pswater/README.md: -------------------------------------------------------------------------------- 1 | A test and example for the Partridge-Schwenke water 2 | monomer potential 3 | 4 | To run the example: 5 | ------------------- 6 | 7 | ipi input.xml 8 | ../../bin/i-pi-driver -u -h driver -m pswater 9 | 10 | Make sure drivers is compiled. Read the README in ROOT/drivers 11 | -------------------------------------------------------------------------------- /examples/pes/pswater/init.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | 3 | O 5.00000 5.00000 5.00000 4 | H 5.98343 5.00000 5.00000 5 | H 4.84583 4.376419 4.10217 6 | -------------------------------------------------------------------------------- /examples/pes/pswater/phonon/init.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 35.23300 35.23300 35.23300 90.00000 90.00000 90.00000 Traj: positions{angstrom} Step: 8 Bead: 0 3 | O -1.96649e+01 2.81536e+01 -4.02277e+01 4 | H -1.92002e+01 2.73195e+01 -4.03040e+01 5 | H -2.03258e+01 2.81244e+01 -4.09204e+01 6 | -------------------------------------------------------------------------------- /examples/pes/pswater/phonon/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal}] 4 | positions{angstrom} 5 | 6 | 1000 7 | 8 | 32342 9 | 10 | 11 |
driver
12 | 13 | 14 | 15 | init.xyz 16 | [35.233, 35.233, 35.233] 17 | 18 | 19 | 20 | 21 | 22 | 23 | 0.001 24 | 25 | 26 | 27 | 28 | -------------------------------------------------------------------------------- /examples/pes/qtip4pf/tun-splitting/TS/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 30 Bead: 0 positions{angstrom} cell{atomic_unit} 3 | O 1.35946e-01 -9.67988e-01 2.41370e-01 4 | H -7.79760e-01 -8.68954e-01 3.01041e-02 5 | H 5.35490e-01 -1.44232e+00 -4.71603e-01 6 | O 1.42452e+00 1.38886e+00 9.26138e-01 7 | H 1.509691 2.100034 1.326755 8 | H 9.82027e-01 5.67085e-01 7.04984e-01 9 | 10 | 11 | -------------------------------------------------------------------------------- /examples/pes/qtip4pf/tun-splitting/instanton/32-lbfgs/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 17 Bead: 0 positions{angstrom} cell{atomic_unit} 3 | O 1.00771e-01 -9.27528e-01 2.18380e-01 4 | H -7.09363e-01 -1.40515e+00 2.94863e-01 5 | H 6.82525e-01 -1.45012e+00 -3.12944e-01 6 | O 1.48338e+00 1.39136e+00 9.15677e-01 7 | H 9.17464e-01 1.92333e+00 1.44553e+00 8 | H 9.80853e-01 6.05825e-01 6.93768e-01 9 | -------------------------------------------------------------------------------- /examples/pes/qtip4pf/tun-splitting/instanton/32/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 17 Bead: 0 positions{angstrom} cell{atomic_unit} 3 | O 1.00771e-01 -9.27528e-01 2.18380e-01 4 | H -7.09363e-01 -1.40515e+00 2.94863e-01 5 | H 6.82525e-01 -1.45012e+00 -3.12944e-01 6 | O 1.48338e+00 1.39136e+00 9.15677e-01 7 | H 9.17464e-01 1.92333e+00 1.44553e+00 8 | H 9.80853e-01 6.05825e-01 6.93768e-01 9 | -------------------------------------------------------------------------------- /examples/pes/qtip4pf/tun-splitting/min-freq/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 30 Bead: 0 positions{angstrom} cell{atomic_unit} 3 | O 1.35946e-01 -9.67988e-01 2.41370e-01 4 | H -7.79760e-01 -8.68954e-01 3.01041e-02 5 | H 5.35490e-01 -1.44232e+00 -4.71603e-01 6 | O 1.42452e+00 1.38886e+00 9.26138e-01 7 | H 1.72081e+00 1.29318e+00 1.81365e+00 8 | H 9.82027e-01 5.67085e-01 7.04984e-01 9 | -------------------------------------------------------------------------------- /examples/pes/qtip4pf/tun-splitting/min-freq/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | positions{angstrom} 6 | 7 | 400 8 | 9 |
localhost
10 | 11 | 12 | 13 | init.xyz 14 | [200.0, 200.0, 200.0 ] 15 | 16 | 17 | 18 | 19 | 20 | 35 21 | 22 | 23 | 24 | 0.01 25 | simulation-fd 26 | 27 | 28 | 29 | 30 | -------------------------------------------------------------------------------- /examples/pes/qtip4pf/tun-splitting/min/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 67 Bead: 0 positions{angstrom} cell{atomic_unit} 3 | O 1.36346e-01 -9.67442e-01 2.40661e-01 4 | H -7.79751e-01 -8.69284e-01 3.06661e-02 5 | H 5.34721e-01 -1.44347e+00 -4.71854e-01 6 | O 1.42482e+00 1.38927e+00 9.26440e-01 7 | H 1.72033e+00 1.29319e+00 1.81419e+00 8 | H 9.82564e-01 5.67597e-01 7.04541e-01 9 | -------------------------------------------------------------------------------- /examples/pes/qtip4pf/tun-splitting/min/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, potential{electronvolt}] 4 | x_centroid{angstrom} 5 | positions{angstrom} 6 | 7 | 400 8 | 9 |
localhost
10 | 11 | 12 | 13 | init.xyz 14 | [200.0, 200.0, 200.0 ] 15 | 16 | 17 | 18 | 19 | 20 | 35 21 | 22 | 23 | 24 | 25 | 1e-5 26 | 1e-5 27 | 1e-5 28 | 29 | 30 | 31 | 32 | 33 | -------------------------------------------------------------------------------- /examples/pes/zundel-systempart/double.xyz: -------------------------------------------------------------------------------- 1 | 14 2 | # positions{angstrom} 3 | O 0.54045 -0.97485 -0.21658 4 | O 2.92484 -0.83925 0.15240 5 | H 0.18386 -1.25804 -1.07875 6 | H 1.74329 -0.90928 -0.10040 7 | H 3.29707 -1.59324 0.64725 8 | H 3.53033 -0.60814 -0.57608 9 | H 0.04233 -0.19486 0.09228 10 | O 2.63827 -0.76870 2.50742 11 | O 0.25387 -0.90430 2.13842 12 | H -0.24423 -0.12430 2.44732 13 | H 3.24377 -0.53750 1.77892 14 | H 1.45677 -0.83870 2.25462 15 | H -0.10263 -1.18740 1.27622 16 | H 3.01057 -1.52260 3.00232 17 | -------------------------------------------------------------------------------- /examples/pes/zundel-systempart/h5o2+.xyz: -------------------------------------------------------------------------------- 1 | 7 2 | # 3 | O 0.54044984 -0.97485007 -0.21657970 4 | O 2.92484146 -0.83925223 0.15239669 5 | H 0.18385954 -1.25804198 -1.07875142 6 | H 1.74328720 -0.90927800 -0.10039502 7 | H 3.29706729 -1.59324218 0.64725255 8 | H 3.53032937 -0.60813812 -0.57607828 9 | H 0.04233158 -0.19485993 0.09228101 10 | -------------------------------------------------------------------------------- /examples/pes/zundel/init.xyz: -------------------------------------------------------------------------------- 1 | 7 2 | # 3 | O 0.54044984 -0.97485007 -0.21657970 4 | O 2.92484146 -0.83925223 0.15239669 5 | H 0.18385954 -1.25804198 -1.07875142 6 | H 1.74328720 -0.90927800 -0.10039502 7 | H 3.29706729 -1.59324218 0.64725255 8 | H 3.53032937 -0.60813812 -0.57607828 9 | H 0.04233158 -0.19485993 0.09228101 10 | -------------------------------------------------------------------------------- /examples/ph2/nvt/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] 4 | positions 5 | extras 6 | 7 | 8 | 100000 9 | 10 | 31415 11 | 12 | 13 |
nvt
14 | 15 | 16 | 17 | init.pdb 18 | 50 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 25 27 | 28 | 1 29 | 30 | 31 | 32 | 25 33 | 34 | 35 | 36 | -------------------------------------------------------------------------------- /examples/ph2/rpmd/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the RPMD post-processing files 2 | # 3 | # Copyright (C) 2013, Joshua More and Michele Ceriotti 4 | # 5 | # This program is free software: you can redistribute it and/or modify 6 | # it under the terms of the GNU General Public License as published by 7 | # the Free Software Foundation, either version 3 of the License, or 8 | # (at your option) any later version. 9 | # 10 | # This program is distributed in the hope that it will be useful, 11 | # but WITHOUT ANY WARRANTY; without even the implied warranty of 12 | # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 13 | # GNU General Public License for more details. 14 | # 15 | # You should have received a copy of the GNU General Public License 16 | # along with this program. If not, see . 17 | 18 | .PHONY: clean scripts postproc 19 | 20 | scripts: consolidate vel_est 21 | 22 | consolidate: consolidate.f 23 | gfortran -O3 -o consolidate consolidate.f 24 | 25 | vel_est: vel_est.f 26 | gfortran -O3 -o vel_est vel_est.f 27 | 28 | postproc: consolidate vel_est 29 | for r in `seq 1 4`; do cd run_$$r; for j in `seq 1 16`; do ../vel_est $$j &> /dev/null; done; cd ..; done; \ 30 | echo "4 16" | ./consolidate 31 | 32 | clean: 33 | rm -f consolidate vel_est vel_corr_tot.out */vel_corr* 34 | 35 | -------------------------------------------------------------------------------- /examples/plumed/zundel/h5o2+.xyz: -------------------------------------------------------------------------------- 1 | 7 2 | # CELL(abcABC): 13.38377 13.38377 13.38377 90.00000 90.00000 90.00000 cell{angstrom} Traj: positions{angstrom} Step: 0 Bead: 10 3 | O 5.40450e-01 -9.74850e-01 -2.16580e-01 4 | O 2.92484e+00 -8.39252e-01 1.52397e-01 5 | H 1.83860e-01 -1.25804e+00 -1.07875e+00 6 | H 1.74329e+00 -9.09278e-01 -1.00395e-01 7 | H 3.29707e+00 -1.59324e+00 6.47253e-01 8 | H 3.53033e+00 -6.08138e-01 -5.76078e-01 9 | H 4.23316e-02 -1.94860e-01 9.22810e-02 10 | -------------------------------------------------------------------------------- /examples/plumed/zundel/plumed/plumed.dat: -------------------------------------------------------------------------------- 1 | # default units are LENGTH=nm ENERGY=kJ/mol TIME=ps 2 | doo: DISTANCE ATOMS=1,2 3 | co1: DISTANCES GROUPA=1 GROUPB=3-7 LESS_THAN={RATIONAL R_0=0.14} 4 | co2: DISTANCES GROUPA=2 GROUPB=3-7 LESS_THAN={RATIONAL R_0=0.14} 5 | dc: COMBINE ARG=co1.lessthan,co2.lessthan COEFFICIENTS=1,-1 PERIODIC=NO 6 | mtd: METAD ARG=doo,dc PACE=20 SIGMA=0.005,0.05 HEIGHT=4 FILE=plumed/HILLS BIASFACTOR=10 TEMP=300 7 | uwall: UPPER_WALLS ARG=doo AT=0.4 KAPPA=250 8 | 9 | PRINT ARG=doo,co1.*,co2.*,mtd.*,uwall.* STRIDE=10 FILE=plumed/COLVAR 10 | FLUSH STRIDE=1 11 | -------------------------------------------------------------------------------- /examples/ppi/LJ/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the harmonic oscillator example 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | .PHONY: all clean lj 8 | all: lj 9 | 10 | driver:=i-pi-driver 11 | IPI:=i-pi 12 | 13 | define run_driver 14 | for i in `seq 1 $1`; do \ 15 | $(driver) -u -h lj_4 -m lj -o 5.270446,1.1663e-4,13.176115 & \ 16 | done; 17 | endef 18 | -include make.in 19 | 20 | lj: 21 | source ../../../env.sh; \ 22 | $(IPI) input.xml & sleep 5; \ 23 | $(call run_driver,4) \ 24 | wait 25 | 26 | clean: 27 | rm -f *simulation* *RESTART* EXIT *.log* *.dat* 28 | 29 | -------------------------------------------------------------------------------- /examples/ppi/LJ/ppi.sh: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/bash 2 | 3 | source ../../../env.sh && wait; 4 | python ../../../tools/py/energies_ppi.py lj 10.0 1000 atomic_unit & 5 | python ../../../tools/py/effective_temperatures.py lj 10.0 1000 > effective_temperatures.log & 6 | python ../../../tools/py/rdf_ppi.py lj 10.0 Ne Ne 50 2.2 4 1000 > rdf_log_$folder.log & 7 | -------------------------------------------------------------------------------- /examples/ppi/harmonic/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the harmonic oscillator example 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | .PHONY: all clean harmonic 8 | all: harmonic 9 | 10 | driver:=i-pi-driver 11 | IPI:=i-pi 12 | 13 | define run_driver 14 | for i in `seq 1 $1`; do \ 15 | $(driver) -u -h harmonic -m harm -o 0.2 & \ 16 | done; 17 | endef 18 | -include make.in 19 | 20 | harmonic: 21 | source ../../../env.sh; \ 22 | $(IPI) input.xml & sleep 5; \ 23 | $(call run_driver,2) \ 24 | wait 25 | 26 | clean: 27 | rm -f *simulation.* *RESTART* EXIT *.log* *.dat* 28 | 29 | -------------------------------------------------------------------------------- /examples/ppi/harmonic/init.pdb: -------------------------------------------------------------------------------- 1 | TITLE cell{atomic_unit} positions{atomic_unit} 2 | CRYST1 71.230 71.230 71.230 90.00 90.00 90.00 P 1 1 3 | ATOM 1 H 1 1 0.108 0.000 0.000 0.00 0.00 0 4 | END 5 | -------------------------------------------------------------------------------- /examples/ppi/harmonic/ppi.sh: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/bash 2 | 3 | source ../../../env.sh && wait; 4 | python ../../../tools/py/energies_ppi.py harm 1841.7060385 1000 electronvolt > energies.log & 5 | python ../../../tools/py/effective_temperatures.py harm 1841.7060385 1000 > effective_temperatures.log & 6 | python ../../../tools/py/heat_capacity_ppi.py harm 1841.7060385 1000 > heat_capacity.log & 7 | -------------------------------------------------------------------------------- /examples/ppi/qtip4pf/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the qtip4pf example 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | # 7 | driver:=i-pi-driver 8 | IPI:=i-pi 9 | 10 | define run_driver 11 | for i in `seq 1 $1`; do \ 12 | $(driver) -u -h qtip4pf -m qtip4pf & \ 13 | done; 14 | endef 15 | -include make.in 16 | 17 | all: 18 | $(IPI) input.xml & sleep 5; \ 19 | $(call run_driver,4) \ 20 | wait 21 | 22 | clean: 23 | rm -f \#* *simulation* *RESTART* EXIT /tmp/ipi_qtip4pf *.log* *.dat* 24 | -------------------------------------------------------------------------------- /examples/ppi/qtip4pf/ppi.sh: -------------------------------------------------------------------------------- 1 | #!/usr/local/bin/bash 2 | 3 | source ../../../env.sh && wait; 4 | python ../../../tools/py/energies_ppi.py qtip4pf 298 100 electronvolt > energies.log & 5 | python ../../../tools/py/kinetic_energy_ppi.py qtip4pf 298 100 electronvolt > kinetic_energy.log & 6 | python ../../../tools/py/potential_energy_ppi.py qtip4pf 298 100 electronvolt > potential_energy.log & 7 | python ../../../tools/py/total_energy_ppi.py qtip4pf 298 100 electronvolt > total_energy.log & 8 | python ../../../tools/py/effective_temperatures.py qtip4pf 298 100 > effective_temperatures.log & 9 | python ../../../tools/py/rdf_ppi.py qtip4pf 298 O O 50 2.4 3.3 100 > rdf_OO.log & 10 | python ../../../tools/py/rdf_ppi.py qtip4pf 298 H H 50 1.0 1.9 100 > rdf_HH.log & 11 | python ../../../tools/py/rdf_ppi.py qtip4pf 298 O H 50 0.7 1.3 100 > rdf_OH.log & 12 | -------------------------------------------------------------------------------- /examples/qespresso/dia-npt-classical/init.xyz: -------------------------------------------------------------------------------- 1 | 8 2 | diamond.pdb 3 | C 0.00000 0.00000 0.00000 4 | C 0.00000 1.78400 1.78400 5 | C 1.78400 1.78400 0.00000 6 | C 1.78400 0.00000 1.78400 7 | C 2.67500 0.89200 2.67500 8 | C 0.89200 0.89200 0.89200 9 | C 0.89200 2.67500 2.67500 10 | C 2.67500 2.67500 0.89200 11 | -------------------------------------------------------------------------------- /examples/qespresso/dia-npt-classical/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='high' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='dia' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | NAT=8 17 | NTYP=1 18 | ECUTWFC=80 19 | ECUTRHO=100 20 | nspin=1 21 | occupations='fixed' 22 | nosym=.true. 23 | / 24 | &ELECTRONS 25 | conv_thr=1.0e-9 26 | mixing_mode='plain' 27 | mixing_beta=0.7 28 | startingpot='atomic' 29 | startingwfc='atomic' 30 | / 31 | &IONS 32 | / 33 | ATOMIC_SPECIES 34 | C 12.01 C.pbe-rrkjus.UPF 35 | ATOMIC_POSITIONS (angstrom) 36 | C 0.000 0.000 0.000 37 | C 0.000 1.784 1.784 38 | C 1.784 1.784 0.000 39 | C 1.784 0.000 1.784 40 | C 2.675 0.892 2.675 41 | C 0.892 0.892 0.892 42 | C 0.892 2.675 2.675 43 | C 2.675 2.675 0.892 44 | K_POINTS (gamma) 45 | CELL_PARAMETERS (bohr) 46 | 6.741 .0 .0 47 | .0 6.741 .0 48 | .0 .0 6.741 49 | 50 | 51 | -------------------------------------------------------------------------------- /examples/qespresso/dia-npt-pimd.4/init.xyz: -------------------------------------------------------------------------------- 1 | 8 2 | diamond.pdb 3 | C 0.00000 0.00000 0.00000 4 | C 0.00000 1.78400 1.78400 5 | C 1.78400 1.78400 0.00000 6 | C 1.78400 0.00000 1.78400 7 | C 2.67500 0.89200 2.67500 8 | C 0.89200 0.89200 0.89200 9 | C 0.89200 2.67500 2.67500 10 | C 2.67500 2.67500 0.89200 11 | -------------------------------------------------------------------------------- /examples/qespresso/dia-npt-pimd.4/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='high' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='dia' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | NAT=8 17 | NTYP=1 18 | ECUTWFC=80 19 | ECUTRHO=100 20 | nspin=1 21 | occupations='fixed' 22 | nosym=.true. 23 | / 24 | &ELECTRONS 25 | conv_thr=1.0e-9 26 | mixing_mode='plain' 27 | mixing_beta=0.7 28 | startingpot='atomic' 29 | startingwfc='atomic' 30 | / 31 | &IONS 32 | / 33 | ATOMIC_SPECIES 34 | C 12.01 C.pbe-rrkjus.UPF 35 | ATOMIC_POSITIONS (angstrom) 36 | C 0.000 0.000 0.000 37 | C 0.000 1.784 1.784 38 | C 1.784 1.784 0.000 39 | C 1.784 0.000 1.784 40 | C 2.675 0.892 2.675 41 | C 0.892 0.892 0.892 42 | C 0.892 2.675 2.675 43 | C 2.675 2.675 0.892 44 | K_POINTS (gamma) 45 | CELL_PARAMETERS (bohr) 46 | 6.741 .0 .0 47 | .0 6.741 .0 48 | .0 .0 6.741 49 | 50 | 51 | -------------------------------------------------------------------------------- /examples/qespresso/h2o/init.pdb: -------------------------------------------------------------------------------- 1 | TITLE cell{atomic_unit} positions{atomic_unit} 2 | CRYST1 10.00 10.00 10.00 90.00 90.00 90.00 P 1 1 3 | ATOM 1 H 1 1 0.610 10.47 6.053 0.00 0.00 0 4 | ATOM 2 H 1 1 1.600 12.78 7.266 0.00 0.00 0 5 | ATOM 3 O 1 1 0.064 12.23 6.458 0.00 0.00 0 6 | END 7 | -------------------------------------------------------------------------------- /examples/qespresso/h2o/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='low' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='h2o' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | celldm(1)= 10.0 17 | NAT=3 18 | NTYP=2 19 | ECUTWFC=18 20 | ECUTRHO=100 21 | nspin=1 22 | occupations='fixed' 23 | nosym=.true. 24 | / 25 | &ELECTRONS 26 | conv_thr=1.0e-9 27 | mixing_mode='plain' 28 | mixing_beta=0.7 29 | startingpot='atomic' 30 | startingwfc='atomic' 31 | / 32 | &IONS 33 | / 34 | ATOMIC_SPECIES 35 | H 1.008 H.pbe-rrkjus.UPF 36 | O 1.008 O.pbe-rrkjus.UPF 37 | ATOMIC_POSITIONS (alat) 38 | H 0.1 0 0 39 | H -0.1 0 0 40 | O 0 0 0 41 | K_POINTS (gamma) 42 | CELL_PARAMETERS 43 | 1 0 0 44 | 0 1 0 45 | 0 0 1 46 | 47 | -------------------------------------------------------------------------------- /examples/qespresso/li4/init.pdb: -------------------------------------------------------------------------------- 1 | TITLE cell{atomic_unit} positions{atomic_unit} 2 | CRYST1 6.570 6.570 6.570 90.00 90.00 90.00 P 1 1 3 | ATOM 1 Li 1 1 0.000 0.000 0.000 0.00 0.00 0 4 | ATOM 2 Li 1 1 3.280 3.280 0.001 0.00 0.00 0 5 | ATOM 3 Li 1 1 0.001 3.281 3.280 0.00 0.00 0 6 | ATOM 4 Li 1 1 3.281 0.000 3.281 0.00 0.00 0 7 | -------------------------------------------------------------------------------- /examples/qespresso/li4/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='high' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='libcc' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | celldm(1)= 6.57 17 | NAT=4 18 | NTYP=1 19 | ECUTWFC=20 20 | ECUTRHO=100 21 | nspin=1 22 | occupations='smearing' 23 | smearing='gauss' 24 | degauss=1e-3 25 | nosym=.true. 26 | / 27 | &ELECTRONS 28 | conv_thr=1.0e-10 29 | mixing_mode='plain' 30 | mixing_beta=0.7 31 | startingpot='atomic' 32 | startingwfc='atomic' 33 | / 34 | &IONS 35 | pot_extrapolation = 'second_order' 36 | wfc_extrapolation = 'second_order' 37 | / 38 | &CELL 39 | / 40 | ATOMIC_SPECIES 41 | Li 6.941 Li.pbe-tm.UPF 42 | ATOMIC_POSITIONS (alat) 43 | Li 0 0 0 44 | Li 0.5 0.5 0 45 | Li 0 0.5 0.5 46 | Li 0.5 0 0.5 47 | K_POINTS (automatic) 48 | 04 04 04 1 1 1 49 | CELL_PARAMETERS 50 | 1 0 0 51 | 0 1 0 52 | 0 0 1 53 | 54 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-md_npt/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-md_nst/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-md_nvt/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-md_nvt_mts/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+mts.4_long 32347 unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-md_nvt_mts/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+mts.4_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-pimd_npt/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-pimd_nst/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-pimd_nvt/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-pimd_nvt_mts/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+mts.4_long 32347 unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-pimd_nvt_mts/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+mts.4_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-repimd_npt/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | pair_style lj/long/tip4p/long long long 1 2 1 1 0.278072379 11.707 4 | bond_style class2 5 | angle_style harmonic 6 | # Adds LJ tail correction 7 | kspace_style pppm/disp/tip4p 0.0001 8 | kspace_modify force/disp/real 0.0001 9 | kspace_modify force/disp/kspace 0.0001 10 | 11 | read_data data.lmp 12 | pair_coeff * * 0 0 13 | pair_coeff 1 1 0.000295147 5.96946 14 | neighbor 2.0 bin 15 | timestep 0.00025 16 | fix 1 all ipi driver 32345 unix 17 | 18 | run 100000000 19 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-rescpimd_nvt/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | pair_style lj/long/tip4p/long long long 1 2 1 1 0.278072379 11.707 4 | bond_style class2 5 | angle_style harmonic 6 | # Adds LJ tail correction 7 | kspace_style pppm/disp/tip4p 0.0001 8 | kspace_modify force/disp/real 0.0001 9 | kspace_modify force/disp/kspace 0.0001 10 | 11 | read_data data.lmp 12 | pair_coeff * * 0 0 13 | pair_coeff 1 1 0.000295147 5.96946 14 | neighbor 2.0 bin 15 | timestep 0.00025 16 | fix 1 all ipi driver 32345 unix 17 | 18 | run 100000000 19 | -------------------------------------------------------------------------------- /examples/regtest/integrators/h2o-scpimd_nvt/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/lammps/benz-graph-slc/data.part: -------------------------------------------------------------------------------- 1 | LAMMPS Description 2 | 3 | 12 atoms 4 | 0 bonds 5 | 0 angles 6 | 0 dihedrals 7 | 8 | 2 atom types 9 | 0 bond types 10 | 0 angle types 11 | 0 dihedral types 12 | 13 | 0 17.1404 xlo xhi 14 | 0 19.792 ylo yhi 15 | 0 30.00000 zlo zhi 16 | 17 | Masses 18 | 19 | 1 12.0110 20 | 2 1.0080 21 | 22 | Atoms 23 | 24 | 1 2 8.43090 -7.64856 3.08149 25 | 2 1 7.88729 -8.59708 3.13791 26 | 3 1 6.49669 -8.60046 3.17688 27 | 4 2 5.94591 -7.65476 3.15118 28 | 5 1 5.80584 -9.80579 3.24864 29 | 6 2 4.71157 -9.80845 3.27940 30 | 7 1 6.50544 -11.00776 3.28138 31 | 8 2 5.96179 -11.95622 3.33785 32 | 9 1 7.89602 -11.00436 3.24246 33 | 10 2 8.44654 -11.95016 3.26834 34 | 11 1 8.58690 -9.79905 3.17069 35 | 12 2 9.68114 -9.79632 3.14005 36 | -------------------------------------------------------------------------------- /examples/regtest/lammps/benz-graph-slc/in.full: -------------------------------------------------------------------------------- 1 | dimension 3 2 | boundary p p p 3 | 4 | atom_style atomic 5 | 6 | units metal 7 | 8 | 9 | read_data data.full 10 | mass 1 12 11 | mass 2 1 12 | 13 | group C type 1 14 | group H type 2 15 | 16 | neighbor 0.5 bin 17 | neigh_modify delay 1 18 | 19 | 20 | pair_style airebo 3 1 1 21 | 22 | pair_coeff * * ./CH.airebo C H 23 | 24 | timestep 0.00025 25 | 26 | fix 1 all ipi fullcent3 13234 unix 27 | 28 | run 1000000000 29 | 30 | -------------------------------------------------------------------------------- /examples/regtest/lammps/benz-graph-slc/in.partbeads: -------------------------------------------------------------------------------- 1 | dimension 3 2 | boundary p p p 3 | 4 | atom_style atomic 5 | 6 | units metal 7 | 8 | 9 | read_data data.part 10 | mass 1 12 11 | mass 2 1 12 | 13 | group C type 1 14 | group H type 2 15 | 16 | neighbor 0.5 bin 17 | neigh_modify delay 1 18 | 19 | 20 | pair_style airebo 3 1 1 21 | 22 | pair_coeff * * ./CH.airebo C H 23 | 24 | timestep 0.00025 25 | 26 | fix 1 all ipi benzenebeads3 13234 unix 27 | 28 | run 1000000000 29 | 30 | -------------------------------------------------------------------------------- /examples/regtest/lammps/benz-graph-slc/in.partcontr: -------------------------------------------------------------------------------- 1 | dimension 3 2 | boundary p p p 3 | 4 | atom_style atomic 5 | 6 | units metal 7 | 8 | 9 | read_data data.part 10 | mass 1 12 11 | mass 2 1 12 | 13 | group C type 1 14 | group H type 2 15 | 16 | neighbor 0.5 bin 17 | neigh_modify delay 1 18 | 19 | 20 | pair_style airebo 3 1 1 21 | 22 | pair_coeff * * ./CH.airebo C H 23 | 24 | timestep 0.00025 25 | 26 | fix 1 all ipi benzenecent3 13234 unix 27 | 28 | run 1000000000 29 | 30 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-alchemical/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 h2o-alchemical 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-fixatoms/in.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut/tip4p/long 1 2 1 1 0.278072379 9.695398182254587 5 | bond_style class2 6 | angle_style harmonic 7 | kspace_style pppm/tip4p 0.0001 8 | 9 | read_data data.lmp 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 h2o-cl-fa 32345 unix 18 | run 100000000 19 | 20 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-fixcom/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 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-fixcom/in.lmp: -------------------------------------------------------------------------------- 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 | kspace_modify compute no 9 | 10 | read_data data.lmp 11 | pair_coeff * * 0 0 12 | pair_coeff 1 1 0.000295147 5.96946 13 | 14 | neighbor 2.0 bin 15 | 16 | timestep 0.00025 17 | 18 | #velocity all create 298.0 2345187 19 | 20 | #thermo_style multi 21 | #thermo 1 22 | 23 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 24 | #fix 1 all nve 25 | fix 1 all ipi h2o-qn-fixcom 32346 unix 26 | 27 | #dump 1 all xyz 25 dump.xyz 28 | 29 | run 100000000 30 | 31 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-fixcom/init.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 35.23300 35.23300 35.23300 90.00000 90.00000 90.00000 Traj: positions{angstrom} Step: 11 Bead: 0 3 | O 0.00000e+00 -2.00000e-02 0.00000e+00 4 | H 7.50000e-01 5.00000e-01 0.00000e+00 5 | H -7.50000e-01 5.00000e-01 0.00000e+00 6 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-piglet.2/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 h2o-piglet.2 32344 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-piglet.8/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 h2o-piglet.8 32342 unix 28 | 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+mts.4/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+mts.4_long 32347 unix 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+mts.4/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+mts.4_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+rpc/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+rpc_long 32347 unix reset 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+rpc/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+rpc_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+sc+mts/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 h2o-pimd+sc+mts 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+sc+rpc/in_long.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_long.lmp 13 | pair_coeff * * 0 0 14 | pair_coeff 1 1 0.000295147 5.96946 15 | 16 | neighbor 2.0 bin 17 | neigh_modify delay 0 every 1 check yes 18 | 19 | timestep 0.00025 20 | 21 | #velocity all create 298.0 2345187 22 | 23 | #thermo_style multi 24 | #thermo 1 25 | 26 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 27 | #fix 1 all nve 28 | fix 1 all ipi h2o-pimd+sc+rpc_long 32347 unix reset 29 | 30 | #dump 1 all xyz 25 dump.xyz 31 | 32 | run 100000000 33 | 34 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+sc+rpc/in_short.lmp: -------------------------------------------------------------------------------- 1 | units electron 2 | atom_style full 3 | 4 | pair_style lj/cut 0.51 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_short.lmp 13 | pair_coeff * * 0 0.1 14 | #pair_coeff 1 1 0.000295147 5.96946 15 | 16 | #atom_modify sort 1 3.00 17 | neighbor 2.0 bin 18 | neigh_modify delay 0 every 1 check yes 19 | 20 | timestep 0.00025 21 | 22 | #velocity all create 298.0 2345187 23 | 24 | #thermo_style multi 25 | #thermo 1 26 | 27 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 28 | #fix 1 all nve 29 | fix 1 all ipi h2o-pimd+sc+rpc_short 32346 unix 30 | 31 | #dump 1 all xyz 25 dump.xyz 32 | 33 | run 100000000 34 | 35 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd+sc/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 h2o-pimd+sc 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/lammps/h2o-pimd.1/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 h2o-pimd.1 32345 unix 28 | 29 | #dump 1 all xyz 25 dump.xyz 30 | 31 | run 100000000 32 | 33 | -------------------------------------------------------------------------------- /examples/regtest/lammps/ice-npt/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. 6 | #bond_style harmonic 7 | bond_style class2 8 | angle_style harmonic 9 | kspace_style ewald 0.0001 10 | 11 | read_data data.lmp 12 | pair_coeff * * 0 0 13 | pair_coeff 1 1 0.000295147 5.96946 14 | 15 | neighbor 2.0 bin 16 | 17 | timestep 0.00025 18 | 19 | #velocity all create 298.0 2345187 20 | 21 | #thermo_style multi 22 | #thermo 1 23 | 24 | #fix 1 all nvt temp 298.0 298.0 30.0 tchain 1 25 | #fix 1 all nve 26 | fix 1 all ipi ice-npt 32345 unix 27 | 28 | #dump 1 all xyz 25 dump.xyz 29 | 30 | run 100000000 31 | 32 | -------------------------------------------------------------------------------- /examples/regtest/lammps/ice-nst/in.lmp: -------------------------------------------------------------------------------- 1 | units real 2 | atom_style full 3 | 4 | read_data data.lmp 5 | 6 | # TIP4PF in current LAMMPS does not give the correct stress with triclinic boxes... 7 | # pair_style lj/cut/tip4p/long 1 2 1 1 0.14714951 7 8 | pair_style lj/cut/coul/long 8 9 | 10 | pair_coeff * * 0 0 11 | pair_coeff 1 1 0.18508368 3.1589022 12 | 13 | bond_style class2 14 | angle_style harmonic 15 | kspace_style ewald 0.0001 16 | 17 | #qtip4pf bond parameters 18 | bond_coeff 1 0.9419 607.19354 -1388.6516 1852.577 19 | angle_coeff 1 43.93 107.4 20 | 21 | neighbor 2.0 bin 22 | 23 | timestep 0.0001 24 | 25 | fix 1 all ipi ice-nst 32345 unix 26 | 27 | run 100000000 28 | 29 | -------------------------------------------------------------------------------- /examples/regtest/pes/CH4_H/instanton_rate/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: 9 Bead: 0 3 | H 1.33370e+00 1.59787e+00 1.35300e+00 4 | C 5.77568e-01 7.10503e-01 5.95431e-01 5 | H 1.00494e-04 1.08773e-01 1.29743e+00 6 | H 1.28079e+00 1.06096e-01 2.22598e-02 7 | H -6.31180e-02 1.31234e+00 -4.92875e-02 8 | H 1.80833e+00 2.15490e+00 1.82860e+00 9 | -------------------------------------------------------------------------------- /examples/regtest/pes/io-units/init-angstrom.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 18.89726 18.89726 18.89726 90.00000 90.00000 90.00000 Step: 40 Bead: 2 positions{angstrom} cell{atomic_unit} 3 | O 4.97336e+00 4.92337e+00 4.96921e+00 4 | H 5.71284e+00 5.57553e+00 4.90940e+00 5 | H 5.01842e+00 4.53605e+00 4.05255e+00 6 | -------------------------------------------------------------------------------- /examples/regtest/pes/io-units/init-nocomment.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | 3 | O 5.00000 5.00000 5.00000 4 | H 5.98343 5.00000 5.00000 5 | H 4.84583 4.376419 4.10217 6 | -------------------------------------------------------------------------------- /examples/regtest/pes/io-units/init-velocities.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 18.89726 18.89726 18.89726 90.00000 90.00000 90.00000 Step: 40 Bead: 2 velocities{atomic_unit} cell{atomic_unit} 3 | O -1.57474e-04 -6.43328e-04 -3.02692e-04 4 | H 4.75131e-04 1.92827e-03 -9.58797e-04 5 | H 1.42102e-03 2.09636e-03 2.30678e-03 6 | -------------------------------------------------------------------------------- /examples/regtest/pes/neb/README.md: -------------------------------------------------------------------------------- 1 | Neb example 2 | ------------- 3 | 4 | Once the env.sh file in the i-pi root directory has been sourced with 5 | 6 | ```bash 7 | source /env.sh 8 | ``` 9 | 10 | Run i-pi with: 11 | 12 | ```bash 13 | i-pi input.xml 14 | ``` 15 | 16 | And the driver: 17 | 18 | ```bash 19 | i-pi-driver -u -h driver -p 20614 -m zundel 20 | ``` 21 | -------------------------------------------------------------------------------- /examples/regtest/pes/pswater/init.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | 3 | O 5.00000 5.00000 5.00000 4 | H 5.98343 5.00000 5.00000 5 | H 4.84583 4.376419 4.10217 6 | -------------------------------------------------------------------------------- /examples/regtest/pes/qtip4pf/tun-splitting/init.xyz: -------------------------------------------------------------------------------- 1 | 6 2 | # CELL(abcABC): 200.00000 200.00000 200.00000 90.00000 90.00000 90.00000 Step: 17 Bead: 0 positions{angstrom} cell{atomic_unit} 3 | O 1.00771e-01 -9.27528e-01 2.18380e-01 4 | H -7.09363e-01 -1.40515e+00 2.94863e-01 5 | H 6.82525e-01 -1.45012e+00 -3.12944e-01 6 | O 1.48338e+00 1.39136e+00 9.15677e-01 7 | H 9.17464e-01 1.92333e+00 1.44553e+00 8 | H 9.80853e-01 6.05825e-01 6.93768e-01 9 | -------------------------------------------------------------------------------- /examples/regtest/pes/zundel/init.xyz: -------------------------------------------------------------------------------- 1 | 7 2 | # 3 | O 0.54044984 -0.97485007 -0.21657970 4 | O 2.92484146 -0.83925223 0.15239669 5 | H 0.18385954 -1.25804198 -1.07875142 6 | H 1.74328720 -0.90927800 -0.10039502 7 | H 3.29706729 -1.59324218 0.64725255 8 | H 3.53032937 -0.60813812 -0.57607828 9 | H 0.04233158 -0.19485993 0.09228101 10 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/dia-npt-classical/init.xyz: -------------------------------------------------------------------------------- 1 | 8 2 | diamond.pdb 3 | C 0.00000 0.00000 0.00000 4 | C 0.00000 1.78400 1.78400 5 | C 1.78400 1.78400 0.00000 6 | C 1.78400 0.00000 1.78400 7 | C 2.67500 0.89200 2.67500 8 | C 0.89200 0.89200 0.89200 9 | C 0.89200 2.67500 2.67500 10 | C 2.67500 2.67500 0.89200 11 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/dia-npt-classical/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='high' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='dia' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | NAT=8 17 | NTYP=1 18 | ECUTWFC=80 19 | ECUTRHO=100 20 | nspin=1 21 | occupations='fixed' 22 | nosym=.true. 23 | / 24 | &ELECTRONS 25 | conv_thr=1.0e-9 26 | mixing_mode='plain' 27 | mixing_beta=0.7 28 | startingpot='atomic' 29 | startingwfc='atomic' 30 | / 31 | &IONS 32 | / 33 | ATOMIC_SPECIES 34 | C 12.01 C.pbe-rrkjus.UPF 35 | ATOMIC_POSITIONS (angstrom) 36 | C 0.000 0.000 0.000 37 | C 0.000 1.784 1.784 38 | C 1.784 1.784 0.000 39 | C 1.784 0.000 1.784 40 | C 2.675 0.892 2.675 41 | C 0.892 0.892 0.892 42 | C 0.892 2.675 2.675 43 | C 2.675 2.675 0.892 44 | K_POINTS (gamma) 45 | CELL_PARAMETERS (bohr) 46 | 6.741 .0 .0 47 | .0 6.741 .0 48 | .0 .0 6.741 49 | 50 | 51 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/dia-npt-pimd.4/init.xyz: -------------------------------------------------------------------------------- 1 | 8 2 | diamond.pdb 3 | C 0.00000 0.00000 0.00000 4 | C 0.00000 1.78400 1.78400 5 | C 1.78400 1.78400 0.00000 6 | C 1.78400 0.00000 1.78400 7 | C 2.67500 0.89200 2.67500 8 | C 0.89200 0.89200 0.89200 9 | C 0.89200 2.67500 2.67500 10 | C 2.67500 2.67500 0.89200 11 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/dia-npt-pimd.4/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='high' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='dia' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | NAT=8 17 | NTYP=1 18 | ECUTWFC=80 19 | ECUTRHO=100 20 | nspin=1 21 | occupations='fixed' 22 | nosym=.true. 23 | / 24 | &ELECTRONS 25 | conv_thr=1.0e-9 26 | mixing_mode='plain' 27 | mixing_beta=0.7 28 | startingpot='atomic' 29 | startingwfc='atomic' 30 | / 31 | &IONS 32 | / 33 | ATOMIC_SPECIES 34 | C 12.01 C.pbe-rrkjus.UPF 35 | ATOMIC_POSITIONS (angstrom) 36 | C 0.000 0.000 0.000 37 | C 0.000 1.784 1.784 38 | C 1.784 1.784 0.000 39 | C 1.784 0.000 1.784 40 | C 2.675 0.892 2.675 41 | C 0.892 0.892 0.892 42 | C 0.892 2.675 2.675 43 | C 2.675 2.675 0.892 44 | K_POINTS (gamma) 45 | CELL_PARAMETERS (bohr) 46 | 6.741 .0 .0 47 | .0 6.741 .0 48 | .0 .0 6.741 49 | 50 | 51 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/h2o/init.pdb: -------------------------------------------------------------------------------- 1 | TITLE cell{atomic_unit} positions{atomic_unit} 2 | CRYST1 10.00 10.00 10.00 90.00 90.00 90.00 P 1 1 3 | ATOM 1 H 1 1 0.610 10.47 6.053 0.00 0.00 0 4 | ATOM 2 H 1 1 1.600 12.78 7.266 0.00 0.00 0 5 | ATOM 3 O 1 1 0.064 12.23 6.458 0.00 0.00 0 6 | END 7 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/h2o/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='low' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='h2o' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | celldm(1)= 10.0 17 | NAT=3 18 | NTYP=2 19 | ECUTWFC=18 20 | ECUTRHO=100 21 | nspin=1 22 | occupations='fixed' 23 | nosym=.true. 24 | / 25 | &ELECTRONS 26 | conv_thr=1.0e-9 27 | mixing_mode='plain' 28 | mixing_beta=0.7 29 | startingpot='atomic' 30 | startingwfc='atomic' 31 | / 32 | &IONS 33 | / 34 | ATOMIC_SPECIES 35 | H 1.008 H.pbe-rrkjus.UPF 36 | O 1.008 O.pbe-rrkjus.UPF 37 | ATOMIC_POSITIONS (alat) 38 | H 0.1 0 0 39 | H -0.1 0 0 40 | O 0 0 0 41 | K_POINTS (gamma) 42 | CELL_PARAMETERS 43 | 1 0 0 44 | 0 1 0 45 | 0 0 1 46 | 47 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/li4/init.pdb: -------------------------------------------------------------------------------- 1 | TITLE cell{atomic_unit} positions{atomic_unit} 2 | CRYST1 6.570 6.570 6.570 90.00 90.00 90.00 P 1 1 3 | ATOM 1 Li 1 1 0.000 0.000 0.000 0.00 0.00 0 4 | ATOM 2 Li 1 1 3.280 3.280 0.001 0.00 0.00 0 5 | ATOM 3 Li 1 1 0.001 3.281 3.280 0.00 0.00 0 6 | ATOM 4 Li 1 1 3.281 0.000 3.281 0.00 0.00 0 7 | -------------------------------------------------------------------------------- /examples/regtest/qespresso/li4/pw.in: -------------------------------------------------------------------------------- 1 | &CONTROL 2 | calculation='scf' 3 | verbosity='high' 4 | restart_mode='from_scratch' 5 | tstress=.true. 6 | tprnfor=.true. 7 | etot_conv_thr=5.0D-5 8 | forc_conv_thr=1.0D-4 9 | prefix='libcc' 10 | outdir='./' 11 | pseudo_dir='../' 12 | max_seconds=7200 13 | / 14 | &SYSTEM 15 | ibrav=0 16 | celldm(1)= 6.57 17 | NAT=4 18 | NTYP=1 19 | ECUTWFC=20 20 | ECUTRHO=100 21 | nspin=1 22 | occupations='smearing' 23 | smearing='gauss' 24 | degauss=1e-3 25 | nosym=.true. 26 | / 27 | &ELECTRONS 28 | conv_thr=1.0e-10 29 | mixing_mode='plain' 30 | mixing_beta=0.7 31 | startingpot='atomic' 32 | startingwfc='atomic' 33 | / 34 | &IONS 35 | pot_extrapolation = 'second_order' 36 | wfc_extrapolation = 'second_order' 37 | / 38 | &CELL 39 | / 40 | ATOMIC_SPECIES 41 | Li 6.941 Li.pbe-tm.UPF 42 | ATOMIC_POSITIONS (alat) 43 | Li 0 0 0 44 | Li 0.5 0.5 0 45 | Li 0 0.5 0.5 46 | Li 0.5 0 0.5 47 | K_POINTS (automatic) 48 | 04 04 04 1 1 1 49 | CELL_PARAMETERS 50 | 1 0 0 51 | 0 1 0 52 | 0 0 1 53 | 54 | -------------------------------------------------------------------------------- /examples/tools/gleacf/h2o-gle/README: -------------------------------------------------------------------------------- 1 | Please run the following to predict the VVAC of a GLE thermostat: 2 | prefix=gle01 3 | ../../../../bin/i-pi-gleacf -iipi input-${prefix}.xml -ivvac simulation-svr.vvac -mrows 5000 -oprefix svrto${prefix} -a conv -dt "1 femtosecond" 4 | 5 | 6 | Please run the following to extract the microcanonical vvac out of a vvac affected by a GLE thermostat: 7 | prefix=gle01 8 | ../../../../bin/i-pi-gleacf -iipi input-${prefix}.xml -ivvac simulation-${prefix}.vvac -mrows 5000 -oprefix ${prefix}tosvr -a deconv -dt "1 femtosecond" -dparam 250 5 9 | 10 | -------------------------------------------------------------------------------- /examples/tools/gleacf/h2o-qt/README: -------------------------------------------------------------------------------- 1 | Please run the following to predict the VVAC of a GLE thermostat: 2 | prefix=qt01 3 | ../../../../bin/i-pi-gleacf -iipi input-${prefix}.xml -ivvac simulation-svr.vvac -mrows 5000 -oprefix svrto${prefix} -a conv -dt "1 femtosecond" 4 | 5 | 6 | Please run the following to extract the microcanonical vvac out of a vvac affected by a GLE thermostat: 7 | prefix=qt01 8 | ../../../../bin/i-pi-gleacf -iipi input-${prefix}.xml -ivvac simulation-${prefix}.vvac -mrows 5000 -oprefix ${prefix}tosvr -a deconv -dt "1 femtosecond" -dparam 250 5 9 | 10 | -------------------------------------------------------------------------------- /examples/tools/gleacf/h2o-wn/README: -------------------------------------------------------------------------------- 1 | Please run the following to predict the VVAC of a GLE thermostat: 2 | prefix=wle1e1 3 | ../../../../bin/i-pi-gleacf -iipi input-${prefix}.xml -ivvac simulation-svr.vvac -mrows 5000 -oprefix svrto${prefix} -a conv -dt "1 femtosecond" 4 | 5 | 6 | Please run the following to extract the microcanonical vvac out of a vvac affected by a GLE thermostat: 7 | prefix=wle1e1 8 | ../../../../bin/i-pi-gleacf -iipi input-${prefix}.xml -ivvac simulation-${prefix}.vvac -mrows 5000 -oprefix ${prefix}tosvr -a deconv -dt "1 femtosecond" -dparam 250 5 9 | 10 | -------------------------------------------------------------------------------- /examples/tools/gleacf/h2o-wn/input.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | [ step, time{picosecond}, conserved{electronvolt}, temperature{kelvin}, kinetic_cv{electronvolt}, potential{electronvolt}, pressure_cv{megapascal} ] 4 | velocities 5 | 6 | 7 | 400000 8 | 9 | 32425 10 | 11 | 12 |
driver-md.8
13 | 14 | 15 | 16 | init.xyz 17 | 300 18 | 19 | 20 | 21 | 22 | 23 | 24 | 0.5 25 | 26 | 10 27 | 28 | 29 | 30 | 31 | 300 32 | 33 | 34 | 35 | -------------------------------------------------------------------------------- /examples/tutorial/README.md: -------------------------------------------------------------------------------- 1 | Example with the rudimentary PH2 code 2 | ===================================== 3 | 4 | This gives an example of para-H2 with the isotropic Silvera-Goldman pair 5 | potential, as discussed in the tutorial section of the user manual. Please 6 | refer to this section for more detailed instructions on how to run this 7 | example. 8 | 9 | To run tutorial 1: 10 | 11 | ```bash 12 | source /env.sh 13 | i-pi tutorial-1.xml 14 | i-pi-driver -m sg -h localhost -o 15 -p 31415 15 | ``` -------------------------------------------------------------------------------- /examples/yaff/Makefile: -------------------------------------------------------------------------------- 1 | # Makefile for the yaff example 2 | # 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | .PHONY: all clean mil53_ffsocket mil53_ffyaff 8 | all: mil53_ffsocket mil53_ffyaff 9 | 10 | IPI:=i-pi 11 | 12 | define run_yaff 13 | for i in `seq 1 $1`; do \ 14 | python run.py & \ 15 | done; 16 | endef 17 | -include make.in 18 | 19 | mil53_ffsocket: 20 | cd mil53_ffsocket; $(IPI) input.xml & sleep 10; \ 21 | $(call run_yaff,4) \ 22 | wait 23 | 24 | mil53_ffyaff: 25 | cd mil53_ffyaff; $(IPI) input.xml; \ 26 | wait 27 | 28 | clean: 29 | rm -f */*.out* */*.log */*.restart* */*RESTART* */EXIT */*pos* */*simulation* */yaffdriver.pyc 30 | -------------------------------------------------------------------------------- /examples/yaff/mil53_ffsocket/run.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | import os 4 | 5 | from yaff import * 6 | 7 | from yaffdriver import YAFFDriver, MySocket 8 | 9 | if __name__ == '__main__': 10 | logf = open('yaff_%s.log' % os.getpid(), 'w') 11 | log._file = logf 12 | servername = 'MIL53' 13 | system = System.from_file('init.chk') 14 | ff = ForceField.generate(system, 'pars.txt', rcut=15 * angstrom, alpha_scale=3.2, gcut_scale=1.5, smooth_ei=True) 15 | 16 | socket = MySocket(servername, verbose=True) 17 | driver = YAFFDriver(socket, ff) 18 | driver.run() 19 | -------------------------------------------------------------------------------- /ipi/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | The i-PI package. 3 | """ 4 | 5 | __all__ = ["clients", "engine", "inputs", "interfaces", "utils"] 6 | -------------------------------------------------------------------------------- /ipi/engine/__init__.py: -------------------------------------------------------------------------------- 1 | """ 2 | Modules used to run simulations. 3 | """ 4 | 5 | # This file is part of i-PI. 6 | # i-PI Copyright (C) 2014-2015 i-PI developers 7 | # See the "licenses" directory for full license information. 8 | 9 | 10 | __all__ = ["atoms", "cell", "simulation", "forces", "ensembles", "properties", 11 | "thermostats", "barostats", "beads", "outputs", "normalmodes", 12 | "initializer", "system", "paratemp"] 13 | -------------------------------------------------------------------------------- /ipi/engine/motion/__init__.py: -------------------------------------------------------------------------------- 1 | """TODO 2 | 3 | """ 4 | 5 | # This file is part of i-PI. 6 | # i-PI Copyright (C) 2014-2015 i-PI developers 7 | # See the "licenses" directory for full license information. 8 | 9 | 10 | from .motion import Motion 11 | from .dynamics import Dynamics 12 | from .replay import Replay 13 | from .geop import GeopMotion 14 | from .instanton import InstantonMotion 15 | from .neb import NEBMover 16 | from .phonons import DynMatrixMover 17 | from .multi import MultiMotion 18 | from .alchemy import AlchemyMC 19 | -------------------------------------------------------------------------------- /ipi/engine/smotion/__init__.py: -------------------------------------------------------------------------------- 1 | """TODO 2 | 3 | """ 4 | 5 | # This file is part of i-PI. 6 | # i-PI Copyright (C) 2014-2015 i-PI developers 7 | # See the "licenses" directory for full license information. 8 | 9 | 10 | from .smotion import Smotion 11 | from .remd import ReplicaExchange 12 | from .metad import MetaDyn 13 | -------------------------------------------------------------------------------- /ipi/external/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/ipi/external/__init__.py -------------------------------------------------------------------------------- /ipi/external/importlib/__init__.py: -------------------------------------------------------------------------------- 1 | try: 2 | # importlib is a python stdlib from python 2.7 on 3 | from importlib import * 4 | except ImportError: 5 | from bundledimportlib import * 6 | -------------------------------------------------------------------------------- /ipi/inputs/__init__.py: -------------------------------------------------------------------------------- 1 | """Modules with all the the input classes.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | __all__ = ['barostats', 'cell', 'ensembles', 'thermostats', 'motion', 9 | 'interface', 'forces', 'forcefields', 'atoms', 'beads', 'prng', 'outputs', 10 | 'normalmodes', 'initializer', 'system', 'simulation'] 11 | -------------------------------------------------------------------------------- /ipi/inputs/motion/__init__.py: -------------------------------------------------------------------------------- 1 | """TODO 2 | 3 | """ 4 | 5 | # This file is part of i-PI. 6 | # i-PI Copyright (C) 2014-2015 i-PI developers 7 | # See the "licenses" directory for full license information. 8 | 9 | 10 | from .motion import InputMotion 11 | -------------------------------------------------------------------------------- /ipi/inputs/smotion/__init__.py: -------------------------------------------------------------------------------- 1 | """TODO 2 | 3 | """ 4 | 5 | # This file is part of i-PI. 6 | # i-PI Copyright (C) 2014-2015 i-PI developers 7 | # See the "licenses" directory for full license information. 8 | 9 | 10 | from .smotion import InputSmotion 11 | -------------------------------------------------------------------------------- /ipi/interfaces/__init__.py: -------------------------------------------------------------------------------- 1 | """Interfaces between i-PI and the drivers.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | __all__ = ["sockets", "clients"] 9 | -------------------------------------------------------------------------------- /ipi/tests/__init__.py: -------------------------------------------------------------------------------- 1 | """Tests that can be run with nosetests.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | -------------------------------------------------------------------------------- /ipi/tests/test.pos_0.pdb: -------------------------------------------------------------------------------- 1 | TITLE positions{angstrom} cell{angstrom} 2 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 3 | ATOM 1 O 1 1 0.000 1.000 2.000 0.00 0.00 0 4 | ATOM 2 H 1 1 3.000 4.000 5.000 0.00 0.00 0 5 | ATOM 3 H 1 1 6.000 7.000 8.000 0.00 0.00 0 6 | END 7 | TITLE positions{angstrom} cell{angstrom} 8 | CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 9 | ATOM 1 O 1 1 0.000 2.000 4.000 0.00 0.00 0 10 | ATOM 2 H 1 1 6.000 8.000 10.000 0.00 0.00 0 11 | ATOM 3 H 1 1 12.000 14.000 16.000 0.00 0.00 0 12 | END 13 | -------------------------------------------------------------------------------- /ipi/tests/test.pos_0.xyz: -------------------------------------------------------------------------------- 1 | 3 2 | # CELL(abcABC): 1.00000 1.00000 1.00000 90.00000 90.00000 90.00000 {atomic_unit} cell{atomic_unit} 3 | O 0.00000e+00 1.00000e+00 2.00000e+00 4 | H 3.00000e+00 4.00000e+00 5.00000e+00 5 | H 6.00000e+00 7.00000e+00 8.00000e+00 6 | 3 7 | # CELL(abcABC): 1.00000 1.00000 1.00000 90.00000 90.00000 90.00000 {atomic_unit} cell{atomic_unit} 8 | O 0.00000e+00 2.00000e+00 4.00000e+00 9 | H 6.00000e+00 8.00000e+00 1.00000e+01 10 | H 1.20000e+01 1.40000e+01 1.60000e+01 11 | -------------------------------------------------------------------------------- /ipi/tests/test_atoms.py: -------------------------------------------------------------------------------- 1 | """Deals with testing the Atoms object.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | from common import local 9 | 10 | from ipi.utils.io import read_file 11 | 12 | 13 | def get_atoms(fin): 14 | """Reads atoms object from file @fin.""" 15 | 16 | with open(local(fin), "r") as f: 17 | ret = read_file("xyz", f) 18 | return ret["atoms"] 19 | 20 | 21 | def test_names(): 22 | """Tests names of Atoms object.""" 23 | atoms = get_atoms("test.pos_0.xyz") 24 | expected = ["O", "H", "H"] 25 | assert len(atoms.names) == 3 26 | for i, name in enumerate(atoms.names): 27 | assert name == expected[i] 28 | assert name == atoms[i].name 29 | 30 | # Same test with iterator instead 31 | for i, atom in enumerate(atoms): 32 | assert atom.name == expected[i] 33 | assert atom.name == atoms.names[i] 34 | -------------------------------------------------------------------------------- /ipi/tests/test_runs.py: -------------------------------------------------------------------------------- 1 | """Tests that the Lennard-Jones test case works properly.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | from common import SimulationTest 9 | 10 | 11 | def test_lj_gas(): 12 | ts = SimulationTest(input="../../test/lj/gas/input.xml", driver="../../drivers/driver.x") 13 | ts.run() 14 | # Test properties (e.g. latest positions/temperature etc) 15 | -------------------------------------------------------------------------------- /ipi/tests/test_units.py: -------------------------------------------------------------------------------- 1 | """Tests unit conversion.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | from ipi.utils import units 9 | 10 | 11 | def test_case_insensitive(): 12 | 13 | angstrom = units.unit_to_internal('length', 'angstrom', 1.0) 14 | Angstrom = units.unit_to_internal('length', 'Angstrom', 1.0) 15 | -------------------------------------------------------------------------------- /ipi/utils/__init__.py: -------------------------------------------------------------------------------- 1 | """Package of utility functions used elsewhere in the code.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | __all__ = ['depend', 'units', 'mathtools', 'prng', 'inputvalue', 'nmtransform', 'messages', 'softexit', 'io'] 9 | -------------------------------------------------------------------------------- /ipi/utils/decorators.py: -------------------------------------------------------------------------------- 1 | """Decorators for easy utilizing i-PI simulations and more.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | def cached(f): 9 | """Cache decorator.""" 10 | 11 | _cache = {} 12 | 13 | def func(*args): 14 | if args in _cache: 15 | return _cache[args] 16 | res = f(*args) 17 | _cache[args] = res 18 | return res 19 | 20 | return func 21 | -------------------------------------------------------------------------------- /ipi/utils/io/backends/__init__.py: -------------------------------------------------------------------------------- 1 | """Contains the different backends for writing/reading atomic positions such as 2 | binary format, pdb and xyz. 3 | """ 4 | 5 | # This file is part of i-PI. 6 | # i-PI Copyright (C) 2014-2015 i-PI developers 7 | # See the "licenses" directory for full license information. 8 | 9 | 10 | __all__ = ["io_pdb", "io_xyz", "io_binary"] 11 | -------------------------------------------------------------------------------- /ipi/utils/io/inputs/__init__.py: -------------------------------------------------------------------------------- 1 | """Contains different implementations for reading/checkpointing an i-PI 2 | simulation. For now only xml, but in future possibly also yml/json. 3 | """ 4 | 5 | # This file is part of i-PI. 6 | # i-PI Copyright (C) 2014-2015 i-PI developers 7 | # See the "licenses" directory for full license information. 8 | 9 | 10 | __all__ = ["io_xml"] 11 | -------------------------------------------------------------------------------- /ipi_tests/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | -------------------------------------------------------------------------------- /ipi_tests/engine/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lab-cosmo/i-pi-dev_archive/ebc6eb56b3c5af0bb8e492e5d98637d61e6c51bb/ipi_tests/engine/__init__.py -------------------------------------------------------------------------------- /ipi_tests/utils/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | -------------------------------------------------------------------------------- /ipi_tests/utils/io/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | -------------------------------------------------------------------------------- /ipi_tests/utils/io/backends/__init__.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | -------------------------------------------------------------------------------- /licenses/license_MIT.txt: -------------------------------------------------------------------------------- 1 | MIT license 2 | Modern Style with sublicense 3 | 4 | Permission is hereby granted, free of charge, to any person obtaining 5 | a copy of this software and associated documentation files (the 6 | "Software"), to deal in the Software without restriction, including 7 | without limitation the rights to use, copy, modify, merge, publish, 8 | distribute, sublicense, and/or sell copies of the Software, and to 9 | permit persons to whom the Software is furnished to do so, subject to 10 | the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included 13 | in all copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, 16 | EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 17 | MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 18 | IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY 19 | CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, 20 | TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE 21 | SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. 22 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | """Setup script used for package installation.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2014-2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | 8 | import os 9 | from setuptools import setup, find_packages 10 | 11 | 12 | def read(fname): 13 | return open(os.path.join(os.path.dirname(__file__), fname)).read() 14 | 15 | 16 | setup( 17 | name='i-PI', 18 | version='1.0', 19 | description='A Python interface for ab initio path integral molecular dynamics simulations.', 20 | long_description=read('README.rst'), 21 | packages=find_packages(), 22 | scripts=['bin/i-pi'], 23 | libraries=[('ipi', {'sources': ['drivers/sockets.c']})], 24 | author="Michele Ceriotti", 25 | author_email="michele.ceriotti@gmail.com", 26 | classifiers=['Development Status :: 5 - Production/Stable'], 27 | license='GPLv3' 28 | ) 29 | -------------------------------------------------------------------------------- /tests/README: -------------------------------------------------------------------------------- 1 | -- tests directory -- 2 | 3 | * This tests other integration tests not directly related to the ipi module, 4 | e.g. building the manual 5 | 6 | * To run the tests, type "nosetests" in the root folder of this repository. 7 | -------------------------------------------------------------------------------- /tests/test_docs.py: -------------------------------------------------------------------------------- 1 | """Ensure that docs can always be built.""" 2 | 3 | # This file is part of i-PI. 4 | # i-PI Copyright (C) 2015 i-PI developers 5 | # See the "licenses" directory for full license information. 6 | 7 | import os 8 | import subprocess 9 | import shlex 10 | 11 | from nose import with_setup 12 | 13 | FNULL = open(os.devnull, 'w') 14 | 15 | 16 | def run_command(cmd): 17 | """Runs `cmd` in doc directory.""" 18 | cwd = os.getcwd() 19 | os.chdir(os.path.join(os.path.split(__file__)[0], "..", "doc")) 20 | ret = subprocess.call(shlex.split(cmd), stdout=FNULL, stderr=FNULL) 21 | os.chdir(cwd) 22 | return ret 23 | 24 | 25 | def distclean(): 26 | """Prepare for documentation build testing.""" 27 | run_command("make distclean") 28 | 29 | 30 | def clean(): 31 | """Clean up the documentation build after testing.""" 32 | run_command("make clean") 33 | 34 | 35 | @with_setup(distclean, None) 36 | def test_make_aux(): 37 | """doc: run make aux""" 38 | ret = run_command("make aux") 39 | assert ret == 0 40 | 41 | 42 | @with_setup(None, clean) 43 | def test_make(): 44 | """doc: run make""" 45 | ret = run_command("make") 46 | assert ret == 0 47 | -------------------------------------------------------------------------------- /tools/bash/update-tool-links.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash 2 | 3 | # This is to be run from the root directory and will create symlinks to 4 | # all the tools under `tools/py` in `bin`, with the `i-pi-` prefix. 5 | 6 | for tool in `ls tools/py` 7 | do 8 | ln -s ../tools/py/$tool bin/i-pi-${tool%.*} 9 | done 10 | -------------------------------------------------------------------------------- /tools/f90/compile.sh: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | f2py --fcompiler=gfortran --f90flags=-ffree-line-length-0 -m fortran -c fortran.f90 4 | -------------------------------------------------------------------------------- /tools/py/bin2xyz.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | 3 | """ bin2xyz.py 4 | 5 | Reads positions of a system in binary format and returns a 6 | xyz file. 7 | 8 | Assumes the input file is in a binary format. 9 | 10 | Syntax: 11 | bin2xyz.py filename 12 | """ 13 | 14 | 15 | import sys 16 | from ipi.utils.io import read_file, print_file 17 | from ipi.utils.depend import * 18 | from ipi.utils.units import * 19 | 20 | 21 | def main(filename): 22 | 23 | ipos = open(filename, "rb") 24 | 25 | natoms = 0 26 | ifr = 0 27 | while True: 28 | try: 29 | ret = read_file("bin", ipos) 30 | pos = ret["atoms"] 31 | cell = ret["cell"] 32 | cell.array_pbc(pos.q) 33 | except EOFError: # finished reading files 34 | sys.exit(0) 35 | 36 | print_file("xyz", pos, cell) 37 | ifr += 1 38 | 39 | 40 | if __name__ == '__main__': 41 | main(*sys.argv[1:]) 42 | -------------------------------------------------------------------------------- /tools/py/xyz2bin.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | 3 | """ xyz2bin.py 4 | 5 | Reads positions of a system in xyz format and returns a 6 | binary file. 7 | 8 | Assumes the input file is in a xyz format. 9 | 10 | Syntax: 11 | xyz2bin.py filename 12 | 13 | """ 14 | 15 | 16 | import sys 17 | from ipi.utils.io import read_file, print_file 18 | from ipi.utils.depend import * 19 | from ipi.utils.units import * 20 | 21 | 22 | def main(filename): 23 | 24 | ipos = open(filename, "r") 25 | 26 | natoms = 0 27 | ifr = 0 28 | while True: 29 | try: 30 | ret = read_file("xyz", ipos) 31 | pos = ret["atoms"] 32 | cell = ret["cell"] 33 | cell.array_pbc(pos.q) 34 | except EOFError: # finished reading files 35 | sys.exit(0) 36 | 37 | print_file("bin", pos, cell) 38 | ifr += 1 39 | 40 | 41 | if __name__ == '__main__': 42 | main(*sys.argv[1:]) 43 | -------------------------------------------------------------------------------- /tools/py/xyz2pdb.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python2 2 | 3 | """ xyz2pdb.py 4 | 5 | Reads positions of a system in xyz format and returns a 6 | pdb file. Also reads the comment line and returns the 7 | positions and the cell in Angstrom. 8 | 9 | Assumes the input file is in a pdb format. 10 | 11 | Syntax: 12 | xyz2pdb.py filename 13 | 14 | """ 15 | 16 | 17 | import sys 18 | from ipi.utils.io import read_file, print_file 19 | from ipi.utils.depend import * 20 | from ipi.utils.units import * 21 | 22 | 23 | def main(filename, wrap=True): 24 | 25 | ipos = open(filename, "r") 26 | if(wrap == "False"): 27 | wrap = False 28 | 29 | natoms = 0 30 | ifr = 0 31 | while True: 32 | try: 33 | ret = read_file("xyz", ipos) 34 | pos = ret["atoms"] 35 | cell = ret["cell"] 36 | if(wrap): cell.array_pbc(pos.q) 37 | except EOFError: # finished reading files 38 | sys.exit(0) 39 | 40 | print_file("pdb", pos, cell) 41 | ifr += 1 42 | 43 | 44 | if __name__ == '__main__': 45 | main(*sys.argv[1:]) 46 | --------------------------------------------------------------------------------