From 169c92e365f05fdad4ddd1d20eca24c8cb61dc05 Mon Sep 17 00:00:00 2001 From: Venkat Kapil Date: Thu, 1 Nov 2018 14:47:25 +0100 Subject: [PATCH 1/2] updated teh description of the instantons motion class --- ipi/inputs/motion/instanton.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ipi/inputs/motion/instanton.py b/ipi/inputs/motion/instanton.py index f61a3e2a..7c291def 100644 --- a/ipi/inputs/motion/instanton.py +++ b/ipi/inputs/motion/instanton.py @@ -144,8 +144,8 @@ class InputInst(InputDictionary): dynamic = {} - default_help = "TODO EXPLAIN WHAT THIS IS" - default_label = "Instanton" + default_help = "A class for instanton calculations" + default_label = "INSTANTON" def store(self, geop): if geop == {}: From 7bf94d34a6ae7f129180cf815121028e055a5d57 Mon Sep 17 00:00:00 2001 From: Venkat Kapil Date: Thu, 1 Nov 2018 15:02:31 +0100 Subject: [PATCH 2/2] added two examples which existed in the main i-pi repo but not here. --- examples/lammps/graphene/C.opt.tersoff | 66 + examples/lammps/graphene/data.lmp | 1939 ++++++++++++++++++++++++ examples/lammps/graphene/in.lmp | 33 + examples/lammps/graphene/init.xyz | 962 ++++++++++++ examples/lammps/graphene/input.xml | 37 + examples/lammps/h2o-repimd/0_init.xyz | 194 +++ examples/lammps/h2o-repimd/10_init.xyz | 194 +++ examples/lammps/h2o-repimd/11_init.xyz | 194 +++ examples/lammps/h2o-repimd/12_init.xyz | 194 +++ examples/lammps/h2o-repimd/13_init.xyz | 194 +++ examples/lammps/h2o-repimd/14_init.xyz | 194 +++ examples/lammps/h2o-repimd/15_init.xyz | 194 +++ examples/lammps/h2o-repimd/16_init.xyz | 194 +++ examples/lammps/h2o-repimd/17_init.xyz | 194 +++ examples/lammps/h2o-repimd/18_init.xyz | 194 +++ examples/lammps/h2o-repimd/19_init.xyz | 194 +++ examples/lammps/h2o-repimd/1_init.xyz | 194 +++ examples/lammps/h2o-repimd/2_init.xyz | 194 +++ examples/lammps/h2o-repimd/3_init.xyz | 194 +++ examples/lammps/h2o-repimd/4_init.xyz | 194 +++ examples/lammps/h2o-repimd/5_init.xyz | 194 +++ examples/lammps/h2o-repimd/6_init.xyz | 194 +++ examples/lammps/h2o-repimd/7_init.xyz | 194 +++ examples/lammps/h2o-repimd/8_init.xyz | 194 +++ examples/lammps/h2o-repimd/9_init.xyz | 194 +++ examples/lammps/h2o-repimd/data.lmp | 419 +++++ examples/lammps/h2o-repimd/in.lmp | 23 + examples/lammps/h2o-repimd/input.xml | 76 + 28 files changed, 7435 insertions(+) create mode 100644 examples/lammps/graphene/C.opt.tersoff create mode 100644 examples/lammps/graphene/data.lmp create mode 100644 examples/lammps/graphene/in.lmp create mode 100644 examples/lammps/graphene/init.xyz create mode 100644 examples/lammps/graphene/input.xml create mode 100644 examples/lammps/h2o-repimd/0_init.xyz create mode 100644 examples/lammps/h2o-repimd/10_init.xyz create mode 100644 examples/lammps/h2o-repimd/11_init.xyz create mode 100644 examples/lammps/h2o-repimd/12_init.xyz create mode 100644 examples/lammps/h2o-repimd/13_init.xyz create mode 100644 examples/lammps/h2o-repimd/14_init.xyz create mode 100644 examples/lammps/h2o-repimd/15_init.xyz create mode 100644 examples/lammps/h2o-repimd/16_init.xyz create mode 100644 examples/lammps/h2o-repimd/17_init.xyz create mode 100644 examples/lammps/h2o-repimd/18_init.xyz create mode 100644 examples/lammps/h2o-repimd/19_init.xyz create mode 100644 examples/lammps/h2o-repimd/1_init.xyz create mode 100644 examples/lammps/h2o-repimd/2_init.xyz create mode 100644 examples/lammps/h2o-repimd/3_init.xyz create mode 100644 examples/lammps/h2o-repimd/4_init.xyz create mode 100644 examples/lammps/h2o-repimd/5_init.xyz create mode 100644 examples/lammps/h2o-repimd/6_init.xyz create mode 100644 examples/lammps/h2o-repimd/7_init.xyz create mode 100644 examples/lammps/h2o-repimd/8_init.xyz create mode 100644 examples/lammps/h2o-repimd/9_init.xyz create mode 100644 examples/lammps/h2o-repimd/data.lmp create mode 100644 examples/lammps/h2o-repimd/in.lmp create mode 100644 examples/lammps/h2o-repimd/input.xml diff --git a/examples/lammps/graphene/C.opt.tersoff b/examples/lammps/graphene/C.opt.tersoff new file mode 100644 index 00000000..3bc19f05 --- /dev/null +++ b/examples/lammps/graphene/C.opt.tersoff @@ -0,0 +1,66 @@ +# Tersoff parameters for various elements and mixtures +# multiple entries can be added to this file, LAMMPS reads the ones it needs +# these entries are in LAMMPS "metal" units: +# A,B = eV; lambda1,lambda2,lambda3 = 1/Angstroms; R,D = Angstroms +# other quantities are unitless + +# Aidan Thompson (athomps at sandia.gov) takes full blame for this +# file. It specifies various potentials published by J. Tersoff for +# silicon, carbon and germanium. Since Tersoff published several +# different silicon potentials, I refer to them using atom types +# Si(B), Si(C) and Si(D). The last two are almost almost identical but +# refer to two different publications. These names should be used in +# the LAMMPS command when the file is invoked. For example: +# pair_coeff * * SiCGe.tersoff Si(B). The Si(D), C and Ge potentials +# can be used pure silicon, pure carbon, pure germanium, binary SiC, +# and binary SiGe, but not binary GeC or ternary SiGeC. LAMMPS will +# generate an error if this file is used with any combination +# involving C and Ge, since there are no entries for the GeC +# interactions (Tersoff did not publish parameters for this +# cross-interaction.) + +# format of a single entry (one or more lines): +# element 1, element 2, element 3, +# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A + +# The original Tersoff potential for Silicon, Si(B) +# J. Tersoff, PRB, 37, 6991 (1988) + +Si(B) Si(B) Si(B) 3.0 1.0 1.3258 4.8381 2.0417 0.0000 22.956 + 0.33675 1.3258 95.373 3.0 0.2 3.2394 3264.7 + +# The later Tersoff potential for Silicon, Si(C) +# J. Tersoff, PRB, 38, 9902 (1988) + +Si(C) Si(C) Si(C) 3.0 1.0 1.7322 1.0039e5 16.218 -0.59826 0.78734 + 1.0999e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8 + +# The later Tersoff potential for Carbon, Silicon, and Germanium +# J. Tersoff, PRB, 39, 5566 (1989) + errata (PRB 41, 3248) +# The Si and C parameters are very close to those in SiC.tersoff + +C C C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 2.2119 346.74 1.95 0.15 3.4879 1393.6 +Si(D) Si(D) Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.7322 471.18 2.85 0.15 2.4799 1830.8 +Ge Ge Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.7047 419.23 2.95 0.15 2.4451 1769.0 + +C Si(D) Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 1.5724e-7 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111 +C Si(D) C 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 1.95 0.15 0.0 0.0 +C C Si(D) 3.0 1.0 0.0 3.8049e4 4.3484 -0.57058 0.72751 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0 + +Si(D) C C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.97205 395.1451 2.3573 0.1527 2.9839 1597.3111 +Si(D) Si(D) C 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.3573 0.1527 0.0 0.0 +Si(D) C Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0 + +Si(D) Ge Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 1.1000e-6 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347 +Si(D) Si(D) Ge 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0 +Si(D) Ge Si(D) 3.0 1.0 0.0 1.0039e5 16.217 -0.59825 0.78734 0.0 0.0 0.0 2.85 0.15 0.0 0.0 + +Ge Si(D) Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 9.0166e-7 1.71845 444.7177 2.8996 0.1500 2.4625 1799.6347 +Ge Si(D) Ge 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.95 0.15 0.0 0.0 +Ge Ge Si(D) 3.0 1.0 0.0 1.0643e5 15.652 -0.43884 0.75627 0.0 0.0 0.0 2.8996 0.1500 0.0 0.0 + +# Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010) +# element 1, element 2, element 3, +# m, gamma, lambda3, c, d, costheta0, n, beta, lambda2, B, R, D, lambda1, A +C(O) C(O) C(O) 3.0 1.0 0.0 3.8049e4 4.3484 -0.930 0.72751 1.5724e-7 2.2119 430.0 1.95 0.15 3.4879 1393.6 + diff --git a/examples/lammps/graphene/data.lmp 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b/examples/lammps/graphene/in.lmp @@ -0,0 +1,33 @@ +atom_style atomic +units metal +dimension 3 +boundary p p p +processors * * 1 + +read_data ./data.lmp +mass 1 12.01 ##Carbon + +### Optimized Tersoff for Carbon: Lindsay and Broido PRB 81, 205441 (2010) +pair_style tersoff +pair_coeff * * C.opt.tersoff C(O) + +variable T equal 300 +variable V equal vol + +variable Lx equal xhi-xlo +variable Ly equal yhi-ylo +print "Lx = ${Lx} A" +print "Ly = ${Ly} A" + +print "Volume simulation box = $V A^(3)" +variable Volume equal v_Lx*v_Ly*3.35 +print "Volume = Lx*Ly*3.35A = ${Volume} A^(3)" + +velocity all create $T 345352 mom yes rot yes dist gaussian +timestep 0.001 # 0.001 picosecond = 1 femtosecond +thermo 1000 +thermo_style custom step temp pe etotal press pxx pyy pzz + +fix 1 all ipi graphene 31415 unix +run 5000000 + diff --git a/examples/lammps/graphene/init.xyz b/examples/lammps/graphene/init.xyz new file mode 100644 index 00000000..98146029 --- /dev/null +++ b/examples/lammps/graphene/init.xyz @@ -0,0 +1,962 @@ +960 +# CELL(abcABC): 5.180e+01 4.984e+01 2.000e+02 90.0 90.0 90.0 positions{angstrom} cell{angstrom} +C 7.6775598001397471e-01 1.2667932797279446e+00 2.1080473899138757e-01 +C 2.1890031462382358e+00 1.2788803931391020e+00 1.4136214742333245e-01 +C 2.9060546960435314e+00 4.4433726498823566e-02 1.2097671772310112e-01 +C 5.0483470945677738e+00 1.2448933511107161e+00 -4.5520905082000782e-02 +C 1.2910065082029972e+01 2.9700150824150690e-02 3.4900846414331060e-01 +C 6.4760090900951939e+00 1.2835307010363712e+00 3.7599922421305818e-02 +C 1.1458516722573021e+01 2.4913603449839325e+01 5.8495604728281449e-02 +C 7.1875253095015319e+00 3.0522334290746869e-02 1.0111992821244095e-01 +C 9.3728425080296773e+00 1.2967280778480161e+00 1.5269060284733313e-01 +C 1.0782485573272096e+01 1.2819930155705055e+00 2.9916328165487305e-01 +C 6.9054075294781869e-01 3.6947230198921983e+00 -9.6524430368314665e-02 +C 7.2200041486136719e+00 2.4889091148203331e+01 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4.2338229294599742e+01 1.2233774923186563e-01 +C 4.7510999315216793e+01 4.2318103710527197e+01 9.7277582114329991e-02 +C 5.0429710537278602e+01 4.2393694657407877e+01 2.5956718510899801e-01 +C 4.7519254646886687e+01 4.7342948785093057e+01 -6.1736343734502833e-02 +C 4.3926111625502102e+01 4.8602116971851743e+01 -1.7199343797354699e-01 +C 3.9607468597413103e+01 4.3579276945031289e+01 -9.7913771679284917e-02 +C 4.1032506326943583e+01 4.3617057561199481e+01 -2.1002919056806818e-02 +C 4.1746351183265105e+01 4.4849906505263817e+01 1.0597590606644908e-02 +C 4.3176046564315008e+01 4.4832224333067671e+01 2.4713883692839486e-02 +C 4.3904123567088263e+01 4.3599617881427925e+01 1.1352137114603467e-01 +C 4.5343772331317396e+01 4.3596249149235234e+01 1.5536725014731215e-01 +C 4.6024426796884100e+01 4.4837057693522411e+01 1.6781919427054950e-01 +C 4.7493224070212293e+01 4.4834554137856983e+01 1.0042912569058128e-01 +C 4.8216648374818909e+01 4.3536475941689616e+01 1.3902958176807645e-01 +C 4.9674636619011572e+01 4.3597960157243278e+01 1.3911445290639693e-01 +C 5.0393600023800921e+01 4.4872455948282600e+01 1.3830788539759933e-01 +C 4.6076473757001750e+01 4.7328051208986608e+01 -7.2051547583144984e-02 +C 3.8851065119076729e+01 4.7328948153954876e+01 -1.5380155403385665e-01 +C 3.9601373643101049e+01 4.6088113809528423e+01 -1.4210221459909309e-01 +C 4.1045190875277100e+01 4.6120105866098065e+01 -1.1916280823440377e-01 +C 4.1796308830672679e+01 4.7353659119384844e+01 -1.6600232029005188e-01 +C 4.3175338571658294e+01 4.7327983667777353e+01 -5.2028650763793163e-02 +C 4.3902440486091052e+01 4.6031887732905354e+01 -1.7128970196839670e-02 +C 4.5351952106565477e+01 4.6097703294474734e+01 -8.0160599617958815e-03 +C 3.8862512188825782e+01 3.7446905674906269e+01 4.1858473402893387e-01 +C 3.8913913720439986e+01 4.4882189608514295e+01 -2.0391628699836786e-01 +C 4.1734254753715135e+01 4.9820642701394910e+01 -2.9506578580670206e-01 +C 4.7522887118468745e+01 4.9806385482988325e+01 -1.7616812023662626e-01 +C 5.0363491597953661e+01 4.9804065572103184e+01 1.6609961281486424e-01 +C 3.8856840261434826e+01 4.9834536037775649e+01 -1.2484495671497083e-01 +C 4.3189339118730445e+01 4.9830229023705698e+01 -2.6516891811201510e-01 +C 4.1737619544657882e+01 2.4958368141690801e+01 -5.4195895871393518e-01 +C 4.3186233450662499e+01 2.4991186885270562e+01 -5.6314074826259475e-01 diff --git a/examples/lammps/graphene/input.xml b/examples/lammps/graphene/input.xml new file mode 100644 index 00000000..478e84e1 --- /dev/null +++ b/examples/lammps/graphene/input.xml @@ -0,0 +1,37 @@ + + + [ step, time{picosecond}, conserved{kelvin}, temperature{kelvin}, kinetic_cv{kelvin}, potential{kelvin}, pressure_cv{megapascal}] + [ isotope_tdfep(1.167;C), isotope_scfep(1.167;0) ] + [ kinetic_cv{kelvin}(C) ] + positions{angstrom} + kinetic_cv + + + 1000000 + + 31415 + + +
graphene
+ + + + init.xyz + 300 + + + + + + + 1.0 + + 100 + + + + + 300 + + + diff --git a/examples/lammps/h2o-repimd/0_init.xyz b/examples/lammps/h2o-repimd/0_init.xyz new file mode 100644 index 00000000..289015b9 --- /dev/null +++ b/examples/lammps/h2o-repimd/0_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.38414 23.38414 23.38414 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -3.30666e+01 5.05897e+01 -1.36898e+01 + H -3.14717e+01 5.00991e+01 -1.43250e+01 + H -3.37033e+01 5.18282e+01 -1.49025e+01 + O 4.20529e+01 9.50998e+01 -6.15593e+01 + H 4.30264e+01 9.64009e+01 -6.21512e+01 + H 4.20618e+01 9.38391e+01 -6.29861e+01 + O 1.20801e+01 2.28772e+01 -4.89727e+01 + H 1.04024e+01 2.25832e+01 -4.84212e+01 + H 1.31024e+01 2.23767e+01 -4.76008e+01 + O 6.25554e+01 -3.60421e+01 -9.67095e+01 + H 6.08640e+01 -3.52562e+01 -9.64318e+01 + H 6.35445e+01 -3.46530e+01 -9.60976e+01 + O 5.45938e+01 1.32963e+02 6.72096e+01 + H 5.30174e+01 1.32638e+02 6.62835e+01 + H 5.56697e+01 1.33718e+02 6.59927e+01 + O -2.77965e+01 2.75490e+01 -1.61761e+00 + H -2.81411e+01 2.58649e+01 -2.25286e+00 + H -2.93217e+01 2.83364e+01 -1.89466e+00 + O 2.05836e+01 -1.94209e+01 3.54063e+00 + H 1.98190e+01 -1.95084e+01 1.81605e+00 + H 2.14288e+01 -1.77729e+01 3.80974e+00 + O 4.94086e+00 3.18422e+00 4.71637e+01 + H 4.34575e+00 3.74687e+00 4.55492e+01 + H 3.43867e+00 2.14064e+00 4.77957e+01 + O 8.15324e+01 -4.31498e+01 8.85347e+01 + H 8.29521e+01 -4.26993e+01 8.74667e+01 + H 8.18501e+01 -4.48310e+01 8.92350e+01 + O -4.69492e+01 -1.09037e+02 -4.14473e+01 + H -4.51846e+01 -1.08840e+02 -4.15498e+01 + H -4.69691e+01 -1.10223e+02 -3.99361e+01 + O -9.62602e+01 6.01823e+01 2.35473e+01 + H -9.49222e+01 5.92820e+01 2.26999e+01 + H -9.57459e+01 6.19320e+01 2.34797e+01 + O -9.92223e+01 6.63199e+01 4.66446e+01 + H -9.94032e+01 6.71881e+01 4.82807e+01 + H -9.76256e+01 6.53858e+01 4.67301e+01 + O 2.30662e+01 -6.96888e+01 -2.91484e+01 + H 2.19783e+01 -6.92108e+01 -3.05803e+01 + H 2.16752e+01 -6.99592e+01 -2.80599e+01 + O 9.72313e+01 -5.74831e+01 3.22836e+01 + H 9.65453e+01 -5.80090e+01 3.38759e+01 + H 9.90888e+01 -5.78439e+01 3.26154e+01 + O -1.40067e+00 -5.42818e+00 2.97239e+01 + H -2.68245e+00 -4.30553e+00 2.91509e+01 + H -1.84067e+00 -7.15128e+00 2.98282e+01 + O -6.87592e+01 -2.78185e+01 -2.93508e+01 + H -6.95491e+01 -2.62077e+01 -2.94526e+01 + H -6.70764e+01 -2.71525e+01 -2.99174e+01 + O -2.21002e+00 -5.73029e+01 -4.14799e+01 + H -2.87873e+00 -5.70309e+01 -4.31594e+01 + H -1.60009e+00 -5.89584e+01 -4.14066e+01 + O -3.80609e+01 1.04329e+02 -8.36784e+01 + H -3.78965e+01 1.03255e+02 -8.22540e+01 + H -3.74185e+01 1.03312e+02 -8.51023e+01 + O 8.43029e+01 1.86725e+01 7.16609e+00 + H 8.38219e+01 1.69242e+01 7.39197e+00 + H 8.39358e+01 1.94551e+01 8.80435e+00 + O 1.16237e+02 6.48552e+01 -2.44601e+01 + H 1.17476e+02 6.49166e+01 -2.31662e+01 + H 1.17118e+02 6.56741e+01 -2.58611e+01 + O -4.38960e+00 4.79154e+01 -9.40336e+00 + H -5.51843e+00 4.93112e+01 -9.12054e+00 + H -4.44277e+00 4.77616e+01 -1.11660e+01 + O 1.60371e+01 1.26720e+01 7.70850e+01 + H 1.62284e+01 1.28824e+01 7.88903e+01 + H 1.78321e+01 1.28621e+01 7.65817e+01 + O 3.39279e+00 8.42552e+01 -5.15829e+01 + H 3.15357e+00 8.32614e+01 -5.31555e+01 + H 2.59952e+00 8.58457e+01 -5.19941e+01 + O 1.05983e+02 -1.87590e+01 5.00025e+01 + H 1.06486e+02 -1.82216e+01 4.83352e+01 + H 1.04261e+02 -1.93456e+01 5.01533e+01 + O -7.09931e+01 5.39601e+01 4.25434e+01 + H -7.09037e+01 5.54880e+01 4.35018e+01 + H -7.21083e+01 5.28692e+01 4.34588e+01 + O 3.96943e+01 -3.27115e+01 -1.14222e+01 + H 4.09075e+01 -3.14589e+01 -1.07271e+01 + H 3.78750e+01 -3.23504e+01 -1.12518e+01 + O -3.26795e+01 -1.74664e+01 2.17216e+01 + H -3.21139e+01 -1.58314e+01 2.10905e+01 + H -3.38144e+01 -1.80835e+01 2.04205e+01 + O 5.25113e+01 2.15729e+01 4.00664e+01 + H 5.29106e+01 2.32615e+01 3.93614e+01 + H 5.27166e+01 2.16622e+01 4.19225e+01 + O 9.79335e+01 -1.09144e+01 -1.97519e+01 + H 9.97737e+01 -1.11653e+01 -1.99255e+01 + H 9.75625e+01 -1.08094e+01 -1.80359e+01 + O 7.88024e+00 -7.49792e+01 1.33434e+01 + H 6.47545e+00 -7.50059e+01 1.22380e+01 + H 7.41823e+00 -7.37127e+01 1.46220e+01 + O -9.74432e+01 4.07862e+01 6.07386e+01 + H -9.67434e+01 4.02775e+01 6.23740e+01 + H -9.89264e+01 4.17145e+01 6.13196e+01 + O 8.04458e+00 -3.97669e+01 4.25391e+01 + H 8.99956e+00 -4.12709e+01 4.22097e+01 + H 6.32611e+00 -4.04322e+01 4.26230e+01 + O -6.32563e+01 4.57265e+01 2.18026e+01 + H -6.31829e+01 4.47097e+01 2.34022e+01 + H -6.37309e+01 4.73457e+01 2.25502e+01 + O 2.17368e+01 3.18343e+01 -9.27564e+00 + H 2.01130e+01 3.21209e+01 -9.68188e+00 + H 2.17180e+01 3.09849e+01 -7.70903e+00 + O -8.93583e+01 -2.89282e+01 -3.70691e+01 + H -9.10493e+01 -2.81992e+01 -3.68596e+01 + H -8.97812e+01 -3.06787e+01 -3.75828e+01 + O 5.62782e+01 -3.71389e+01 -4.34035e+01 + H 5.68370e+01 -3.55084e+01 -4.27426e+01 + H 5.68988e+01 -3.72028e+01 -4.51420e+01 + O 3.08345e+01 3.09046e+01 6.09241e+01 + H 3.11792e+01 3.09504e+01 6.26903e+01 + H 3.03428e+01 2.92152e+01 6.05414e+01 + O -3.10751e+01 6.75516e+01 8.54413e+01 + H -2.95597e+01 6.86319e+01 8.52430e+01 + H -3.21384e+01 6.76619e+01 8.39341e+01 + O -3.39693e+01 1.24974e+02 1.00769e+02 + H -3.30645e+01 1.26519e+02 1.01003e+02 + H -3.41316e+01 1.24816e+02 9.89345e+01 + O 3.34200e+01 1.09557e+01 4.49048e+01 + H 3.23643e+01 9.67113e+00 4.39795e+01 + H 3.26336e+01 1.25733e+01 4.46788e+01 + O 5.55694e+01 2.08179e+00 -1.43332e+01 + H 5.72937e+01 2.65978e+00 -1.43123e+01 + H 5.48379e+01 2.79100e+00 -1.58493e+01 + O 1.94522e+02 -2.83572e+01 2.50218e+01 + H 1.92749e+02 -2.88515e+01 2.55039e+01 + H 1.94627e+02 -2.93164e+01 2.34661e+01 + O -2.07121e+01 -1.21128e+01 -3.24230e+01 + H -1.92910e+01 -1.32072e+01 -3.26208e+01 + H -2.22169e+01 -1.31451e+01 -3.24168e+01 + O 4.83392e+00 -2.50909e+01 -4.03799e+01 + H 6.49258e+00 -2.44880e+01 -4.06126e+01 + H 4.97858e+00 -2.64569e+01 -3.92419e+01 + O 3.55661e+01 -2.15996e+00 5.81308e+01 + H 3.47821e+01 -6.74316e-01 5.73646e+01 + H 3.41972e+01 -3.19375e+00 5.86453e+01 + O 1.24894e+01 -5.18341e+01 -4.84899e+00 + H 1.36451e+01 -5.14447e+01 -6.18823e+00 + H 1.22342e+01 -5.03083e+01 -3.85017e+00 + O -2.85187e+01 -9.57392e+01 -8.85275e+01 + H -3.00687e+01 -9.66433e+01 -8.79298e+01 + H -2.91734e+01 -9.42434e+01 -8.93907e+01 + O -1.74301e+01 2.55490e+01 3.65545e+01 + H -1.60667e+01 2.53155e+01 3.51895e+01 + H -1.90554e+01 2.49205e+01 3.59057e+01 + O -4.76652e+01 2.85780e+01 3.30942e+01 + H -4.74544e+01 2.95292e+01 3.46376e+01 + H -4.66664e+01 2.70040e+01 3.33085e+01 + O -9.17858e+01 8.09002e+01 -8.28285e-01 + H -9.10011e+01 8.10374e+01 8.40797e-01 + H -9.08043e+01 8.20005e+01 -1.94465e+00 + O -5.37217e+01 9.83442e+00 -8.66855e+00 + H -5.41556e+01 1.04980e+01 -7.02458e+00 + H -5.39084e+01 1.13057e+01 -9.79823e+00 + O 1.43059e+01 5.07446e-03 4.93203e+01 + H 1.29112e+01 -4.64052e-01 5.03917e+01 + H 1.41523e+01 1.76793e+00 4.94909e+01 + O 2.42774e+01 2.80013e-01 1.66836e+02 + H 2.28916e+01 1.42690e+00 1.67221e+02 + H 2.51450e+01 -3.28811e-01 1.68218e+02 + O -9.27901e+00 -7.77466e+00 4.64908e+01 + H -1.03485e+01 -6.92499e+00 4.52574e+01 + H -8.21364e+00 -6.46689e+00 4.70046e+01 + O -6.76183e+01 1.76207e+01 -9.07021e+01 + H -6.86680e+01 1.83129e+01 -8.93835e+01 + H -6.74999e+01 1.58460e+01 -9.04308e+01 + O 1.54563e+01 5.15694e+01 1.08227e+02 + H 1.58019e+01 5.33329e+01 1.08259e+02 + H 1.50345e+01 5.15075e+01 1.06449e+02 + O 3.48042e+00 -4.25934e+01 4.25790e+01 + H 2.56926e+00 -4.40116e+01 4.18992e+01 + H 2.20768e+00 -4.13187e+01 4.30474e+01 + O -1.29013e+01 2.17130e+01 7.52496e+01 + H -1.39849e+01 2.06897e+01 7.42129e+01 + H -1.16856e+01 2.05242e+01 7.59815e+01 + O 8.15156e+01 3.86076e+01 -1.17941e+01 + H 8.04326e+01 3.71649e+01 -1.23985e+01 + H 8.02323e+01 3.97486e+01 -1.12545e+01 + O 5.81125e+01 -3.21588e+01 7.48508e+01 + H 5.96163e+01 -3.30115e+01 7.52871e+01 + H 5.86072e+01 -3.13108e+01 7.32361e+01 + O -5.10458e+00 2.31837e+01 4.28768e+01 + H -5.46875e+00 2.18719e+01 4.41679e+01 + H -6.54405e+00 2.30318e+01 4.18596e+01 + O 1.63142e+02 1.97250e+01 -1.23561e+01 + H 1.62570e+02 1.92678e+01 -1.40071e+01 + H 1.61580e+02 1.92688e+01 -1.13379e+01 + O -6.26538e+01 9.83431e+01 -4.20451e+01 + H -6.17299e+01 9.99669e+01 -4.22216e+01 + H -6.39924e+01 9.83106e+01 -4.32511e+01 + O -6.84586e+01 -2.26416e+01 3.33611e+01 + H -6.93966e+01 -2.40657e+01 3.40751e+01 + H -6.70588e+01 -2.33044e+01 3.24378e+01 diff --git a/examples/lammps/h2o-repimd/10_init.xyz b/examples/lammps/h2o-repimd/10_init.xyz new file mode 100644 index 00000000..51022a7a --- /dev/null +++ b/examples/lammps/h2o-repimd/10_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.23964 23.23964 23.23964 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -9.49031e+00 5.82837e+01 -2.31601e+01 + H -1.11632e+01 5.79669e+01 -2.37609e+01 + H -8.33195e+00 5.79969e+01 -2.45829e+01 + O 4.09489e+01 1.03904e+02 -5.02961e+01 + H 4.19143e+01 1.02629e+02 -4.95152e+01 + H 4.02344e+01 1.03346e+02 -5.18875e+01 + O 2.92622e+01 7.75002e+00 -5.61628e+01 + H 2.98537e+01 9.65284e+00 -5.62079e+01 + H 2.81084e+01 7.60228e+00 -5.76798e+01 + O 6.54586e+01 -3.86589e+01 -8.36717e+01 + H 6.37541e+01 -3.79772e+01 -8.38709e+01 + H 6.54415e+01 -4.04862e+01 -8.33490e+01 + O 7.39990e+01 1.27398e+02 6.77142e+01 + H 7.30997e+01 1.27349e+02 6.92929e+01 + H 7.35121e+01 1.25995e+02 6.66647e+01 + O -4.68357e+01 2.75348e+01 6.69888e+00 + H -4.58039e+01 2.87265e+01 7.60891e+00 + H -4.57694e+01 2.71110e+01 5.30881e+00 + O 4.60780e+00 -2.65418e+01 -5.26553e+00 + H 5.97760e+00 -2.68981e+01 -4.18033e+00 + H 5.28066e+00 -2.62627e+01 -7.00895e+00 + O 2.31869e+01 2.01091e+01 5.98642e+01 + H 2.33755e+01 2.13519e+01 5.85355e+01 + H 2.23361e+01 2.07867e+01 6.12741e+01 + O 8.09812e+01 -3.42541e+01 8.61934e+01 + H 8.17250e+01 -3.26632e+01 8.66449e+01 + H 8.03705e+01 -3.49201e+01 8.78355e+01 + O -5.04543e+01 -1.09406e+02 -4.28806e+01 + H -4.99777e+01 -1.07664e+02 -4.28672e+01 + H -4.91874e+01 -1.09981e+02 -4.16191e+01 + O -7.40130e+01 4.91200e+01 1.09874e+01 + H -7.43401e+01 4.74531e+01 1.07705e+01 + H -7.53828e+01 4.99408e+01 1.17930e+01 + O -9.71134e+01 6.82033e+01 6.31832e+01 + H -9.58855e+01 6.83835e+01 6.45096e+01 + H -9.81070e+01 6.96737e+01 6.33574e+01 + O 1.31758e+00 -4.26282e+01 -2.56461e+01 + H 2.35520e+00 -4.17351e+01 -2.67926e+01 + H -1.67005e-01 -4.16324e+01 -2.55967e+01 + O 6.32343e+01 -5.12772e+01 3.01708e+00 + H 6.47400e+01 -5.19077e+01 2.09744e+00 + H 6.35402e+01 -4.94965e+01 3.18910e+00 + O 1.26442e+01 -2.28419e+01 2.20811e+01 + H 1.32295e+01 -2.30891e+01 2.36845e+01 + H 1.11639e+01 -2.38046e+01 2.19862e+01 + O -9.68741e+01 -4.65020e+01 -1.86308e+01 + H -9.62690e+01 -4.77496e+01 -1.75182e+01 + H -9.60990e+01 -4.49643e+01 -1.80810e+01 + O -1.57668e+01 -4.17970e+01 -6.71963e+01 + H -1.57604e+01 -4.01799e+01 -6.64902e+01 + H -1.47521e+01 -4.16779e+01 -6.86318e+01 + O -3.99145e+01 7.85460e+01 -8.76384e+01 + H -3.89695e+01 7.94745e+01 -8.63860e+01 + H -4.12680e+01 7.96515e+01 -8.81887e+01 + 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7.75442e+00 -1.39566e+01 + H -4.37883e+01 9.43909e+00 -1.32778e+01 + H -4.22520e+01 7.99876e+00 -1.54332e+01 + O -1.29358e+00 1.53118e+01 3.78824e+01 + H 7.01702e-02 1.50340e+01 3.90271e+01 + H -9.49788e-01 1.70025e+01 3.72713e+01 + O 1.09977e+01 1.59460e+01 1.69078e+02 + H 1.22766e+01 1.53553e+01 1.68078e+02 + H 1.18547e+01 1.68454e+01 1.70349e+02 + O 7.26960e+00 -2.24482e+01 5.66549e+01 + H 8.05556e+00 -2.27478e+01 5.49976e+01 + H 8.30318e+00 -2.10687e+01 5.72991e+01 + O -4.82619e+01 9.04347e+00 -1.01566e+02 + H -4.91457e+01 9.17553e+00 -1.03168e+02 + H -4.95729e+01 8.35428e+00 -1.00471e+02 + O 2.04339e+01 3.93135e+01 1.16632e+02 + H 2.15142e+01 4.07738e+01 1.16536e+02 + H 1.97233e+01 3.90141e+01 1.15006e+02 + O 2.12415e+01 -5.02165e+01 3.06761e+01 + H 1.99508e+01 -4.99354e+01 3.18957e+01 + H 2.25451e+01 -4.89280e+01 3.09854e+01 + O -1.42670e+01 2.39433e+01 7.51709e+01 + H -1.44594e+01 2.55041e+01 7.41970e+01 + H -1.24664e+01 2.35782e+01 7.50366e+01 + O 8.84077e+01 6.21185e+01 -4.66669e+00 + H 8.81718e+01 6.02864e+01 -4.45529e+00 + H 8.96688e+01 6.22465e+01 -5.94553e+00 + O 7.66349e+01 -5.73014e+01 1.06609e+02 + H 7.54003e+01 -5.66292e+01 1.07785e+02 + H 7.81235e+01 -5.74662e+01 1.07576e+02 + O 6.90824e+00 1.89421e+01 3.64770e+01 + H 6.47518e+00 2.05705e+01 3.58656e+01 + H 6.06724e+00 1.77813e+01 3.53116e+01 + O 1.71125e+02 2.03424e+01 -2.48276e+01 + H 1.72225e+02 1.91091e+01 -2.41224e+01 + H 1.69770e+02 2.05544e+01 -2.36552e+01 + O -6.86934e+01 6.95167e+01 -3.71209e+01 + H -6.69683e+01 7.01269e+01 -3.71030e+01 + H -6.97834e+01 7.09336e+01 -3.73972e+01 + O -4.49279e+01 -3.40237e+01 1.08364e+01 + H -4.59540e+01 -3.31540e+01 1.20170e+01 + H -4.36376e+01 -3.26630e+01 1.04966e+01 diff --git a/examples/lammps/h2o-repimd/11_init.xyz b/examples/lammps/h2o-repimd/11_init.xyz new file mode 100644 index 00000000..2d65b67d --- /dev/null +++ b/examples/lammps/h2o-repimd/11_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.64520 23.64520 23.64520 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -5.07785e+01 3.85429e+01 -1.75896e+01 + H -5.21696e+01 3.86218e+01 -1.87973e+01 + H -4.94627e+01 3.76021e+01 -1.82407e+01 + O 4.63115e+01 1.09784e+02 -5.65499e+01 + H 4.78714e+01 1.08722e+02 -5.66637e+01 + H 4.70258e+01 1.11444e+02 -5.64767e+01 + O 9.31081e+00 2.92140e+01 -6.89337e+01 + H 9.34480e+00 2.97998e+01 -6.71882e+01 + H 1.10741e+01 2.89168e+01 -6.93565e+01 + O 6.98487e+01 -4.26719e+01 -8.79640e+01 + H 6.96025e+01 -4.38860e+01 -8.92865e+01 + H 7.11073e+01 -4.15533e+01 -8.85940e+01 + O 5.90699e+01 1.34684e+02 7.59769e+01 + H 5.82515e+01 1.36279e+02 7.61525e+01 + H 5.77248e+01 1.33471e+02 7.63559e+01 + O -2.94269e+01 1.10483e+01 8.95726e+00 + H -2.85651e+01 1.23351e+01 7.95487e+00 + H -2.96151e+01 9.54380e+00 7.93079e+00 + O 1.71038e+01 -1.69297e+01 -1.76093e+01 + H 1.72630e+01 -1.60636e+01 -1.92321e+01 + H 1.87298e+01 -1.75406e+01 -1.72653e+01 + O 1.16584e+01 1.49119e+01 6.75885e+01 + H 1.16829e+01 1.31147e+01 6.72460e+01 + H 1.06549e+01 1.50787e+01 6.91362e+01 + O 6.59460e+01 -3.77092e+01 9.66794e+01 + H 6.64301e+01 -3.78237e+01 9.49944e+01 + H 6.49109e+01 -3.61929e+01 9.68505e+01 + O -5.19573e+01 -1.05375e+02 -5.32106e+01 + H -5.10198e+01 -1.04145e+02 -5.41062e+01 + H -5.28206e+01 -1.06343e+02 -5.45202e+01 + O -1.10875e+02 4.91233e+01 1.88460e+01 + H -1.10402e+02 4.97878e+01 1.71830e+01 + H -1.10932e+02 5.07967e+01 1.96600e+01 + O -1.04137e+02 7.47044e+01 4.70740e+01 + H -1.03425e+02 7.55707e+01 4.56120e+01 + H -1.02776e+02 7.38554e+01 4.79910e+01 + O 5.36853e+00 -5.53003e+01 -3.96020e+01 + H 3.76058e+00 -5.51196e+01 -3.89106e+01 + H 5.37005e+00 -5.42855e+01 -4.10908e+01 + O 8.74123e+01 -5.57414e+01 2.15647e+01 + H 8.84613e+01 -5.63970e+01 2.02462e+01 + H 8.58978e+01 -5.54680e+01 2.05793e+01 + O -6.57806e+00 -1.73840e+00 3.13870e+01 + H -5.46316e+00 -6.31528e-01 3.22508e+01 + H -6.65681e+00 -1.12722e+00 2.96717e+01 + O -8.10530e+01 -4.00875e+01 -3.42524e+01 + H -8.21705e+01 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+ H -5.72452e+01 -2.28790e+01 -2.67518e+00 diff --git a/examples/lammps/h2o-repimd/12_init.xyz b/examples/lammps/h2o-repimd/12_init.xyz new file mode 100644 index 00000000..b450ac31 --- /dev/null +++ b/examples/lammps/h2o-repimd/12_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.62434 23.62434 23.62434 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -1.44830e+01 3.85425e+01 -2.01672e+01 + H -1.29218e+01 3.87874e+01 -2.10086e+01 + H -1.56691e+01 3.78168e+01 -2.13948e+01 + O 6.55666e+01 9.32671e+01 -3.94350e+01 + H 6.53496e+01 9.32730e+01 -3.75439e+01 + H 6.43798e+01 9.20443e+01 -4.01101e+01 + O 1.23514e+01 5.05406e+01 -6.51774e+01 + H 1.09579e+01 4.99061e+01 -6.42937e+01 + H 1.27384e+01 4.91413e+01 -6.62830e+01 + O 5.96196e+01 -4.96837e+01 -8.26668e+01 + H 6.13214e+01 -4.90340e+01 -8.24064e+01 + H 5.88672e+01 -4.99547e+01 -8.10166e+01 + O 6.91993e+01 1.31494e+02 4.54647e+01 + H 6.85857e+01 1.33124e+02 4.50159e+01 + H 6.80423e+01 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1.61851e+02 + O 7.73368e-02 -1.58823e+00 3.25898e+01 + H -1.49940e+00 -1.43902e+00 3.16876e+01 + H -3.79343e-01 -2.68248e+00 3.39289e+01 + O -6.49453e+01 8.27898e+00 -9.03589e+01 + H -6.32682e+01 7.82232e+00 -9.08970e+01 + H -6.57992e+01 6.75914e+00 -8.98470e+01 + O 2.05553e+01 5.48200e+01 1.11515e+02 + H 2.21891e+01 5.54929e+01 1.11783e+02 + H 1.95527e+01 5.60103e+01 1.12457e+02 + O 3.31374e+01 -5.20946e+01 2.12702e+01 + H 3.34011e+01 -5.11992e+01 1.96454e+01 + H 3.28804e+01 -5.08398e+01 2.26662e+01 + O -4.17817e+00 4.35982e+01 1.20750e+02 + H -2.50041e+00 4.35359e+01 1.20155e+02 + H -5.13181e+00 4.45742e+01 1.19624e+02 + O 8.20352e+01 5.84305e+01 6.78063e+00 + H 8.19879e+01 5.71994e+01 5.47489e+00 + H 8.18101e+01 5.99392e+01 5.84453e+00 + O 6.57997e+01 -4.46070e+01 6.46112e+01 + H 6.74116e+01 -4.54809e+01 6.51040e+01 + H 6.62619e+01 -4.29591e+01 6.42695e+01 + O -1.71906e+01 5.51764e-01 6.45071e+01 + H -1.67366e+01 1.47872e+00 6.59609e+01 + H -1.71019e+01 1.83928e+00 6.31606e+01 + O 1.48018e+02 1.89141e+01 6.94136e+00 + H 1.49172e+02 1.80494e+01 5.91201e+00 + H 1.47172e+02 1.75147e+01 7.86996e+00 + O -8.12775e+01 9.35052e+01 -6.78680e+01 + H -8.29033e+01 9.36421e+01 -6.86031e+01 + H -8.04326e+01 9.28653e+01 -6.93764e+01 + O -6.63028e+01 -3.33541e+01 -6.32280e+00 + H -6.48074e+01 -3.42541e+01 -6.87426e+00 + H -6.70905e+01 -3.28244e+01 -7.82127e+00 diff --git a/examples/lammps/h2o-repimd/13_init.xyz b/examples/lammps/h2o-repimd/13_init.xyz new file mode 100644 index 00000000..9d36d8ab --- /dev/null +++ b/examples/lammps/h2o-repimd/13_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.19110 23.19110 23.19110 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -3.74399e+01 4.52902e+01 -3.16683e+01 + H -3.67384e+01 4.54605e+01 -2.99526e+01 + H -3.59706e+01 4.50858e+01 -3.26928e+01 + O 4.72344e+01 9.30344e+01 -4.51581e+01 + H 4.74151e+01 9.18787e+01 -4.37425e+01 + H 4.57347e+01 9.38512e+01 -4.47747e+01 + O 1.91573e+01 4.54128e+01 -4.94727e+01 + H 1.95757e+01 4.65383e+01 -4.80487e+01 + H 1.99249e+01 4.61154e+01 -5.09682e+01 + O 4.94316e+01 -3.90419e+01 -1.01797e+02 + H 4.97265e+01 -3.99980e+01 -1.03307e+02 + H 5.09281e+01 -3.79858e+01 -1.01517e+02 + O 6.16345e+01 1.34290e+02 7.26136e+01 + H 6.11127e+01 1.32692e+02 7.33339e+01 + H 6.30707e+01 1.34038e+02 7.15453e+01 + O -3.16389e+01 2.60864e+01 1.82529e+01 + H -3.07363e+01 2.68132e+01 1.96322e+01 + H -3.27270e+01 2.73892e+01 1.75760e+01 + O 1.40715e+00 -1.10865e+01 3.26414e+00 + H 1.15190e+00 -1.08671e+01 5.05705e+00 + H 6.42530e-01 -1.27679e+01 3.09972e+00 + O -2.10370e+00 1.44303e+01 6.13415e+01 + H -3.63854e+00 1.51165e+01 6.05344e+01 + H -9.78295e-01 1.57547e+01 6.15604e+01 + O 6.90038e+01 -3.58275e+01 8.17251e+01 + H 7.04160e+01 -3.68142e+01 8.24354e+01 + H 6.87869e+01 -3.43947e+01 8.28367e+01 + O -5.03043e+01 -9.10007e+01 -5.43463e+01 + H -5.17799e+01 -9.09340e+01 -5.33878e+01 + H -5.03264e+01 -8.93588e+01 -5.51566e+01 + O -8.79861e+01 4.40346e+01 1.03983e+01 + H -8.98180e+01 4.42992e+01 1.00825e+01 + H -8.74628e+01 4.51921e+01 1.16839e+01 + O -1.09907e+02 8.21904e+01 6.87877e+01 + H -1.09995e+02 8.04369e+01 6.90039e+01 + H -1.09945e+02 8.26110e+01 6.70013e+01 + O 1.08239e+01 -5.48368e+01 -2.85080e+01 + H 1.18545e+01 -5.62401e+01 -2.82364e+01 + H 1.14140e+01 -5.36276e+01 -2.73027e+01 + O 1.11876e+02 -5.39779e+01 2.95449e+01 + H 1.11395e+02 -5.52357e+01 2.83985e+01 + H 1.13591e+02 -5.44007e+01 2.97473e+01 + O 8.41942e+00 -7.31587e+00 2.58913e+01 + H 7.29097e+00 -6.45570e+00 2.70073e+01 + H 7.49360e+00 -8.74477e+00 2.51806e+01 + O -6.92466e+01 -4.12248e+01 -2.85609e+01 + H -6.85612e+01 -4.28658e+01 -2.82132e+01 + H -6.85179e+01 -4.05937e+01 -3.00810e+01 + O 1.94001e+01 -3.99107e+01 -3.39153e+01 + H 1.97177e+01 -4.04890e+01 -3.55654e+01 + H 2.02725e+01 -3.82743e+01 -3.40029e+01 + O -2.21641e+01 8.93123e+01 -7.82210e+01 + H -2.08727e+01 8.81339e+01 -7.87227e+01 + H -2.34396e+01 8.89903e+01 -7.94383e+01 + O 9.92902e+01 5.27842e+00 3.08605e+01 + H 9.89092e+01 6.73198e+00 2.98221e+01 + H 9.94371e+01 3.91383e+00 2.97100e+01 + O 9.73981e+01 6.27942e+01 -1.03922e+01 + H 9.78263e+01 6.15650e+01 -1.17021e+01 + H 9.80075e+01 6.43764e+01 -1.10867e+01 + O -1.77285e+01 6.46348e+01 -1.70260e+01 + H -1.73743e+01 6.55346e+01 -1.54564e+01 + H -1.95876e+01 6.47093e+01 -1.72930e+01 + O 1.16905e+01 6.58862e+00 8.58587e+01 + H 9.93769e+00 6.47305e+00 8.62197e+01 + H 1.19299e+01 6.86960e+00 8.40983e+01 + O 4.95714e+00 7.12068e+01 -5.49718e+01 + H 6.60040e+00 7.02518e+01 -5.48596e+01 + H 3.90536e+00 7.05277e+01 -5.35612e+01 + O 1.21872e+02 -3.18826e+01 4.05885e+01 + H 1.21422e+02 -3.10169e+01 3.90904e+01 + H 1.23670e+02 -3.17513e+01 4.08495e+01 + O -6.37954e+01 3.29539e+01 2.84033e+01 + H -6.24334e+01 3.32160e+01 2.72220e+01 + H -6.53159e+01 3.35348e+01 2.75762e+01 + O 4.71435e+01 -7.99135e+00 2.22714e+01 + H 4.69985e+01 -9.42938e+00 2.34719e+01 + H 4.88347e+01 -7.67759e+00 2.25604e+01 + O -4.08207e+01 -2.06672e+01 2.60442e+01 + H -4.24200e+01 -2.12771e+01 2.54002e+01 + H -3.97350e+01 -2.20891e+01 2.57894e+01 + O 4.04790e+01 1.57073e+01 3.45633e+01 + H 4.11746e+01 1.56997e+01 3.28023e+01 + H 3.86898e+01 1.60151e+01 3.41948e+01 + O 8.69100e+01 -1.76689e+01 -1.23831e+00 + H 8.61220e+01 -1.64940e+01 2.65349e-02 + H 8.75563e+01 -1.64863e+01 -2.38218e+00 + O -4.12830e-01 -6.06259e+01 2.12729e+01 + H -1.45221e+00 -5.92859e+01 2.05835e+01 + H -3.21909e-01 -6.18538e+01 1.97925e+01 + O -8.83660e+01 3.07808e+01 6.93886e+01 + H -9.00195e+01 3.09771e+01 6.87148e+01 + H -8.86022e+01 2.94644e+01 7.06114e+01 + O 1.23444e+00 -5.65969e+01 3.13638e+01 + H 5.99445e-01 -5.73838e+01 3.30233e+01 + H 2.81071e+00 -5.58196e+01 3.16434e+01 + O -5.75199e+01 4.05111e+01 -1.15416e+00 + H -5.88204e+01 3.95438e+01 -3.68065e-01 + H -5.65388e+01 4.11066e+01 2.07864e-01 + O 1.14607e+01 3.59677e+01 -1.03006e+01 + H 1.31272e+01 3.52617e+01 -1.01134e+01 + H 1.09527e+01 3.64610e+01 -8.66231e+00 + O -7.86105e+01 -3.64242e+01 -3.86862e+01 + H -7.94336e+01 -3.71261e+01 -3.71619e+01 + H -7.85187e+01 -3.79086e+01 -3.97978e+01 + O 5.88986e+01 -2.94300e+01 -3.63156e+01 + H 5.79804e+01 -3.08159e+01 -3.56076e+01 + H 5.93149e+01 -3.01636e+01 -3.78762e+01 + O 3.38687e+01 2.89553e+01 4.81217e+01 + H 3.39750e+01 2.78661e+01 4.94816e+01 + H 3.23656e+01 2.86389e+01 4.73302e+01 + O -3.02778e+01 8.01807e+01 8.29696e+01 + H -2.94396e+01 8.13131e+01 8.18573e+01 + H -2.93702e+01 7.86097e+01 8.27944e+01 + O -3.64947e+01 1.17279e+02 8.92384e+01 + H -3.48837e+01 1.17501e+02 8.84872e+01 + H -3.73925e+01 1.18721e+02 8.84190e+01 + O 3.68419e+01 2.13525e+01 3.59060e+01 + H 3.76762e+01 2.08352e+01 3.74366e+01 + H 3.66048e+01 1.97248e+01 3.49962e+01 + O 6.70278e+01 4.36593e+00 -1.58094e+01 + H 6.66961e+01 2.75729e+00 -1.65283e+01 + H 6.79389e+01 5.19137e+00 -1.71668e+01 + O 1.80773e+02 -3.43792e+01 1.87544e+01 + H 1.80338e+02 -3.28065e+01 1.94619e+01 + H 1.81313e+02 -3.40412e+01 1.70402e+01 + O -3.03288e+01 -2.75016e+01 -2.91990e+01 + H -3.16786e+01 -2.80131e+01 -2.80569e+01 + H -2.93652e+01 -2.62675e+01 -2.82084e+01 + O 2.34960e+01 -2.67933e+01 -4.15411e+01 + H 2.20386e+01 -2.70387e+01 -4.25062e+01 + H 2.31902e+01 -2.56497e+01 -4.02294e+01 + O 1.91388e+01 -2.12505e+01 7.14309e+01 + H 1.86017e+01 -1.98941e+01 7.03410e+01 + H 1.76707e+01 -2.17883e+01 7.22993e+01 + O 4.07521e+01 -4.77364e+01 -1.70256e+01 + H 4.10938e+01 -4.79768e+01 -1.53032e+01 + H 4.03995e+01 -4.94984e+01 -1.75515e+01 + O -5.05468e+01 -4.84344e+01 -8.15051e+01 + H -5.16252e+01 -4.98252e+01 -8.10883e+01 + H -5.04465e+01 -4.73400e+01 -8.00456e+01 + O -1.10238e+01 -1.04596e-01 2.68650e+01 + H -9.42438e+00 -1.01523e+00 2.69608e+01 + H -1.19583e+01 -6.52396e-01 2.54763e+01 + O -5.50695e+01 5.59601e+01 4.73274e+01 + H -5.55327e+01 5.60437e+01 4.55657e+01 + H -5.62960e+01 5.47277e+01 4.79597e+01 + O -6.95694e+01 6.90717e+01 -1.42656e+01 + H -7.09589e+01 6.88007e+01 -1.30947e+01 + H -6.90493e+01 7.08571e+01 -1.38577e+01 + O -3.36704e+01 1.43707e+01 -1.75519e+01 + H -3.33706e+01 1.26231e+01 -1.68948e+01 + H -3.52640e+01 1.45463e+01 -1.85299e+01 + O 6.69224e+00 5.14934e+00 4.15512e+01 + H 5.25595e+00 4.82180e+00 4.05049e+01 + H 6.00463e+00 6.32785e+00 4.26877e+01 + O 1.56910e+01 5.33874e+00 1.67416e+02 + H 1.74146e+01 5.51769e+00 1.67991e+02 + H 1.48618e+01 4.28593e+00 1.68642e+02 + O -1.65673e+01 -9.52154e+00 5.51208e+01 + H -1.65046e+01 -8.42206e+00 5.36904e+01 + H -1.68793e+01 -1.12039e+01 5.43265e+01 + O -7.91198e+01 1.05206e+01 -7.34978e+01 + H -7.96815e+01 9.01135e+00 -7.43619e+01 + H -7.73092e+01 1.07046e+01 -7.38539e+01 + O 1.35358e+01 4.82479e+01 1.24899e+02 + H 1.27730e+01 4.72247e+01 1.23572e+02 + H 1.37271e+01 4.72152e+01 1.26536e+02 + O -4.57661e+00 -5.90055e+01 2.72276e+01 + H -5.39486e+00 -5.88198e+01 2.88663e+01 + H -5.68507e+00 -5.93134e+01 2.58274e+01 + O -2.06916e+01 2.70732e+01 8.03126e+01 + H -1.93783e+01 2.76249e+01 7.92259e+01 + H -2.00150e+01 2.60985e+01 8.16468e+01 + O 8.94376e+01 4.09953e+01 3.01161e-01 + H 8.97681e+01 4.24229e+01 -7.34818e-01 + H 9.10498e+01 4.02014e+01 1.33265e-01 + O 7.65918e+01 -3.60118e+01 6.07476e+01 + H 7.63747e+01 -3.45345e+01 6.17164e+01 + H 7.80139e+01 -3.57576e+01 5.97962e+01 + O -2.09067e+01 2.31234e+01 4.16998e+01 + H -2.11043e+01 2.25069e+01 4.33509e+01 + H -2.16474e+01 2.18623e+01 4.05928e+01 + O 1.73967e+02 6.00068e+00 -1.21615e+01 + H 1.72349e+02 5.61158e+00 -1.29427e+01 + H 1.75109e+02 4.72500e+00 -1.29119e+01 + O -7.04846e+01 1.00070e+02 -6.63960e+01 + H -7.02291e+01 1.00433e+02 -6.81898e+01 + H -7.18928e+01 1.01244e+02 -6.61105e+01 + O -6.12720e+01 -2.49081e+01 5.10247e-01 + H -6.05494e+01 -2.65434e+01 4.36601e-01 + H -6.08666e+01 -2.42416e+01 -1.03135e+00 diff --git a/examples/lammps/h2o-repimd/14_init.xyz b/examples/lammps/h2o-repimd/14_init.xyz new file mode 100644 index 00000000..6e0c61d3 --- /dev/null +++ b/examples/lammps/h2o-repimd/14_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.60263 23.60263 23.60263 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -1.70553e+01 5.92439e+01 -2.58777e+01 + H -1.72946e+01 6.05075e+01 -2.46819e+01 + H -1.79331e+01 5.78434e+01 -2.51325e+01 + O 4.44538e+01 1.37079e+02 -4.57758e+01 + H 4.27185e+01 1.37302e+02 -4.57718e+01 + H 4.51914e+01 1.38711e+02 -4.62773e+01 + O 2.28414e+01 -1.03728e+01 -5.94149e+01 + H 2.45484e+01 -1.02256e+01 -6.03097e+01 + H 2.32097e+01 -1.00393e+01 -5.76952e+01 + O 5.05733e+01 -8.83195e+00 -8.63632e+01 + H 4.98192e+01 -7.38151e+00 -8.73152e+01 + H 5.18291e+01 -7.82631e+00 -8.53119e+01 + O 4.60792e+01 1.26156e+02 8.13707e+01 + H 4.68871e+01 1.25796e+02 7.98213e+01 + H 4.58853e+01 1.27952e+02 8.14146e+01 + O -2.96636e+01 1.78112e+01 -4.84378e+00 + H -2.98071e+01 1.61080e+01 -5.83483e+00 + H -2.80144e+01 1.85533e+01 -5.29301e+00 + O 1.18150e+01 1.19320e+01 2.25814e+01 + H 1.00840e+01 1.17012e+01 2.21828e+01 + H 1.23968e+01 1.09736e+01 2.11062e+01 + O -1.06241e+01 -1.48128e+01 6.56042e+01 + H -9.31084e+00 -1.54378e+01 6.45495e+01 + H -1.14878e+01 -1.37735e+01 6.44441e+01 + O 1.09651e+02 -8.82792e+01 8.51580e+01 + H 1.11370e+02 -8.79666e+01 8.45864e+01 + H 1.09587e+02 -8.95971e+01 8.63646e+01 + O -5.13874e+01 -8.91444e+01 -2.77204e+01 + H -5.24773e+01 -9.04251e+01 -2.83983e+01 + H -4.97102e+01 -8.97679e+01 -2.80472e+01 + O -1.19174e+02 4.23713e+01 1.65998e+01 + H -1.19110e+02 4.29145e+01 1.49124e+01 + H -1.18766e+02 4.05905e+01 1.63114e+01 + O -1.08612e+02 5.97432e+01 7.46968e+01 + H -1.10154e+02 5.91526e+01 7.54442e+01 + H -1.08648e+02 5.88201e+01 7.30907e+01 + O -1.86297e+01 -6.01730e+01 -1.80294e+01 + H -1.80411e+01 -6.16432e+01 -1.69485e+01 + H -1.92687e+01 -5.90906e+01 -1.67398e+01 + O 8.66711e+01 -6.26216e+01 6.44885e+00 + H 8.55575e+01 -6.15067e+01 7.37706e+00 + H 8.78188e+01 -6.16185e+01 5.59093e+00 + O -7.85503e+00 1.79862e+01 6.97642e+00 + H -6.75399e+00 1.73506e+01 8.15291e+00 + H -7.73131e+00 1.97365e+01 7.11099e+00 + O -7.50670e+01 -5.98691e+01 -4.35771e+01 + H -7.64382e+01 -5.86892e+01 -4.42212e+01 + H -7.48978e+01 -6.12805e+01 -4.48286e+01 + O 3.38777e+01 -7.43270e+01 -4.76623e+01 + H 3.55999e+01 -7.49743e+01 -4.76576e+01 + H 3.31219e+01 -7.51661e+01 -4.61992e+01 + O -1.37850e+01 1.14379e+02 -7.93107e+01 + H -1.48000e+01 1.13469e+02 -8.05341e+01 + H -1.50254e+01 1.14701e+02 -7.80671e+01 + O 8.31739e+01 1.13805e+01 8.68203e+00 + H 8.20380e+01 1.13931e+01 7.24000e+00 + H 8.24564e+01 1.01990e+01 9.98655e+00 + O 1.38302e+02 4.69989e+01 -1.80224e+01 + H 1.39584e+02 4.57899e+01 -1.81200e+01 + H 1.37497e+02 4.69138e+01 -1.64274e+01 + O -3.98650e+01 9.23829e+01 -4.09568e+01 + H -3.87307e+01 9.38969e+01 -4.06692e+01 + H -3.90788e+01 9.13045e+01 -4.22155e+01 + O 2.39239e+01 2.82903e+01 6.41354e+01 + H 2.37898e+01 2.74449e+01 6.25553e+01 + H 2.54991e+01 2.75887e+01 6.49007e+01 + O 1.19482e+01 6.36426e+01 -6.03838e+01 + H 1.17531e+01 6.22402e+01 -6.14554e+01 + H 1.31298e+01 6.47945e+01 -6.13235e+01 + O 1.22283e+02 -3.11425e+01 4.80349e+01 + H 1.21267e+02 -2.99846e+01 4.71333e+01 + H 1.21155e+02 -3.20866e+01 4.89381e+01 + O -6.52451e+01 4.94649e+01 6.51286e+01 + H -6.48096e+01 5.05019e+01 6.37054e+01 + H -6.45133e+01 5.02897e+01 6.65326e+01 + O 4.63401e+01 -4.55004e+01 1.17542e+01 + H 4.49554e+01 -4.46074e+01 1.08992e+01 + H 4.76483e+01 -4.52359e+01 1.05340e+01 + O -1.85581e+01 8.51321e+00 4.81566e+01 + H -1.74322e+01 7.04689e+00 4.80039e+01 + H -1.85045e+01 8.86322e+00 5.00126e+01 + O 4.35955e+01 2.98614e+01 2.44526e+01 + H 4.33336e+01 2.95907e+01 2.26203e+01 + H 4.27737e+01 2.83545e+01 2.51502e+01 + O 8.78028e+01 2.41374e+01 -2.19316e+01 + H 8.72465e+01 2.24679e+01 -2.22442e+01 + H 8.90033e+01 2.38377e+01 -2.06104e+01 + O -2.33209e+01 -9.47181e+01 2.97604e-01 + H -2.24933e+01 -9.57002e+01 -9.49892e-01 + H -2.28887e+01 -9.29283e+01 1.51091e-01 + O -5.53324e+01 3.76834e+01 7.27672e+01 + H -5.59372e+01 3.80459e+01 7.44733e+01 + H -5.64806e+01 3.66016e+01 7.18549e+01 + O -1.12774e+01 -4.57708e+01 -1.44299e+00 + H -1.19016e+01 -4.73776e+01 -1.17905e+00 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2.48447e+01 1.93281e+01 3.19002e+01 + O 6.11073e+01 2.74563e+01 -1.94691e+01 + H 6.17863e+01 2.92243e+01 -1.90387e+01 + H 6.24383e+01 2.63929e+01 -2.02053e+01 + O 1.84089e+02 -6.65449e+01 -1.43957e+01 + H 1.82918e+02 -6.53907e+01 -1.52957e+01 + H 1.85409e+02 -6.53840e+01 -1.39926e+01 + O -3.97130e+01 -1.96850e+01 -8.94721e-01 + H -3.78579e+01 -2.00906e+01 -1.04157e+00 + H -4.03535e+01 -2.13856e+01 -2.46386e-01 + O -1.81479e+01 -1.11229e+01 -3.09236e+01 + H -1.91998e+01 -1.25464e+01 -3.13724e+01 + H -1.79029e+01 -1.11448e+01 -2.90763e+01 + O 3.93330e+01 -4.48333e+00 7.05312e+01 + H 4.00091e+01 -4.51077e+00 6.87741e+01 + H 3.94818e+01 -6.09678e+00 7.12513e+01 + O 2.39240e+01 -5.69260e+01 1.64843e+01 + H 2.33811e+01 -5.74982e+01 1.81713e+01 + H 2.57150e+01 -5.67812e+01 1.64841e+01 + O -2.43884e+01 -5.08725e+01 -5.95140e+01 + H -2.60487e+01 -5.15752e+01 -5.92882e+01 + H -2.43555e+01 -4.91158e+01 -5.92264e+01 + O -2.57604e-01 1.42177e+01 2.69535e+01 + H -3.88246e-01 1.59301e+01 2.72052e+01 + H -1.78537e+00 1.34750e+01 2.75549e+01 + O -4.43936e+01 5.55457e+01 3.80858e+01 + H -4.52123e+01 5.45152e+01 3.93127e+01 + H -4.55842e+01 5.56254e+01 3.66461e+01 + O -3.74450e+01 7.32165e+01 6.62890e+00 + H -3.64172e+01 7.27630e+01 8.09473e+00 + H -3.59867e+01 7.37579e+01 5.68645e+00 + O -7.58317e+01 1.66727e+01 -1.22714e+01 + H -7.69456e+01 1.57068e+01 -1.12054e+01 + H -7.46612e+01 1.54089e+01 -1.25712e+01 + O 1.69338e+01 -1.10027e+00 3.35705e+01 + H 1.69673e+01 -2.06853e+00 3.50395e+01 + H 1.56248e+01 -6.27543e-02 3.39474e+01 + O 2.54359e+01 1.97435e+01 2.09699e+02 + H 2.72985e+01 1.99217e+01 2.09126e+02 + H 2.46471e+01 1.90159e+01 2.08257e+02 + O -2.20782e+01 -1.90445e+01 7.07997e+01 + H -2.07878e+01 -1.77650e+01 7.09988e+01 + H -2.37151e+01 -1.82999e+01 7.11976e+01 + O -3.49032e+01 -2.19384e+01 -8.34889e+01 + H -3.42960e+01 -2.01702e+01 -8.36208e+01 + H -3.62749e+01 -2.18982e+01 -8.22107e+01 + O 1.13911e+01 3.63373e+01 1.09540e+02 + H 9.65614e+00 3.63499e+01 1.10234e+02 + H 1.14618e+01 3.78869e+01 1.08499e+02 + O -1.88500e+01 -6.97020e+01 3.36559e+01 + H -1.95930e+01 -6.91620e+01 3.20534e+01 + H -1.78601e+01 -7.10397e+01 3.30464e+01 + O -2.34726e+01 5.53523e+01 9.97845e+01 + H -2.48480e+01 5.63256e+01 9.90448e+01 + H -2.19450e+01 5.62723e+01 9.95342e+01 + O 6.89273e+01 6.10369e+01 -2.53037e+01 + H 6.80635e+01 6.25718e+01 -2.55135e+01 + H 6.97043e+01 6.10628e+01 -2.36947e+01 + O 5.27811e+01 -7.10458e+01 7.23031e+01 + H 5.30264e+01 -7.18306e+01 7.38793e+01 + H 5.08700e+01 -7.11357e+01 7.23351e+01 + O -3.95704e+00 3.24721e+01 1.54037e+01 + H -2.24215e+00 3.29039e+01 1.54440e+01 + H -4.40406e+00 3.17540e+01 1.70927e+01 + O 1.48153e+02 2.82586e+01 -1.00073e+01 + H 1.47054e+02 2.97783e+01 -1.02352e+01 + H 1.47382e+02 2.68799e+01 -1.09258e+01 + O -5.39179e+01 8.44158e+01 -5.56933e+01 + H -5.27392e+01 8.30199e+01 -5.58124e+01 + H -5.55465e+01 8.36280e+01 -5.60935e+01 + O -3.23672e+01 -2.63575e+01 1.51796e+01 + H -3.41244e+01 -2.68157e+01 1.53423e+01 + H -3.16138e+01 -2.74615e+01 1.63806e+01 diff --git a/examples/lammps/h2o-repimd/15_init.xyz b/examples/lammps/h2o-repimd/15_init.xyz new file mode 100644 index 00000000..288d3927 --- /dev/null +++ b/examples/lammps/h2o-repimd/15_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.40444 23.40444 23.40444 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -2.59816e+01 9.68373e+01 -4.48977e-01 + H -2.66581e+01 9.51306e+01 -7.06115e-01 + H -2.66323e+01 9.79959e+01 -1.60111e+00 + O 4.89416e+01 8.03513e+01 -4.69650e+01 + H 4.78635e+01 7.92077e+01 -4.62414e+01 + H 4.83031e+01 8.19261e+01 -4.62236e+01 + O 1.38810e+01 3.76130e+01 -8.48836e+01 + H 1.52319e+01 3.64584e+01 -8.54252e+01 + H 1.30297e+01 3.85147e+01 -8.61978e+01 + O 7.72644e+01 -4.51976e+01 -7.30627e+01 + H 7.76018e+01 -4.57314e+01 -7.46822e+01 + H 7.54603e+01 -4.50282e+01 -7.30112e+01 + O 8.33530e+01 1.18279e+02 1.99889e+01 + H 8.27208e+01 1.16687e+02 1.96362e+01 + H 8.28255e+01 1.18753e+02 2.16501e+01 + O -1.32762e+01 1.92094e+01 3.77800e+01 + H -1.24208e+01 2.08398e+01 3.77489e+01 + H -1.18675e+01 1.80506e+01 3.72415e+01 + O 1.87337e+01 -2.89506e+01 -1.36290e+01 + H 1.91477e+01 -2.91999e+01 -1.53710e+01 + H 1.96920e+01 -2.74003e+01 -1.30687e+01 + O -2.90011e+01 2.28120e+01 6.86902e+01 + H -3.00147e+01 2.21579e+01 7.01009e+01 + H -2.99555e+01 2.42897e+01 6.81330e+01 + O 6.78800e+01 -3.19795e+01 6.03510e+01 + H 6.94556e+01 -3.12697e+01 6.05725e+01 + H 6.70879e+01 -3.09398e+01 5.91385e+01 + O -3.95774e+01 -7.04240e+01 -3.12361e+01 + H -4.04867e+01 -6.95596e+01 -3.25316e+01 + H -3.94239e+01 -7.20633e+01 -3.19298e+01 + O -1.10058e+02 6.20536e+01 1.78219e+01 + H -1.09522e+02 6.17324e+01 1.95450e+01 + H -1.08858e+02 6.16134e+01 1.65437e+01 + O -1.17951e+02 5.99457e+01 9.61149e+01 + H -1.18489e+02 6.14399e+01 9.54992e+01 + H -1.18940e+02 5.99289e+01 9.76056e+01 + O 2.65697e+01 -1.04616e+02 -1.32031e+01 + H 2.79678e+01 -1.04694e+02 -1.44019e+01 + H 2.58300e+01 -1.02986e+02 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-6.69236e-01 + H 8.63468e+01 6.44795e+01 1.37673e-01 + H 8.77422e+01 6.70428e+01 -6.16588e-01 + O 6.98921e+01 -3.56013e+01 6.60736e+01 + H 6.98157e+01 -3.38014e+01 6.59940e+01 + H 7.02609e+01 -3.61176e+01 6.43466e+01 + O -8.54182e+00 1.63428e+01 4.19027e+01 + H -7.58328e+00 1.73084e+01 4.07379e+01 + H -8.35831e+00 1.71237e+01 4.35594e+01 + O 1.78365e+02 1.85369e+01 -1.80458e+01 + H 1.80046e+02 1.89999e+01 -1.75577e+01 + H 1.77558e+02 1.79619e+01 -1.65595e+01 + O -6.36502e+01 8.52512e+01 -4.96472e+01 + H -6.26538e+01 8.41365e+01 -5.07807e+01 + H -6.24825e+01 8.61616e+01 -4.85979e+01 + O -6.25700e+01 -2.51201e+01 2.88409e+00 + H -6.34589e+01 -2.58717e+01 1.49653e+00 + H -6.19117e+01 -2.66100e+01 3.84669e+00 diff --git a/examples/lammps/h2o-repimd/17_init.xyz b/examples/lammps/h2o-repimd/17_init.xyz new file mode 100644 index 00000000..d1b0a6a0 --- /dev/null +++ b/examples/lammps/h2o-repimd/17_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.35215 23.35215 23.35215 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -4.70207e+01 7.06726e+01 -2.52633e+01 + H -4.71485e+01 7.22869e+01 -2.59329e+01 + H -4.57594e+01 7.05724e+01 -2.38785e+01 + O 1.40209e+01 9.88768e+01 -6.37605e+01 + H 1.52603e+01 9.91074e+01 -6.49862e+01 + H 1.44768e+01 9.76521e+01 -6.25633e+01 + O 3.87578e+01 5.78346e+01 -5.60271e+01 + H 3.71469e+01 5.71942e+01 -5.56905e+01 + H 3.93543e+01 5.70485e+01 -5.75157e+01 + O 7.29551e+01 -3.84706e+01 -9.71579e+01 + H 7.21206e+01 -3.70445e+01 -9.64346e+01 + H 7.15996e+01 -3.95333e+01 -9.78520e+01 + O 8.49083e+01 1.40989e+02 5.61481e+01 + H 8.61596e+01 1.39861e+02 5.54079e+01 + H 8.33106e+01 1.40573e+02 5.52546e+01 + O -1.18148e+01 3.37238e+01 -2.10038e+01 + H -1.03628e+01 3.40991e+01 -2.01596e+01 + H -1.31902e+01 3.44892e+01 -1.99773e+01 + O 1.11723e+00 -3.50133e+01 2.35650e+01 + H 2.69980e+00 -3.56082e+01 2.41154e+01 + H 1.74659e+00 -3.34353e+01 2.29522e+01 + O -9.74217e+00 -3.04545e+00 7.30228e+01 + H -9.13275e+00 -4.71738e+00 7.33053e+01 + H -1.02140e+01 -2.90906e+00 7.12805e+01 + O 7.68751e+01 -1.80238e+01 1.11493e+02 + H 7.77036e+01 -1.91911e+01 1.12666e+02 + H 7.55057e+01 -1.74366e+01 1.12442e+02 + O -4.97788e+01 -9.92517e+01 -5.34788e+01 + H -4.90001e+01 -9.77859e+01 -5.43528e+01 + H -5.03788e+01 -1.00571e+02 -5.44997e+01 + O -7.05605e+01 3.28330e+01 5.21790e+00 + H -6.93758e+01 3.32225e+01 3.88708e+00 + H -7.09480e+01 3.11288e+01 4.71306e+00 + O -1.18192e+02 7.57858e+01 6.01101e+01 + H -1.19638e+02 7.58165e+01 6.12593e+01 + H -1.19034e+02 7.53020e+01 5.84465e+01 + O 6.97285e+00 -7.96263e+01 -1.27233e+01 + H 5.91334e+00 -8.09439e+01 -1.33576e+01 + H 5.94203e+00 -7.86781e+01 -1.15689e+01 + O 7.35312e+01 -6.00056e+01 9.32544e+00 + H 7.28694e+01 -6.03843e+01 7.62300e+00 + H 7.20046e+01 -5.99299e+01 1.02920e+01 + O -5.93941e+01 -2.76126e-01 2.93821e+01 + H -6.03827e+01 -1.17984e+00 3.06897e+01 + H -5.84605e+01 -1.58114e+00 2.85140e+01 + O -8.28795e+01 -4.11588e+01 2.56548e+00 + H -8.18495e+01 -4.15346e+01 4.05348e+00 + H -8.28336e+01 -3.92976e+01 2.44745e+00 + O -1.75761e+00 -4.08761e+01 -5.02315e+01 + H -1.90887e+00 -3.95115e+01 -4.89734e+01 + H -3.46613e+00 -4.10200e+01 -5.06544e+01 + O -4.22515e+01 1.04613e+02 -7.79733e+01 + H -4.08904e+01 1.05904e+02 -7.77186e+01 + H -4.22694e+01 1.03763e+02 -7.63654e+01 + O 5.79457e+01 4.06249e+01 1.37078e+01 + H 5.94887e+01 4.01309e+01 1.28008e+01 + H 5.81154e+01 4.24751e+01 1.36241e+01 + O 1.10959e+02 5.84155e+01 -4.81235e+00 + H 1.10541e+02 5.83904e+01 -6.52412e+00 + H 1.10775e+02 6.01458e+01 -4.27189e+00 + O -2.00683e+01 6.79394e+01 1.82789e+01 + H -1.91367e+01 6.92240e+01 1.72800e+01 + H -2.13139e+01 6.88526e+01 1.91780e+01 + O 2.55948e+01 4.10037e+01 9.70979e+01 + H 2.73411e+01 4.10350e+01 9.67020e+01 + H 2.55041e+01 4.24208e+01 9.81860e+01 + O 1.73192e+01 3.43809e+01 -6.49395e+01 + H 1.68982e+01 3.61512e+01 -6.49173e+01 + H 1.88927e+01 3.41066e+01 -6.57255e+01 + O 1.15747e+02 -2.65706e+01 3.31535e+01 + H 1.15848e+02 -2.82402e+01 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4.49156e+01 + H 3.46773e+01 1.18108e+01 4.58205e+01 + O 9.67967e+01 1.68702e+01 -1.00893e+01 + H 9.73864e+01 1.80494e+01 -8.91016e+00 + H 9.60845e+01 1.55993e+01 -9.00637e+00 + O 1.86654e+02 1.08517e+01 1.24949e+01 + H 1.86169e+02 9.24608e+00 1.31558e+01 + H 1.87780e+02 1.14366e+01 1.37656e+01 + O -3.43871e+01 -1.56067e+01 -5.94254e+00 + H -3.61185e+01 -1.61178e+01 -5.37654e+00 + H -3.41115e+01 -1.43817e+01 -4.70638e+00 + O -3.38503e+01 -2.68367e+01 -2.53961e+01 + H -3.52892e+01 -2.75770e+01 -2.63102e+01 + H -3.36697e+01 -2.51299e+01 -2.61043e+01 + O 4.13390e+01 -2.64262e+01 7.73293e+01 + H 4.16922e+01 -2.58168e+01 7.57019e+01 + H 4.29963e+01 -2.63319e+01 7.83723e+01 + O 4.46340e+01 -6.55066e+01 2.71599e+01 + H 4.32376e+01 -6.46947e+01 2.62848e+01 + H 4.40826e+01 -6.71846e+01 2.70467e+01 + O -5.07245e+01 -3.65899e+01 -9.35532e+01 + H -5.16073e+01 -3.60171e+01 -9.50111e+01 + H -4.91832e+01 -3.56322e+01 -9.37811e+01 + O 4.70053e+00 5.67644e+01 5.03446e+01 + H 5.41371e+00 5.51319e+01 5.05716e+01 + H 6.00121e+00 5.78725e+01 5.12674e+01 + O -2.46578e+01 6.13856e+01 5.21830e+01 + H -2.31681e+01 6.22089e+01 5.14734e+01 + H -2.42620e+01 5.95959e+01 5.23288e+01 + O -3.55342e+01 9.27565e+01 -1.02909e+01 + H -3.41690e+01 9.35546e+01 -9.43845e+00 + H -3.68231e+01 9.30783e+01 -9.09710e+00 + O -6.19573e+01 -1.27072e+00 1.51708e+00 + H -6.10681e+01 -6.96705e-01 2.97244e+00 + H -6.17229e+01 2.66009e-02 3.36941e-01 + O 3.27293e+01 2.60867e+01 2.17700e+01 + H 3.26555e+01 2.73585e+01 2.30850e+01 + H 3.44344e+01 2.55915e+01 2.14346e+01 + O 5.00373e+01 2.43033e+01 1.88620e+02 + H 4.98867e+01 2.57964e+01 1.89614e+02 + H 5.17942e+01 2.37336e+01 1.88689e+02 + O -2.27796e+01 -3.05838e+01 4.36150e+01 + H -2.18755e+01 -2.90986e+01 4.36573e+01 + H -2.39646e+01 -3.00610e+01 4.24314e+01 + O -4.27881e+01 1.12789e-01 -6.05865e+01 + H -4.11698e+01 -8.55309e-01 -6.05371e+01 + H -4.26216e+01 1.23863e+00 -6.19995e+01 + O 2.13115e+01 3.85095e+01 1.04577e+02 + H 2.15455e+01 3.82204e+01 1.02860e+02 + H 2.15955e+01 3.68583e+01 1.05188e+02 + O -1.34134e+01 -6.11417e+01 3.58534e+01 + H -1.44552e+01 -5.96717e+01 3.55968e+01 + H -1.36425e+01 -6.15515e+01 3.75362e+01 + O -3.13831e+01 1.59292e+01 9.93325e+01 + H -3.06093e+01 1.74045e+01 1.00249e+02 + H -3.28277e+01 1.53901e+01 1.00389e+02 + O 7.67734e+01 5.25555e+01 -1.37130e+01 + H 7.79099e+01 5.35911e+01 -1.27192e+01 + H 7.52060e+01 5.34513e+01 -1.35513e+01 + O 7.84275e+01 -3.35273e+01 7.57507e+01 + H 7.79089e+01 -3.20185e+01 7.48981e+01 + H 7.82431e+01 -3.30578e+01 7.75922e+01 + O -2.89234e+01 -5.64236e-02 4.86761e+01 + H -3.06134e+01 -7.53860e-01 4.88697e+01 + H -2.85265e+01 -1.58117e-01 4.68503e+01 + O 1.48503e+02 1.82268e+01 -5.09662e+01 + H 1.48619e+02 1.66757e+01 -5.18738e+01 + H 1.47017e+02 1.90638e+01 -5.12139e+01 + O -8.61429e+01 8.70227e+01 -6.80927e+01 + H -8.56368e+01 8.86503e+01 -6.77898e+01 + H -8.59905e+01 8.70080e+01 -6.98560e+01 + O -5.34163e+01 -1.75375e+01 2.48343e+01 + H -5.47974e+01 -1.82264e+01 2.41637e+01 + H -5.30381e+01 -1.59727e+01 2.41119e+01 diff --git a/examples/lammps/h2o-repimd/18_init.xyz b/examples/lammps/h2o-repimd/18_init.xyz new file mode 100644 index 00000000..08053f89 --- /dev/null +++ b/examples/lammps/h2o-repimd/18_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.52896 23.52896 23.52896 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -4.16234e+01 4.42940e+01 -1.90981e+01 + H -4.22955e+01 4.52655e+01 -2.04287e+01 + H -4.01231e+01 4.49547e+01 -1.86257e+01 + O 4.60177e+01 9.47767e+01 -4.03538e+01 + H 4.63535e+01 9.52061e+01 -4.21426e+01 + H 4.58519e+01 9.29928e+01 -4.05089e+01 + O 9.93002e+00 2.31222e+01 -6.57520e+01 + H 9.43035e+00 2.38021e+01 -6.73111e+01 + H 9.65608e+00 2.42430e+01 -6.44086e+01 + O 6.99176e+01 -5.18337e+01 -8.34877e+01 + H 6.89477e+01 -5.24078e+01 -8.49375e+01 + H 6.88904e+01 -5.06984e+01 -8.25038e+01 + O 6.57349e+01 1.09940e+02 6.76028e+01 + H 6.67808e+01 1.09437e+02 6.62441e+01 + H 6.46166e+01 1.11403e+02 6.72319e+01 + O -2.12081e+01 3.43860e+01 -4.80608e+00 + H -1.97454e+01 3.53682e+01 -5.07219e+00 + H -2.24550e+01 3.55639e+01 -4.48238e+00 + O 7.49094e+00 -2.51047e+01 1.26433e+01 + H 6.34406e+00 -2.56260e+01 1.13858e+01 + H 9.03688e+00 -2.48551e+01 1.16541e+01 + O -1.21116e+01 1.00823e+01 6.90544e+01 + H -1.07500e+01 8.97480e+00 6.88741e+01 + H -1.21877e+01 1.09744e+01 7.06436e+01 + O 9.97020e+01 -6.00617e+01 7.84166e+01 + H 9.87124e+01 -5.86075e+01 7.84777e+01 + H 1.01307e+02 -5.94426e+01 7.89358e+01 + O -5.30561e+01 -1.04869e+02 -3.84871e+01 + H -5.42079e+01 -1.06191e+02 -3.85072e+01 + H -5.13537e+01 -1.05586e+02 -3.88360e+01 + O -9.07523e+01 7.02277e+01 2.40935e+01 + H -8.93046e+01 7.11832e+01 2.35859e+01 + H -9.19848e+01 7.14547e+01 2.48053e+01 + O -1.10618e+02 8.38666e+01 6.58235e+01 + H -1.09497e+02 8.32911e+01 6.70098e+01 + H -1.10288e+02 8.55860e+01 6.61647e+01 + O 1.74099e+01 -5.02990e+01 -3.37676e+01 + H 1.83578e+01 -4.86932e+01 -3.37915e+01 + H 1.59533e+01 -5.01658e+01 -3.47493e+01 + O 1.03486e+02 -5.67082e+01 1.01170e+01 + H 1.03672e+02 -5.53996e+01 8.93611e+00 + H 1.02361e+02 -5.60940e+01 1.14778e+01 + O -3.02956e+01 -1.93751e+01 3.33965e+01 + H -2.99511e+01 -2.10768e+01 3.28885e+01 + H -2.99461e+01 -1.83071e+01 3.20476e+01 + O -7.31393e+01 -5.53002e+01 -3.15326e+01 + H -7.35067e+01 -5.68061e+01 -3.25681e+01 + H -7.34669e+01 -5.39371e+01 -3.26581e+01 + O 1.93391e+01 -4.05435e+01 -4.15205e+01 + H 1.93771e+01 -3.88641e+01 -4.21602e+01 + H 2.07539e+01 -4.14064e+01 -4.22313e+01 + O -3.03554e+01 9.35235e+01 -1.09508e+02 + H -2.88922e+01 9.23811e+01 -1.09779e+02 + H -3.19127e+01 9.26252e+01 -1.09443e+02 + O 1.06345e+02 -2.82735e+00 1.04955e+01 + H 1.06626e+02 -1.36395e+00 1.15529e+01 + H 1.06620e+02 -4.36650e+00 1.16064e+01 + O 9.42676e+01 4.32879e+01 -1.46508e+00 + H 9.57263e+01 4.40288e+01 -8.30130e-01 + H 9.48267e+01 4.20552e+01 -2.74583e+00 + O -2.50030e+01 5.76630e+01 -2.14472e+01 + H -2.50663e+01 5.94642e+01 -2.09722e+01 + H -2.32437e+01 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-1.41278e+01 -6.59292e+00 2.95355e+01 + H -1.42709e+01 -7.39671e+00 2.78897e+01 + H -1.40272e+01 -4.81478e+00 2.91735e+01 + O -7.37572e+01 -2.37475e+01 -9.52833e+01 + H -7.49670e+01 -2.45795e+01 -9.40678e+01 + H -7.25149e+01 -2.50529e+01 -9.55220e+01 + O 1.47676e+00 4.99106e+01 1.28205e+02 + H 3.16573e+00 4.99789e+01 1.27860e+02 + H 8.42230e-01 4.92285e+01 1.26742e+02 + O -1.13292e+01 -6.10370e+01 3.42141e+01 + H -1.20709e+01 -5.94615e+01 3.38134e+01 + H -1.17261e+01 -6.12322e+01 3.58944e+01 + O -6.62223e-01 2.65355e+01 9.56804e+01 + H -2.42382e-01 2.78921e+01 9.44567e+01 + H -1.52547e+00 2.52700e+01 9.46686e+01 + O 9.85710e+01 4.27636e+01 -1.40086e+01 + H 9.87171e+01 4.30981e+01 -1.58810e+01 + H 9.69538e+01 4.34213e+01 -1.36284e+01 + O 8.32451e+01 -3.00668e+01 8.52061e+01 + H 8.42767e+01 -2.89074e+01 8.62905e+01 + H 8.45518e+01 -3.12042e+01 8.47587e+01 + O -1.01809e+01 2.49484e+01 5.98592e+01 + H -9.24593e+00 2.59403e+01 5.87523e+01 + H -1.02208e+01 2.56064e+01 6.15925e+01 + O 1.72207e+02 2.96980e+01 2.23942e+00 + H 1.72833e+02 3.07289e+01 3.67013e+00 + H 1.70775e+02 3.06539e+01 1.53852e+00 + O -4.31244e+01 8.61441e+01 -4.41448e+01 + H -4.27223e+01 8.78894e+01 -4.39974e+01 + H -4.37583e+01 8.57034e+01 -4.24707e+01 + O -5.63497e+01 -3.57527e+01 3.63312e+00 + H -5.72346e+01 -3.62403e+01 5.04069e+00 + H -5.54284e+01 -3.43485e+01 4.39378e+00 diff --git a/examples/lammps/h2o-repimd/19_init.xyz b/examples/lammps/h2o-repimd/19_init.xyz new file mode 100644 index 00000000..b8770d48 --- /dev/null +++ b/examples/lammps/h2o-repimd/19_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.84559 23.84559 23.84559 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -3.23938e+01 5.92321e+01 -2.24749e+01 + H -3.22299e+01 5.79750e+01 -2.11066e+01 + H -3.17359e+01 5.84537e+01 -2.40015e+01 + O 5.07695e+01 8.40478e+01 -5.88802e+01 + H 5.12033e+01 8.29053e+01 -6.02021e+01 + H 5.23373e+01 8.49227e+01 -5.88429e+01 + O 1.05272e+01 2.97933e+01 -5.09895e+01 + H 1.04655e+01 2.93208e+01 -4.92386e+01 + H 1.06960e+01 2.84324e+01 -5.20301e+01 + O 7.64396e+01 -6.07400e+01 -1.01813e+02 + H 7.59218e+01 -5.99711e+01 -1.03371e+02 + H 7.54087e+01 -5.98164e+01 -1.00557e+02 + O 7.26229e+01 1.15540e+02 5.58335e+01 + H 7.33098e+01 1.17079e+02 5.54166e+01 + H 7.17930e+01 1.15925e+02 5.73665e+01 + O -3.07313e+01 1.81493e+01 -4.67385e+00 + H -2.95738e+01 1.69583e+01 -4.02632e+00 + H -3.03918e+01 1.82364e+01 -6.51996e+00 + O 1.56747e+01 -1.51938e+01 -8.24734e+00 + H 1.42544e+01 -1.42682e+01 -9.11134e+00 + H 1.58807e+01 -1.48623e+01 -6.40221e+00 + O -7.85342e+00 3.27530e+01 9.24079e+01 + H -6.38965e+00 3.16499e+01 9.25778e+01 + H -9.14005e+00 3.15333e+01 9.26489e+01 + O 7.66547e+01 -4.66432e+01 7.30224e+01 + H 7.52244e+01 -4.72368e+01 7.19480e+01 + H 7.74284e+01 -4.81140e+01 7.37603e+01 + O -2.80180e+01 -1.06170e+02 -4.41111e+01 + H -2.83671e+01 -1.05916e+02 -4.23682e+01 + H -2.96152e+01 -1.06551e+02 -4.49037e+01 + O -9.62275e+01 3.87227e+01 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4.06437e+00 diff --git a/examples/lammps/h2o-repimd/2_init.xyz b/examples/lammps/h2o-repimd/2_init.xyz new file mode 100644 index 00000000..fc471dc5 --- /dev/null +++ b/examples/lammps/h2o-repimd/2_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.44524 23.44524 23.44524 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -2.95577e+01 4.56766e+01 -2.77471e+01 + H -2.82624e+01 4.58789e+01 -2.89817e+01 + H -2.92458e+01 4.39546e+01 -2.72921e+01 + O 3.67356e+01 1.12637e+02 -3.53009e+01 + H 3.83854e+01 1.12992e+02 -3.58905e+01 + H 3.67752e+01 1.13387e+02 -3.37217e+01 + O 2.31544e+01 3.29215e+01 -3.96023e+01 + H 2.20509e+01 3.27176e+01 -3.81808e+01 + H 2.39877e+01 3.45349e+01 -3.92387e+01 + O 5.63663e+01 -5.61655e+01 -8.66965e+01 + H 5.57872e+01 -5.47475e+01 -8.57007e+01 + H 5.74629e+01 -5.53303e+01 -8.79618e+01 + O 6.37551e+01 1.06595e+02 7.69901e+01 + H 6.39373e+01 1.04823e+02 7.67289e+01 + H 6.24414e+01 1.06888e+02 7.58832e+01 + O -3.29612e+01 3.74641e+01 -8.45618e+00 + H -3.31035e+01 3.62309e+01 -7.15350e+00 + H -3.37380e+01 3.68564e+01 -9.92623e+00 + O 2.62221e+01 -2.05856e+01 1.83960e+01 + H 2.55907e+01 -2.00159e+01 2.00497e+01 + H 2.65118e+01 -2.24152e+01 1.86494e+01 + O 6.50476e+00 2.64971e+01 6.05071e+01 + H 6.66857e+00 2.58688e+01 6.21515e+01 + H 5.49138e+00 2.53118e+01 5.96580e+01 + O 9.56226e+01 -3.05515e+01 8.65210e+01 + H 9.38683e+01 -3.01505e+01 8.62834e+01 + H 9.60847e+01 -2.97710e+01 8.81067e+01 + O -5.16475e+01 -8.47560e+01 -4.67938e+01 + H -5.07601e+01 -8.32061e+01 -4.73464e+01 + H -5.17557e+01 -8.57830e+01 -4.82999e+01 + O -1.02917e+02 5.38282e+01 1.04849e+01 + H -1.04310e+02 5.26413e+01 1.00656e+01 + H -1.03728e+02 5.53874e+01 1.09175e+01 + O -8.82905e+01 8.08927e+01 6.82637e+01 + H -8.69504e+01 8.20586e+01 6.83491e+01 + H -8.78120e+01 7.95643e+01 6.92931e+01 + O 1.28445e+00 -6.65722e+01 -4.68165e+01 + H 1.14281e-01 -6.79577e+01 -4.65680e+01 + H 6.34486e-01 -6.51910e+01 -4.57717e+01 + O 1.03145e+02 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-2.42340e+00 + H 2.62572e+01 -7.46214e+01 -2.73914e+00 + H 2.48219e+01 -7.62537e+01 -8.88393e-01 + O -3.96252e+01 -5.99785e+01 -7.91566e+01 + H -4.01525e+01 -5.95079e+01 -7.75230e+01 + H -4.07992e+01 -6.10308e+01 -8.00052e+01 + O -9.02774e+00 1.40363e+01 2.21242e+01 + H -8.82273e+00 1.23570e+01 2.14095e+01 + H -7.70630e+00 1.49571e+01 2.14538e+01 + O -5.71408e+01 4.44584e+01 2.66207e+01 + H -5.74548e+01 4.54699e+01 2.80221e+01 + H -5.85261e+01 4.50765e+01 2.55695e+01 + O -7.10969e+01 7.85187e+01 -7.07121e+00 + H -7.05417e+01 8.01466e+01 -6.26713e+00 + H -6.98806e+01 7.78218e+01 -8.26788e+00 + O -4.27206e+01 1.75423e+01 -1.85007e+01 + H -4.23874e+01 1.92114e+01 -1.79493e+01 + H -4.13366e+01 1.70974e+01 -1.96244e+01 + O 1.36438e+01 9.27188e+00 2.60078e+01 + H 1.51937e+01 9.37213e+00 2.51335e+01 + H 1.40751e+01 8.63249e+00 2.76679e+01 + O 1.81823e+01 7.51852e+00 1.58662e+02 + H 1.76482e+01 6.05514e+00 1.57706e+02 + H 1.99204e+01 7.68451e+00 1.58169e+02 + O -1.15165e+01 5.19689e+00 6.46453e+01 + H -1.00557e+01 4.71321e+00 6.35628e+01 + H -1.10450e+01 4.95435e+00 6.64254e+01 + O -6.40186e+01 -6.65929e-02 -8.80881e+01 + H -6.52012e+01 5.77882e-01 -8.69219e+01 + H -6.41563e+01 8.91261e-01 -8.97171e+01 + O 1.02886e+01 6.42762e+01 1.10129e+02 + H 1.10956e+01 6.58705e+01 1.10425e+02 + H 1.16948e+01 6.31839e+01 1.10027e+02 + O -1.40687e+01 -4.79885e+01 2.37619e+01 + H -1.51512e+01 -4.66806e+01 2.44553e+01 + H -1.49287e+01 -4.96507e+01 2.40915e+01 + O -1.96540e+01 2.99095e+01 7.86559e+01 + H -2.12311e+01 3.08761e+01 7.82847e+01 + H -1.83328e+01 3.07099e+01 7.77487e+01 + O 9.00702e+01 4.08623e+01 -8.08993e+00 + H 8.98077e+01 4.27013e+01 -8.47738e+00 + H 8.96317e+01 4.02160e+01 -9.70604e+00 + O 7.05546e+01 -2.21894e+01 8.45255e+01 + H 7.13024e+01 -2.12573e+01 8.59077e+01 + H 7.17495e+01 -2.21924e+01 8.31710e+01 + O -5.05871e+00 3.74051e+01 3.49145e+01 + H -5.88240e+00 3.70731e+01 3.32862e+01 + H -6.43374e+00 3.76347e+01 3.60111e+01 + O 1.51763e+02 -4.72650e-01 -1.54427e+01 + H 1.51832e+02 -1.76331e+00 -1.41651e+01 + H 1.49907e+02 -5.21981e-01 -1.58239e+01 + O -7.34429e+01 7.47786e+01 -3.72485e+01 + H -7.20044e+01 7.49956e+01 -3.61494e+01 + H -7.44968e+01 7.61958e+01 -3.68612e+01 + O -5.35248e+01 -1.59134e+01 6.35560e+00 + H -5.24410e+01 -1.72188e+01 6.38965e+00 + H -5.43964e+01 -1.60702e+01 7.95034e+00 diff --git a/examples/lammps/h2o-repimd/3_init.xyz b/examples/lammps/h2o-repimd/3_init.xyz new file mode 100644 index 00000000..0425cfa6 --- /dev/null +++ b/examples/lammps/h2o-repimd/3_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 22.91558 22.91558 22.91558 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -3.16228e+01 4.39361e+01 -2.90922e+01 + H -3.10953e+01 4.34203e+01 -3.07702e+01 + H -3.11155e+01 4.24717e+01 -2.81889e+01 + O 3.61197e+01 1.06551e+02 -4.59553e+01 + H 3.70410e+01 1.05312e+02 -4.49809e+01 + H 3.58743e+01 1.07926e+02 -4.47669e+01 + O 1.87540e+01 3.00010e+01 -4.97391e+01 + H 1.95676e+01 2.86183e+01 -5.05498e+01 + H 1.79447e+01 3.08830e+01 -5.10200e+01 + O 7.67395e+01 -3.36467e+01 -1.00740e+02 + H 7.77541e+01 -3.21463e+01 -1.00514e+02 + H 7.67024e+01 -3.36413e+01 -1.02563e+02 + O 5.74195e+01 1.23258e+02 7.49700e+01 + H 5.85545e+01 1.24192e+02 7.59673e+01 + H 5.69414e+01 1.21969e+02 7.61115e+01 + O -4.06694e+01 2.86660e+01 2.17489e+00 + H -3.93267e+01 2.92854e+01 3.12843e+00 + H -4.20717e+01 2.91993e+01 3.12566e+00 + O 2.71615e+01 -1.13409e+01 1.95995e+01 + H 2.73037e+01 -9.99001e+00 1.84340e+01 + H 2.86721e+01 -1.12441e+01 2.07421e+01 + O 7.36019e+00 2.04034e+01 5.11099e+01 + H 8.54998e+00 1.90256e+01 5.09155e+01 + H 6.20342e+00 1.99517e+01 5.24016e+01 + O 9.17612e+01 -3.80094e+01 8.10459e+01 + H 9.04029e+01 -3.88055e+01 8.02691e+01 + H 9.09843e+01 -3.64723e+01 8.16044e+01 + O -4.93359e+01 -1.00848e+02 -5.13229e+01 + H -5.03786e+01 -1.02141e+02 -5.20113e+01 + H -4.86384e+01 -1.01387e+02 -4.97253e+01 + O -1.20719e+02 4.16768e+01 7.56631e+00 + H -1.20462e+02 4.32159e+01 6.64803e+00 + H -1.19234e+02 4.07314e+01 7.45410e+00 + O -1.11379e+02 7.29215e+01 6.58194e+01 + H -1.10280e+02 7.14745e+01 6.56390e+01 + H -1.10600e+02 7.38461e+01 6.70724e+01 + O 1.43354e+01 -5.73971e+01 -3.61582e+01 + H 1.35517e+01 -5.67639e+01 -3.46786e+01 + H 1.61505e+01 -5.75162e+01 -3.60095e+01 + O 9.05188e+01 -5.60356e+01 1.29290e+01 + H 9.20132e+01 -5.51852e+01 1.31903e+01 + H 8.96914e+01 -5.61381e+01 1.45532e+01 + O -2.36718e+00 1.37423e+01 2.58478e+01 + H -1.49277e+00 1.29103e+01 2.44863e+01 + H -3.94269e+00 1.28460e+01 2.57762e+01 + O -5.87926e+01 -3.10769e+01 -6.41280e+01 + H -5.97473e+01 -3.18517e+01 -6.27911e+01 + H -5.70679e+01 -3.14814e+01 -6.36408e+01 + O 7.24488e+00 -4.97509e+01 -3.49352e+01 + H 9.07793e+00 -4.98104e+01 -3.48919e+01 + H 6.81993e+00 -4.91518e+01 -3.32056e+01 + O -1.66029e+01 9.18365e+01 -7.17933e+01 + H -1.53249e+01 9.29890e+01 -7.12026e+01 + H -1.73216e+01 9.09904e+01 -7.03520e+01 + O 7.81363e+01 5.05733e+00 1.98475e+01 + H 7.93889e+01 4.05895e+00 1.89252e+01 + H 7.72350e+01 6.19475e+00 1.88227e+01 + O 9.61355e+01 5.37624e+01 -1.41999e+01 + H 9.48607e+01 5.39937e+01 -1.54476e+01 + H 9.52943e+01 5.33286e+01 -1.26693e+01 + O 5.11473e+00 4.19820e+01 8.36432e-01 + H 3.28727e+00 4.24244e+01 7.68836e-01 + H 5.59211e+00 4.23941e+01 2.61119e+00 + O 1.45656e+01 2.42445e+00 6.52043e+01 + H 1.49794e+01 3.68129e+00 6.39659e+01 + H 1.46720e+01 8.69570e-01 6.41999e+01 + O 2.14941e+01 7.08428e+01 -7.04539e+01 + H 2.28487e+01 7.17667e+01 -7.12842e+01 + H 2.04782e+01 6.98230e+01 -7.16257e+01 + O 1.07891e+02 -2.86107e+01 4.23149e+01 + H 1.06701e+02 -2.94523e+01 4.33916e+01 + H 1.08998e+02 -2.98642e+01 4.16172e+01 + O -8.09555e+01 6.18946e+01 3.81219e+01 + H -8.19209e+01 6.25948e+01 3.95205e+01 + H -8.04262e+01 6.32231e+01 3.70101e+01 + O 4.63293e+01 -1.74976e+00 2.39103e+01 + H 4.54869e+01 -5.38214e-01 2.28556e+01 + H 4.49248e+01 -2.59265e+00 2.45038e+01 + O -1.05544e+01 -1.09107e+01 1.81621e+01 + H -1.14385e+01 -1.09977e+01 1.97077e+01 + H -1.09889e+01 -9.38051e+00 1.73065e+01 + O 3.92325e+01 9.78191e+00 1.55573e+01 + H 3.80148e+01 1.05311e+01 1.67033e+01 + H 3.86037e+01 8.03662e+00 1.49414e+01 + O 9.12811e+01 -2.04039e+01 -1.83267e+01 + H 9.28003e+01 -2.03255e+01 -1.71620e+01 + H 9.17006e+01 -2.15000e+01 -1.96521e+01 + O -8.33250e+00 -6.33581e+01 1.42219e+01 + H -9.59788e+00 -6.27722e+01 1.31722e+01 + H -7.50734e+00 -6.44778e+01 1.30424e+01 + O -7.97981e+01 3.11625e+01 6.91343e+01 + H -8.08615e+01 3.01529e+01 6.80302e+01 + H -7.95996e+01 3.01297e+01 7.05974e+01 + O 1.00953e+01 -4.50850e+01 1.53329e+01 + H 1.15050e+01 -4.61574e+01 1.58056e+01 + H 8.60325e+00 -4.61475e+01 1.52928e+01 + O -5.16363e+01 6.13540e+01 -1.02854e+01 + H -5.13664e+01 6.21832e+01 -8.66689e+00 + H -4.99615e+01 6.09455e+01 -1.07053e+01 + O 2.62207e+01 4.82374e+01 7.99686e+00 + H 2.60451e+01 4.78191e+01 9.76090e+00 + H 2.72649e+01 4.96832e+01 7.96455e+00 + O -7.26760e+01 -4.96150e+01 -2.02915e+01 + H -7.21161e+01 -5.12736e+01 -1.99482e+01 + H -7.29438e+01 -4.96040e+01 -2.19983e+01 + O 4.32103e+01 -3.89718e+01 -2.19127e+01 + H 4.22762e+01 -3.91153e+01 -2.35193e+01 + H 4.34927e+01 -4.04948e+01 -2.10890e+01 + O 1.36284e+01 1.95419e+01 7.05217e+01 + H 1.51230e+01 1.94143e+01 7.14290e+01 + H 1.35273e+01 2.11287e+01 6.99472e+01 + O -4.65243e+01 8.03471e+01 9.02838e+01 + H -4.48368e+01 8.03123e+01 8.95705e+01 + H -4.70611e+01 7.87195e+01 9.01907e+01 + O -3.51174e+01 1.42467e+02 1.01503e+02 + H -3.68073e+01 1.42627e+02 1.02211e+02 + H -3.47569e+01 1.40729e+02 1.01372e+02 + O 2.07001e+01 -1.45700e+00 4.07183e+01 + H 2.03741e+01 -1.74453e+00 3.89257e+01 + H 1.96336e+01 -2.63002e+00 4.15759e+01 + O 5.38893e+01 1.13156e+01 -1.45613e+01 + H 5.24597e+01 1.01831e+01 -1.45554e+01 + H 5.52232e+01 1.03626e+01 -1.53054e+01 + O 1.91740e+02 -2.90117e+01 1.99259e+01 + H 1.92918e+02 -2.97873e+01 2.09789e+01 + H 1.90743e+02 -2.81681e+01 2.11154e+01 + O -4.14819e+01 -3.08034e+01 -7.03707e+00 + H -4.10682e+01 -2.90913e+01 -7.29045e+00 + H -4.00603e+01 -3.18548e+01 -7.76845e+00 + O -4.12862e-01 -4.13017e+01 -2.99017e+01 + H 1.11824e+00 -4.08930e+01 -2.90724e+01 + H -4.62250e-01 -4.00850e+01 -3.12132e+01 + O 2.93509e+01 -1.87359e+01 8.21383e+01 + H 2.91320e+01 -1.74481e+01 8.34258e+01 + H 3.06769e+01 -1.98147e+01 8.27882e+01 + O 3.43554e+01 -6.85274e+01 -1.54291e+01 + H 3.55784e+01 -6.85576e+01 -1.68312e+01 + H 3.29443e+01 -6.95297e+01 -1.60898e+01 + O -3.23993e+01 -6.67393e+01 -6.73467e+01 + H -3.42318e+01 -6.69725e+01 -6.72922e+01 + H -3.19748e+01 -6.60948e+01 -6.90080e+01 + O -1.62627e+01 3.08536e+01 1.70009e+01 + H -1.73396e+01 3.17365e+01 1.81012e+01 + H -1.57399e+01 3.21411e+01 1.57252e+01 + O -4.43512e+01 5.43497e+01 2.75400e+01 + H -4.41619e+01 5.60650e+01 2.70900e+01 + H -4.58654e+01 5.38908e+01 2.65091e+01 + O -6.76500e+01 6.92561e+01 -1.02099e+01 + H -6.88105e+01 6.79812e+01 -1.04137e+01 + H -6.85060e+01 7.03912e+01 -9.16225e+00 + O -4.97563e+01 2.09596e+01 -9.94390e+00 + H -5.02748e+01 2.25803e+01 -1.06370e+01 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4.15542e+01 -1.24521e+01 + O 5.41779e+01 -3.41675e+01 6.92767e+01 + H 5.48871e+01 -3.28554e+01 7.03168e+01 + H 5.55148e+01 -3.53411e+01 6.92681e+01 + O -3.31123e+00 1.08555e+01 3.12290e+01 + H -2.73576e+00 1.16076e+01 2.96772e+01 + H -2.25119e+00 1.16208e+01 3.25284e+01 + O 1.63067e+02 1.94343e+01 -1.45487e+01 + H 1.62777e+02 2.11384e+01 -1.40660e+01 + H 1.64353e+02 1.86759e+01 -1.34847e+01 + O -6.50084e+01 5.93213e+01 -4.26945e+01 + H -6.34588e+01 5.83952e+01 -4.32040e+01 + H -6.47077e+01 6.09523e+01 -4.33818e+01 + O -7.00696e+01 -2.96879e+01 3.02178e+01 + H -6.99933e+01 -3.03385e+01 2.85927e+01 + H -6.84628e+01 -2.87813e+01 3.05560e+01 diff --git a/examples/lammps/h2o-repimd/4_init.xyz b/examples/lammps/h2o-repimd/4_init.xyz new file mode 100644 index 00000000..7e2b8e57 --- /dev/null +++ b/examples/lammps/h2o-repimd/4_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.84275 23.84275 23.84275 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -2.86164e+01 3.20629e+01 -3.53776e+01 + H -2.97789e+01 3.07495e+01 -3.48833e+01 + H -2.89361e+01 3.36587e+01 -3.44474e+01 + O 1.15781e+01 1.07799e+02 -6.24087e+01 + H 1.15817e+01 1.09400e+02 -6.31169e+01 + H 1.10284e+01 1.06663e+02 -6.37784e+01 + O 1.79666e+01 5.07985e+01 -7.16332e+01 + H 1.62322e+01 5.08040e+01 -7.21711e+01 + H 1.84914e+01 4.91306e+01 -7.15222e+01 + O 7.80692e+01 -2.72974e+01 -1.14599e+02 + H 7.64321e+01 -2.81003e+01 -1.14298e+02 + H 7.79848e+01 -2.73242e+01 -1.16474e+02 + O 6.88683e+01 1.40006e+02 8.32764e+01 + H 6.77656e+01 1.38593e+02 8.30954e+01 + H 6.86755e+01 1.41079e+02 8.16670e+01 + O -2.27500e+01 2.97573e+01 1.62038e+01 + H -2.19436e+01 2.83448e+01 1.66938e+01 + H -2.44736e+01 2.94357e+01 1.66757e+01 + O 5.18509e+00 -1.67628e+01 -3.82150e-01 + H 3.47298e+00 -1.63659e+01 -4.95264e-01 + H 5.90921e+00 -1.71832e+01 -2.03306e+00 + O 3.11661e+01 -9.03226e+00 3.98271e+01 + H 3.21371e+01 -8.87621e+00 4.13501e+01 + H 2.95877e+01 -9.93776e+00 4.02232e+01 + O 8.29542e+01 -5.03617e+01 1.11774e+02 + H 8.31275e+01 -5.20672e+01 1.11169e+02 + H 8.24537e+01 -4.95204e+01 1.10246e+02 + O -2.83716e+01 -7.99695e+01 -6.05728e+01 + H -2.98405e+01 -8.06308e+01 -5.96564e+01 + H -2.70061e+01 -8.07411e+01 -5.97058e+01 + O -1.03263e+02 6.93334e+01 1.86178e+01 + H -1.04798e+02 6.97832e+01 1.77988e+01 + H -1.02006e+02 7.02989e+01 1.76218e+01 + O -8.83959e+01 7.80963e+01 4.22422e+01 + H -8.66956e+01 7.80104e+01 4.15114e+01 + H -8.93522e+01 7.65661e+01 4.19103e+01 + O -1.31243e+01 -6.77306e+01 -1.78208e+01 + H -1.21655e+01 -6.80155e+01 -1.63512e+01 + H -1.47884e+01 -6.87144e+01 -1.76767e+01 + O 8.70681e+01 -5.41558e+01 2.50358e+01 + H 8.56094e+01 -5.29856e+01 2.51525e+01 + H 8.73725e+01 -5.47080e+01 2.66974e+01 + O -1.54802e+01 -1.32212e+00 2.03195e+01 + H -1.41779e+01 -3.18364e-01 2.10792e+01 + H -1.45695e+01 -2.21004e+00 1.89858e+01 + O -6.94668e+01 -1.28713e+01 -3.99066e+01 + H -6.88467e+01 -1.28538e+01 -3.80930e+01 + H -7.10551e+01 -1.36989e+01 -3.98897e+01 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H 1.37933e+01 -6.05648e+01 1.59102e+01 + H 1.32940e+01 -5.97135e+01 1.86676e+01 + O 8.90928e-01 2.40764e+01 9.38635e+01 + H 8.17287e-01 2.46567e+01 9.55421e+01 + H 7.17783e-01 2.22259e+01 9.41275e+01 + O 9.30319e+01 7.52529e+01 -3.93134e+00 + H 9.16608e+01 7.53852e+01 -2.72832e+00 + H 9.42415e+01 7.41691e+01 -3.26263e+00 + O 6.92243e+01 -3.58903e+01 7.39787e+01 + H 6.79872e+01 -3.46348e+01 7.38930e+01 + H 6.91158e+01 -3.66498e+01 7.56238e+01 + O -2.93311e+01 2.11000e+01 4.69365e+01 + H -3.02959e+01 2.16566e+01 4.54951e+01 + H -3.05250e+01 1.98456e+01 4.74690e+01 + O 1.64193e+02 3.24177e+01 7.66579e+00 + H 1.63668e+02 3.23530e+01 9.40023e+00 + H 1.62814e+02 3.17116e+01 6.74733e+00 + O -5.22102e+01 9.61393e+01 -7.94799e+01 + H -5.10744e+01 9.69008e+01 -7.84407e+01 + H -5.12807e+01 9.51033e+01 -8.06049e+01 + O -3.54014e+01 -4.22592e+01 -6.76284e+00 + H -3.54268e+01 -4.05360e+01 -6.46873e+00 + H -3.62340e+01 -4.25525e+01 -8.39170e+00 diff --git a/examples/lammps/h2o-repimd/5_init.xyz b/examples/lammps/h2o-repimd/5_init.xyz new file mode 100644 index 00000000..09f2d794 --- /dev/null +++ b/examples/lammps/h2o-repimd/5_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.43997 23.43997 23.43997 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -3.39272e+01 5.13669e+01 -1.21490e+01 + H -3.56790e+01 5.16103e+01 -1.16232e+01 + H -3.29968e+01 5.08967e+01 -1.06949e+01 + O 4.68087e+01 1.12353e+02 -5.23731e+01 + H 4.62891e+01 1.12185e+02 -5.06001e+01 + H 4.66626e+01 1.10714e+02 -5.31346e+01 + O 3.12091e+01 2.25857e+01 -5.56665e+01 + H 3.09245e+01 2.19979e+01 -5.73633e+01 + H 2.98760e+01 2.36671e+01 -5.54594e+01 + O 4.94249e+01 -4.32979e+01 -8.32557e+01 + H 4.91814e+01 -4.34437e+01 -8.49875e+01 + H 4.99516e+01 -4.50009e+01 -8.28335e+01 + O 5.22390e+01 1.36106e+02 6.52482e+01 + H 5.04547e+01 1.36443e+02 6.49826e+01 + H 5.27763e+01 1.37022e+02 6.38649e+01 + O -4.33492e+01 2.51590e+01 4.67509e+00 + H -4.39177e+01 2.63643e+01 3.47911e+00 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4.35726e+01 + O -7.36654e+01 4.53152e+00 -8.56115e+01 + H -7.28606e+01 2.91626e+00 -8.59895e+01 + H -7.28413e+01 5.83703e+00 -8.64794e+01 + O 7.41255e+00 5.29869e+01 1.28067e+02 + H 7.46068e+00 5.41614e+01 1.26602e+02 + H 6.03602e+00 5.17393e+01 1.27989e+02 + O 1.47934e+01 -6.24105e+01 4.09006e+01 + H 1.44724e+01 -6.41160e+01 4.09070e+01 + H 1.36259e+01 -6.16498e+01 3.97252e+01 + O -4.89368e+00 2.52304e+01 8.40403e+01 + H -4.51060e+00 2.64463e+01 8.26566e+01 + H -3.48998e+00 2.49198e+01 8.50253e+01 + O 1.01149e+02 4.92204e+01 -1.87648e+00 + H 1.00199e+02 4.98690e+01 -5.24712e-01 + H 1.02750e+02 4.96066e+01 -1.25428e+00 + O 5.84589e+01 -3.58703e+01 6.16418e+01 + H 5.88746e+01 -3.46621e+01 6.04748e+01 + H 5.81607e+01 -3.53704e+01 6.33397e+01 + O -1.42432e+01 1.49739e+01 4.21642e+01 + H -1.58610e+01 1.57759e+01 4.20497e+01 + H -1.32758e+01 1.61296e+01 4.11545e+01 + O 1.68787e+02 1.21143e+01 -1.71333e+01 + H 1.69120e+02 1.03237e+01 -1.70043e+01 + H 1.67161e+02 1.20719e+01 -1.79550e+01 + O -6.27291e+01 9.03185e+01 -4.05895e+01 + H -6.12067e+01 9.03799e+01 -4.14118e+01 + H -6.40083e+01 9.07556e+01 -4.18166e+01 + O -5.11216e+01 -2.68511e+01 1.19221e+01 + H -5.24969e+01 -2.65039e+01 1.07738e+01 + H -5.08228e+01 -2.51957e+01 1.25942e+01 diff --git a/examples/lammps/h2o-repimd/6_init.xyz b/examples/lammps/h2o-repimd/6_init.xyz new file mode 100644 index 00000000..ee0fe6e5 --- /dev/null +++ b/examples/lammps/h2o-repimd/6_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.40135 23.40135 23.40135 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -2.14603e+01 6.50851e+01 5.17265e+00 + H -2.25421e+01 6.66156e+01 4.86631e+00 + H -2.22130e+01 6.40947e+01 6.49510e+00 + O 4.46781e+01 7.68118e+01 -3.54354e+01 + H 4.43794e+01 7.77696e+01 -3.69359e+01 + H 4.52400e+01 7.81113e+01 -3.42617e+01 + O 1.18637e+01 3.67433e+01 -7.21253e+01 + H 1.32364e+01 3.58339e+01 -7.12318e+01 + H 1.11195e+01 3.55452e+01 -7.32286e+01 + O 6.84939e+01 -4.69882e+01 -7.45256e+01 + H 6.90939e+01 -4.54702e+01 -7.54023e+01 + H 6.68543e+01 -4.71187e+01 -7.52272e+01 + O 4.60004e+01 1.33351e+02 6.73996e+01 + H 4.43354e+01 1.33136e+02 6.79026e+01 + H 4.62357e+01 1.34857e+02 6.83294e+01 + O -4.22501e+01 3.26849e+01 -6.14221e+00 + H -4.31017e+01 3.23548e+01 -4.50592e+00 + H -4.20186e+01 3.44741e+01 -6.33675e+00 + O 4.03741e+00 -1.38826e+01 6.97226e+00 + H 2.93659e+00 -1.45729e+01 8.27222e+00 + H 3.32603e+00 -1.24202e+01 6.16928e+00 + O -3.29713e+01 -6.60824e+00 6.54739e+01 + H -3.33589e+01 -7.37579e+00 6.38354e+01 + H -3.36294e+01 -7.72287e+00 6.67396e+01 + O 8.62540e+01 -5.87517e+01 7.83349e+01 + H 8.64911e+01 -6.04542e+01 7.76533e+01 + H 8.43726e+01 -5.88452e+01 7.85873e+01 + O -6.49338e+01 -8.90250e+01 -3.20479e+01 + H -6.61670e+01 -8.88239e+01 -3.33126e+01 + H -6.53455e+01 -8.74350e+01 -3.11732e+01 + O -8.87440e+01 4.78098e+01 4.40502e+00 + H -8.95749e+01 4.91965e+01 3.59039e+00 + H -8.82931e+01 4.67753e+01 3.02976e+00 + O -9.03082e+01 9.31432e+01 3.84708e+01 + H -9.01748e+01 9.48840e+01 3.90217e+01 + H -9.04432e+01 9.33214e+01 3.67091e+01 + O -1.61637e+01 -6.26522e+01 -2.42232e+01 + H -1.67971e+01 -6.10356e+01 -2.38747e+01 + H -1.76693e+01 -6.35300e+01 -2.47233e+01 + O 9.77929e+01 -5.66313e+01 3.56442e+01 + H 9.61428e+01 -5.63873e+01 3.65239e+01 + H 9.83223e+01 -5.49186e+01 3.50124e+01 + O -1.96696e+00 -1.44068e+01 7.04056e+00 + H -2.03120e+00 -1.31257e+01 5.77169e+00 + H -2.59446e+00 -1.57811e+01 6.06461e+00 + O -3.44180e+01 -4.88501e+01 -7.72724e+01 + H -3.46698e+01 -4.93805e+01 -7.90393e+01 + H -3.42006e+01 -5.04989e+01 -7.65569e+01 + O 1.02766e+01 -1.90952e+01 -3.24694e+01 + H 8.56449e+00 -1.90657e+01 -3.21851e+01 + H 1.09156e+01 -2.01458e+01 -3.11992e+01 + O -2.68013e+01 7.45128e+01 -6.61968e+01 + H -2.66548e+01 7.47898e+01 -6.80917e+01 + H -2.83852e+01 7.38081e+01 -6.60803e+01 + O 9.54775e+01 1.33944e+01 3.85991e+00 + H 9.66539e+01 1.26968e+01 2.61322e+00 + H 9.61767e+01 1.49709e+01 4.22534e+00 + O 1.13926e+02 2.81515e+01 -2.45427e+01 + H 1.14957e+02 2.79398e+01 -2.60055e+01 + H 1.12369e+02 2.73689e+01 -2.49012e+01 + O 3.46302e+00 7.00785e+01 -1.36543e+01 + H 4.36223e+00 6.85597e+01 -1.31693e+01 + H 3.62007e+00 7.01682e+01 -1.55057e+01 + O -2.28277e+01 2.08987e+01 6.98365e+01 + H -2.35873e+01 2.18896e+01 6.83567e+01 + H -2.39615e+01 2.12887e+01 7.11812e+01 + O 1.18805e+01 6.61650e+01 -5.86827e+01 + H 1.36412e+01 6.63725e+01 -5.92552e+01 + H 1.20877e+01 6.44921e+01 -5.80516e+01 + O 1.14102e+02 -1.23812e+01 4.84879e+01 + H 1.14829e+02 -1.26270e+01 4.69796e+01 + H 1.14902e+02 -1.07950e+01 4.89203e+01 + O -6.43985e+01 1.99184e+01 4.72878e+01 + H -6.60825e+01 1.91392e+01 4.72515e+01 + H -6.35181e+01 1.89300e+01 4.84915e+01 + O 2.60331e+01 5.06326e+00 -1.29830e+01 + H 2.64898e+01 3.44139e+00 -1.36299e+01 + H 2.43105e+01 5.09410e+00 -1.24056e+01 + O -6.22525e+00 -2.00385e+01 3.53733e+01 + H -4.93133e+00 -1.88860e+01 3.49462e+01 + H -5.83876e+00 -2.07039e+01 3.70856e+01 + O 6.42195e+01 -2.70793e+01 4.45695e+01 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1.06960e+01 -4.25210e+01 -2.10191e+01 + H 1.10531e+01 -4.09032e+01 -2.33879e+01 + O 2.89518e+01 -8.86251e+00 6.42016e+01 + H 2.81935e+01 -8.64878e+00 6.26613e+01 + H 2.98414e+01 -7.33088e+00 6.46562e+01 + O 5.64624e+01 -4.59462e+01 1.02585e+01 + H 5.64958e+01 -4.48299e+01 1.17946e+01 + H 5.70762e+01 -4.75946e+01 1.07303e+01 + O -5.25578e+01 -3.06942e+01 -6.26220e+01 + H -5.28575e+01 -3.25270e+01 -6.26414e+01 + H -5.41268e+01 -2.99398e+01 -6.22780e+01 + O -1.71437e+01 2.43833e+01 2.07363e+01 + H -1.75885e+01 2.32639e+01 1.92974e+01 + H -1.71016e+01 2.32421e+01 2.20894e+01 + O -6.14753e+01 5.81163e+01 3.68341e+01 + H -6.30701e+01 5.86800e+01 3.64975e+01 + H -6.15314e+01 5.73231e+01 3.84538e+01 + O -3.58849e+01 5.87979e+01 7.83100e+00 + H -3.69060e+01 5.74240e+01 8.62555e+00 + H -3.68066e+01 6.02324e+01 8.17019e+00 + O -3.09197e+01 1.46337e+00 -2.31487e+01 + H -3.13452e+01 4.68456e-01 -2.16856e+01 + H -3.20676e+01 2.82345e+00 -2.29025e+01 + O 2.31910e+01 2.84059e+01 4.09934e+01 + H 2.24653e+01 2.99774e+01 4.04992e+01 + H 2.45899e+01 2.86142e+01 4.20257e+01 + O 1.03358e+01 1.87741e+01 1.93531e+02 + H 1.04502e+01 1.86523e+01 1.95312e+02 + H 1.14557e+01 2.01569e+01 1.92906e+02 + O 9.41363e+00 2.69607e+00 2.88962e+01 + H 9.61594e+00 2.19594e+00 3.06897e+01 + H 7.75125e+00 2.16096e+00 2.84678e+01 + O -9.45694e+01 1.52471e+01 -8.45232e+01 + H -9.62739e+01 1.54286e+01 -8.51802e+01 + H -9.46334e+01 1.46153e+01 -8.27602e+01 + O -6.57916e+00 2.46009e+01 1.10372e+02 + H -7.16071e+00 2.58705e+01 1.11507e+02 + H -8.00212e+00 2.33949e+01 1.10339e+02 + O -3.23415e+01 -6.30803e+01 2.85267e+01 + H -3.34367e+01 -6.30748e+01 2.99289e+01 + H -3.31756e+01 -6.40757e+01 2.72218e+01 + O -4.12566e+01 1.82829e+01 8.08794e+01 + H -3.95383e+01 1.82996e+01 8.07657e+01 + H -4.18951e+01 1.78344e+01 7.92377e+01 + O 9.33525e+01 8.91591e+01 -3.10533e+01 + H 9.30706e+01 8.95720e+01 -2.92740e+01 + H 9.44941e+01 9.05445e+01 -3.12793e+01 + O 6.97438e+01 -3.26398e+01 8.45244e+01 + H 6.99759e+01 -3.11346e+01 8.54926e+01 + H 6.97501e+01 -3.41249e+01 8.56681e+01 + O -2.06368e+01 4.97480e+00 4.50792e+01 + H -1.95122e+01 3.59009e+00 4.53737e+01 + H -2.12996e+01 5.27714e+00 4.67410e+01 + O 1.61735e+02 -1.15691e+00 4.81907e+00 + H 1.62107e+02 -1.40809e+00 6.60265e+00 + H 1.61529e+02 6.51547e-01 4.47580e+00 + O -5.92507e+01 7.22143e+01 -7.50357e+01 + H -5.89601e+01 7.05095e+01 -7.56348e+01 + H -6.07916e+01 7.17876e+01 -7.43116e+01 + O -4.65785e+01 -3.61088e+01 1.96909e+01 + H -4.80355e+01 -3.63962e+01 1.86377e+01 + H -4.67475e+01 -3.43897e+01 2.01929e+01 diff --git a/examples/lammps/h2o-repimd/7_init.xyz b/examples/lammps/h2o-repimd/7_init.xyz new file mode 100644 index 00000000..9fe32564 --- /dev/null +++ b/examples/lammps/h2o-repimd/7_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.36303 23.36303 23.36303 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -2.32202e+00 8.25747e+01 -1.27652e+01 + H -3.10581e+00 8.14348e+01 -1.16584e+01 + H -2.49125e+00 8.17450e+01 -1.43476e+01 + O 6.24234e+01 8.54078e+01 -1.99324e+01 + H 6.06638e+01 8.57598e+01 -1.99223e+01 + H 6.32439e+01 8.66650e+01 -1.87990e+01 + O 1.92755e+01 1.73489e+01 -4.69251e+01 + H 2.09902e+01 1.71109e+01 -4.64301e+01 + H 1.83285e+01 1.65888e+01 -4.55348e+01 + O 5.93896e+01 -2.92550e+00 -8.25520e+01 + H 5.94713e+01 -4.58659e+00 -8.33058e+01 + H 5.94884e+01 -1.85401e+00 -8.40048e+01 + O 4.06870e+01 1.36231e+02 7.61303e+01 + H 4.12243e+01 1.36031e+02 7.78495e+01 + H 3.91602e+01 1.37182e+02 7.63127e+01 + O -2.31141e+01 2.83354e+01 -7.86301e+00 + H -2.21750e+01 2.74464e+01 -9.09222e+00 + H -2.20114e+01 2.91306e+01 -6.70551e+00 + O 6.62882e+00 -1.66833e+01 5.21614e+00 + H 5.34631e+00 -1.79495e+01 5.03020e+00 + H 5.70202e+00 -1.51754e+01 5.31965e+00 + O -2.01163e+01 1.03369e+01 3.60657e+01 + H -1.93459e+01 9.77021e+00 3.75457e+01 + H -2.18372e+01 1.08460e+01 3.66394e+01 + O 7.91775e+01 -4.31118e+01 8.14659e+01 + H 7.92007e+01 -4.13459e+01 8.18701e+01 + H 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new file mode 100644 index 00000000..d2e7995f --- /dev/null +++ b/examples/lammps/h2o-repimd/8_init.xyz @@ -0,0 +1,194 @@ +192 +# CELL(abcABC): 23.77957 23.77957 23.77957 90.00000 90.00000 90.00000 Step: 60000 Bead: 0 x_centroid{atomic_unit} cell{atomic_unit} + O -3.38143e+01 5.06750e+01 1.30931e+01 + H -3.47873e+01 5.17079e+01 1.20665e+01 + H -3.39389e+01 4.90435e+01 1.23228e+01 + O 4.38068e+01 7.43082e+01 -7.82185e+01 + H 4.28403e+01 7.47663e+01 -7.97261e+01 + H 4.45324e+01 7.58609e+01 -7.76269e+01 + O 1.26024e+01 4.07197e+01 -7.91334e+01 + H 1.43112e+01 4.10341e+01 -7.86987e+01 + H 1.25964e+01 3.90501e+01 -7.98366e+01 + O 6.70765e+01 -4.64723e+01 -9.73479e+01 + H 6.79303e+01 -4.61132e+01 -9.89816e+01 + H 6.57462e+01 -4.74983e+01 -9.77080e+01 + O 1.78486e+01 1.13580e+02 8.72528e+01 + H 1.90446e+01 1.12170e+02 8.76501e+01 + H 1.78490e+01 1.13366e+02 8.54512e+01 + O -2.09635e+01 4.88317e+01 1.23471e+01 + H -2.19426e+01 4.89136e+01 1.09503e+01 + H -2.19684e+01 4.78752e+01 1.34058e+01 + 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+ 63 1 188 187 189 + 64 1 191 190 192 diff --git a/examples/lammps/h2o-repimd/in.lmp b/examples/lammps/h2o-repimd/in.lmp new file mode 100644 index 00000000..5a5ced26 --- /dev/null +++ b/examples/lammps/h2o-repimd/in.lmp @@ -0,0 +1,23 @@ +units electron +atom_style full + +#pair_style lj/long/tip4p/long cut long 1 2 1 1 0.278072379 11.7 +#bond_style class2 +#angle_style harmonic +#kspace_style pppm/disp/tip4p 1e-4 + +pair_style lj/long/tip4p/long long long 1 2 1 1 0.278072379 11.707 +bond_style class2 +angle_style harmonic +kspace_style pppm/disp/tip4p 0.0001 +kspace_modify force/disp/real 0.0001 +kspace_modify force/disp/kspace 0.0001 + +read_data data.lmp +pair_coeff * * 0 0 +pair_coeff 1 1 0.000295147 5.96946 +neighbor 2.0 bin +timestep 0.00025 +fix 1 all ipi f1 32345 unix + +run 100000000 diff --git a/examples/lammps/h2o-repimd/input.xml b/examples/lammps/h2o-repimd/input.xml new file mode 100644 index 00000000..0b49799f --- /dev/null +++ b/examples/lammps/h2o-repimd/input.xml @@ -0,0 +1,76 @@ + + + [ step, time{picosecond}, conserved, temperature{kelvin}, kinetic_cv, potential, pressure_cv, volume, ensemble_temperature ] + x_centroid + positions + positions + positions + positions + + + 400000 + 3400 + 31415 + +
f1
+ 1e-3 + + + [ IDX, TEMP, PRESSURE ,INITFILE] + [ 0, 250, 1.0, 0_init.xyz ] + [ 1, 260, 1.0, 1_init.xyz ] + [ 2, 270, 1.0, 2_init.xyz ] + [ 3, 280, 1.0, 3_init.xyz ] + [ 4, 290, 1.0, 4_init.xyz ] + [ 5, 300, 1.0, 5_init.xyz ] + [ 6, 310, 1.0, 6_init.xyz ] + [ 7, 320, 1.0, 7_init.xyz ] + [ 8, 330, 1.0, 8_init.xyz ] + [ 9, 340, 1.0, 9_init.xyz ] + [ 10, 250, 100, 0_init.xyz ] + [ 11, 260, 100, 11_init.xyz ] + [ 12, 270, 100, 12_init.xyz ] + [ 13, 280, 100, 13_init.xyz ] + [ 14, 290, 100, 14_init.xyz ] + [ 15, 300, 100, 15_init.xyz ] + [ 16, 310, 100, 16_init.xyz ] + [ 17, 320, 100, 17_init.xyz ] + [ 18, 330, 100, 18_init.xyz ] + [ 19, 340, 100, 19_init.xyz ] + + + + + + 1 + + +