135 lines
8.6 KiB
Plaintext
135 lines
8.6 KiB
Plaintext
# Demonstrate bispectrum computes for triclinic cell
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# This triclinic cell has 6 times the volume of the single
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# unit cell used by in.grid
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# and contains 12 atoms. It is a 3x2x1 supercell
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# with each unit cell containing 2 atoms and the
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# reduced lattice vectors are [1 0 0], [1 1 0], and [1 1 1].
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# The grid is listed in x-fastest order
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# CORRECTNESS: thermo output for c_mygrid[*][7] should contain
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# the same 2 values that appear in c_mygrid[*][7] for in.grid,
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# 7.0663376 and 13.808803, corresponding to atom and insterstitial sites,
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# respectively, and with occurrences 12 and 36, respectively.
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# Initialize simulation
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variable nsteps index 0
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variable nrep index 1
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variable a index 3.316
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variable ngrid index 4
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variable ngridx equal 3*${ngrid}
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variable ngridy equal 2*${ngrid}
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variable ngridz equal 1*${ngrid}
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variable nrepx equal 1*${nrep}
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variable nrepy equal 1*${nrep}
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variable nrepz equal 1*${nrep}
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrepx}
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variable ny equal ${nrepy}
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variable nz equal ${nrepz}
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boundary p p p
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lattice custom $a &
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a1 1 0 0 &
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a2 1 1 0 &
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a3 1 1 1 &
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basis 0 0 0 &
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basis 0.0 0.0 0.5 &
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# origin 0.25 0.25 0.25
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box tilt large
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region box prism 0 ${nx} 0 ${ny} 0 ${nz} ${ny} ${nz} ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 180.88
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# choose potential
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include Ta06A.snap
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# define grid compute and atom compute
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group snapgroup type 1
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variable twojmax equal 2
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variable rcutfac equal 4.67637
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable wj equal 1
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variable radelem equal 0.5
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variable bzero equal 0
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variable quad equal 0
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variable switch equal 1
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compute b all sna/atom &
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${rcutfac} ${rfac0} ${twojmax} ${radelem} &
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${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
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quadraticflag ${quad} switchflag ${switch}
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compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} &
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${rcutfac} ${rfac0} ${twojmax} ${radelem} &
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${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
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quadraticflag ${quad} switchflag ${switch}
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# define output
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# mygrid is ngrid by (3+nbis) = 384x8
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thermo_style custom step temp ke pe vol &
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c_mygrid[1][7] c_mygrid[2][7] c_mygrid[3][7] c_mygrid[4][7] c_mygrid[5][7] c_mygrid[6][7] c_mygrid[7][7] c_mygrid[8][7] c_mygrid[9][7] &
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c_mygrid[10][7] c_mygrid[11][7] c_mygrid[12][7] c_mygrid[13][7] c_mygrid[14][7] c_mygrid[15][7] c_mygrid[16][7] c_mygrid[17][7] c_mygrid[18][7] c_mygrid[19][7] &
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c_mygrid[20][7] c_mygrid[21][7] c_mygrid[22][7] c_mygrid[23][7] c_mygrid[24][7] c_mygrid[25][7] c_mygrid[26][7] c_mygrid[27][7] c_mygrid[28][7] c_mygrid[29][7] &
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c_mygrid[30][7] c_mygrid[31][7] c_mygrid[32][7] c_mygrid[33][7] c_mygrid[34][7] c_mygrid[35][7] c_mygrid[36][7] c_mygrid[37][7] c_mygrid[38][7] c_mygrid[39][7] &
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c_mygrid[40][7] c_mygrid[41][7] c_mygrid[42][7] c_mygrid[43][7] c_mygrid[44][7] c_mygrid[45][7] c_mygrid[46][7] c_mygrid[47][7] c_mygrid[48][7] c_mygrid[49][7] &
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c_mygrid[50][7] c_mygrid[51][7] c_mygrid[52][7] c_mygrid[53][7] c_mygrid[54][7] c_mygrid[55][7] c_mygrid[56][7] c_mygrid[57][7] c_mygrid[58][7] c_mygrid[59][7] &
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c_mygrid[60][7] c_mygrid[61][7] c_mygrid[62][7] c_mygrid[63][7] c_mygrid[64][7] c_mygrid[65][7] c_mygrid[66][7] c_mygrid[67][7] c_mygrid[68][7] c_mygrid[69][7] &
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c_mygrid[70][7] c_mygrid[71][7] c_mygrid[72][7] c_mygrid[73][7] c_mygrid[74][7] c_mygrid[75][7] c_mygrid[76][7] c_mygrid[77][7] c_mygrid[78][7] c_mygrid[79][7] &
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c_mygrid[80][7] c_mygrid[81][7] c_mygrid[82][7] c_mygrid[83][7] c_mygrid[84][7] c_mygrid[85][7] c_mygrid[86][7] c_mygrid[87][7] c_mygrid[88][7] c_mygrid[89][7] &
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c_mygrid[90][7] c_mygrid[91][7] c_mygrid[92][7] c_mygrid[93][7] c_mygrid[94][7] c_mygrid[95][7] c_mygrid[96][7] c_mygrid[97][7] c_mygrid[98][7] c_mygrid[99][7] &
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c_mygrid[100][7] c_mygrid[101][7] c_mygrid[102][7] c_mygrid[103][7] c_mygrid[104][7] c_mygrid[105][7] c_mygrid[106][7] c_mygrid[107][7] c_mygrid[108][7] c_mygrid[109][7] &
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c_mygrid[110][7] c_mygrid[111][7] c_mygrid[112][7] c_mygrid[113][7] c_mygrid[114][7] c_mygrid[115][7] c_mygrid[116][7] c_mygrid[117][7] c_mygrid[118][7] c_mygrid[119][7] &
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c_mygrid[120][7] c_mygrid[121][7] c_mygrid[122][7] c_mygrid[123][7] c_mygrid[124][7] c_mygrid[125][7] c_mygrid[126][7] c_mygrid[127][7] c_mygrid[128][7] c_mygrid[129][7] &
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c_mygrid[130][7] c_mygrid[131][7] c_mygrid[132][7] c_mygrid[133][7] c_mygrid[134][7] c_mygrid[135][7] c_mygrid[136][7] c_mygrid[137][7] c_mygrid[138][7] c_mygrid[139][7] &
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c_mygrid[140][7] c_mygrid[141][7] c_mygrid[142][7] c_mygrid[143][7] c_mygrid[144][7] c_mygrid[145][7] c_mygrid[146][7] c_mygrid[147][7] c_mygrid[148][7] c_mygrid[149][7] &
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c_mygrid[150][7] c_mygrid[151][7] c_mygrid[152][7] c_mygrid[153][7] c_mygrid[154][7] c_mygrid[155][7] c_mygrid[156][7] c_mygrid[157][7] c_mygrid[158][7] c_mygrid[159][7] &
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c_mygrid[160][7] c_mygrid[161][7] c_mygrid[162][7] c_mygrid[163][7] c_mygrid[164][7] c_mygrid[165][7] c_mygrid[166][7] c_mygrid[167][7] c_mygrid[168][7] c_mygrid[169][7] &
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c_mygrid[170][7] c_mygrid[171][7] c_mygrid[172][7] c_mygrid[173][7] c_mygrid[174][7] c_mygrid[175][7] c_mygrid[176][7] c_mygrid[177][7] c_mygrid[178][7] c_mygrid[179][7] &
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c_mygrid[180][7] c_mygrid[181][7] c_mygrid[182][7] c_mygrid[183][7] c_mygrid[184][7] c_mygrid[185][7] c_mygrid[186][7] c_mygrid[187][7] c_mygrid[188][7] c_mygrid[189][7] &
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c_mygrid[190][7] c_mygrid[191][7] c_mygrid[192][7] c_mygrid[193][7] c_mygrid[194][7] c_mygrid[195][7] c_mygrid[196][7] c_mygrid[197][7] c_mygrid[198][7] c_mygrid[199][7] &
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c_mygrid[200][7] c_mygrid[201][7] c_mygrid[202][7] c_mygrid[203][7] c_mygrid[204][7] c_mygrid[205][7] c_mygrid[206][7] c_mygrid[207][7] c_mygrid[208][7] c_mygrid[209][7] &
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c_mygrid[210][7] c_mygrid[211][7] c_mygrid[212][7] c_mygrid[213][7] c_mygrid[214][7] c_mygrid[215][7] c_mygrid[216][7] c_mygrid[217][7] c_mygrid[218][7] c_mygrid[219][7] &
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c_mygrid[220][7] c_mygrid[221][7] c_mygrid[222][7] c_mygrid[223][7] c_mygrid[224][7] c_mygrid[225][7] c_mygrid[226][7] c_mygrid[227][7] c_mygrid[228][7] c_mygrid[229][7] &
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c_mygrid[230][7] c_mygrid[231][7] c_mygrid[232][7] c_mygrid[233][7] c_mygrid[234][7] c_mygrid[235][7] c_mygrid[236][7] c_mygrid[237][7] c_mygrid[238][7] c_mygrid[239][7] &
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c_mygrid[240][7] c_mygrid[241][7] c_mygrid[242][7] c_mygrid[243][7] c_mygrid[244][7] c_mygrid[245][7] c_mygrid[246][7] c_mygrid[247][7] c_mygrid[248][7] c_mygrid[249][7] &
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c_mygrid[250][7] c_mygrid[251][7] c_mygrid[252][7] c_mygrid[253][7] c_mygrid[254][7] c_mygrid[255][7] c_mygrid[256][7] c_mygrid[257][7] c_mygrid[258][7] c_mygrid[259][7] &
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c_mygrid[260][7] c_mygrid[261][7] c_mygrid[262][7] c_mygrid[263][7] c_mygrid[264][7] c_mygrid[265][7] c_mygrid[266][7] c_mygrid[267][7] c_mygrid[268][7] c_mygrid[269][7] &
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c_mygrid[270][7] c_mygrid[271][7] c_mygrid[272][7] c_mygrid[273][7] c_mygrid[274][7] c_mygrid[275][7] c_mygrid[276][7] c_mygrid[277][7] c_mygrid[278][7] c_mygrid[279][7] &
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c_mygrid[280][7] c_mygrid[281][7] c_mygrid[282][7] c_mygrid[283][7] c_mygrid[284][7] c_mygrid[285][7] c_mygrid[286][7] c_mygrid[287][7] c_mygrid[288][7] c_mygrid[289][7] &
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c_mygrid[290][7] c_mygrid[291][7] c_mygrid[292][7] c_mygrid[293][7] c_mygrid[294][7] c_mygrid[295][7] c_mygrid[296][7] c_mygrid[297][7] c_mygrid[298][7] c_mygrid[299][7] &
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c_mygrid[300][7] c_mygrid[301][7] c_mygrid[302][7] c_mygrid[303][7] c_mygrid[304][7] c_mygrid[305][7] c_mygrid[306][7] c_mygrid[307][7] c_mygrid[308][7] c_mygrid[309][7] &
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c_mygrid[310][7] c_mygrid[311][7] c_mygrid[312][7] c_mygrid[313][7] c_mygrid[314][7] c_mygrid[315][7] c_mygrid[316][7] c_mygrid[317][7] c_mygrid[318][7] c_mygrid[319][7] &
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c_mygrid[320][7] c_mygrid[321][7] c_mygrid[322][7] c_mygrid[323][7] c_mygrid[324][7] c_mygrid[325][7] c_mygrid[326][7] c_mygrid[327][7] c_mygrid[328][7] c_mygrid[329][7] &
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c_mygrid[330][7] c_mygrid[331][7] c_mygrid[332][7] c_mygrid[333][7] c_mygrid[334][7] c_mygrid[335][7] c_mygrid[336][7] c_mygrid[337][7] c_mygrid[338][7] c_mygrid[339][7] &
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c_mygrid[340][7] c_mygrid[341][7] c_mygrid[342][7] c_mygrid[343][7] c_mygrid[344][7] c_mygrid[345][7] c_mygrid[346][7] c_mygrid[347][7] c_mygrid[348][7] c_mygrid[349][7] &
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c_mygrid[350][7] c_mygrid[351][7] c_mygrid[352][7] c_mygrid[353][7] c_mygrid[354][7] c_mygrid[355][7] c_mygrid[356][7] c_mygrid[357][7] c_mygrid[358][7] c_mygrid[359][7] &
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c_mygrid[360][7] c_mygrid[361][7] c_mygrid[362][7] c_mygrid[363][7] c_mygrid[364][7] c_mygrid[365][7] c_mygrid[366][7] c_mygrid[367][7] c_mygrid[368][7] c_mygrid[369][7] &
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c_mygrid[370][7] c_mygrid[371][7] c_mygrid[372][7] c_mygrid[373][7] c_mygrid[374][7] c_mygrid[375][7] c_mygrid[376][7] c_mygrid[377][7] c_mygrid[378][7] c_mygrid[379][7] &
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c_mygrid[380][7] c_mygrid[381][7] c_mygrid[382][7] c_mygrid[383][7] c_mygrid[384][7]
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thermo_modify norm yes
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dump mydump_b all custom 1000 dump_b id c_b[*]
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# run
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run 0
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