Got a first pass working for ortho and tri grids
This commit is contained in:
Aidan Thompson
71
examples/snap/in.grid
Normal file
71
examples/snap/in.grid
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@ -0,0 +1,71 @@
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# Demonstrate bispectrum computes
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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 2
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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 ${nrep}
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variable ny equal ${nrep}
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variable nz equal ${nrep}
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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 0 1 0 &
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a3 0 0 1 &
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basis 0 0 0 &
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basis 0.5 0.5 0.5 &
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# origin 0.25 0.25 0.25
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region box block 0 ${nx} 0 ${ny} 0 ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 180.88
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# choose potential
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include Ta06A.snap
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# define grid compute and atom compute
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group snapgroup type 1
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variable twojmax equal 2
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variable rcutfac equal 4.67637
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable wj equal 1
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variable radelem equal 0.5
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variable bzero equal 0
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variable quad equal 0
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variable switch equal 0
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compute b all sna/atom &
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${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 ${ngrid} ${ngrid} ${ngrid} &
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${rcutfac} ${rfac0} ${twojmax} ${radelem} &
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${wj} rmin0 ${rmin0} bzeroflag ${bzero} &
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quadraticflag ${quad} switchflag ${switch}
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# define output
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thermo_style custom step temp ke pe vol c_mygrid[1][1] c_mygrid[2][1] c_mygrid[3][1] c_mygrid[4][1] c_mygrid[5][1] c_mygrid[6][1] c_mygrid[7][1] c_mygrid[8][1]
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thermo_modify norm yes
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dump mydump_b all custom 1000 dump_b id c_b[*]
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# run
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run 0
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116
examples/snap/in.grid.tri
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116
examples/snap/in.grid.tri
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@ -0,0 +1,116 @@
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# Demonstrate bispectrum computes
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# Initialize simulation
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variable nsteps index 0
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variable nrep index 1
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variable a index 3.316
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variable ngrid index 4
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variable ngridx equal 3*${ngrid}
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variable ngridy equal 2*${ngrid}
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variable ngridz equal 1*${ngrid}
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units metal
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# generate the box and atom positions using a BCC lattice
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variable nx equal ${nrep}
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variable ny equal ${nrep}
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variable nz equal ${nrep}
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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} ${nz}
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create_box 1 box
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create_atoms 1 box
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mass 1 180.88
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# choose potential
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include Ta06A.snap
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# define grid compute and atom compute
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group snapgroup type 1
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variable twojmax equal 2
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variable rcutfac equal 4.67637
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variable rfac0 equal 0.99363
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variable rmin0 equal 0
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variable wj equal 1
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variable radelem equal 0.5
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variable bzero equal 0
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variable quad equal 0
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variable switch equal 0
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compute b all sna/atom &
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${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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thermo_style custom step temp ke pe vol &
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c_mygrid[1][1] c_mygrid[2][1] c_mygrid[3][1] c_mygrid[4][1] c_mygrid[5][1] c_mygrid[6][1] c_mygrid[7][1] c_mygrid[8][1] c_mygrid[9][1] &
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c_mygrid[10][1] c_mygrid[11][1] c_mygrid[12][1] c_mygrid[13][1] c_mygrid[14][1] c_mygrid[15][1] c_mygrid[16][1] c_mygrid[17][1] c_mygrid[18][1] c_mygrid[19][1] &
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c_mygrid[20][1] c_mygrid[21][1] c_mygrid[22][1] c_mygrid[23][1] c_mygrid[24][1] c_mygrid[25][1] c_mygrid[26][1] c_mygrid[27][1] c_mygrid[28][1] c_mygrid[29][1] &
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c_mygrid[30][1] c_mygrid[31][1] c_mygrid[32][1] c_mygrid[33][1] c_mygrid[34][1] c_mygrid[35][1] c_mygrid[36][1] c_mygrid[37][1] c_mygrid[38][1] c_mygrid[39][1] &
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c_mygrid[40][1] c_mygrid[41][1] c_mygrid[42][1] c_mygrid[43][1] c_mygrid[44][1] c_mygrid[45][1] c_mygrid[46][1] c_mygrid[47][1] c_mygrid[48][1] c_mygrid[49][1] &
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c_mygrid[50][1] c_mygrid[51][1] c_mygrid[52][1] c_mygrid[53][1] c_mygrid[54][1] c_mygrid[55][1] c_mygrid[56][1] c_mygrid[57][1] c_mygrid[58][1] c_mygrid[59][1] &
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c_mygrid[60][1] c_mygrid[61][1] c_mygrid[62][1] c_mygrid[63][1] c_mygrid[64][1] c_mygrid[65][1] c_mygrid[66][1] c_mygrid[67][1] c_mygrid[68][1] c_mygrid[69][1] &
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c_mygrid[70][1] c_mygrid[71][1] c_mygrid[72][1] c_mygrid[73][1] c_mygrid[74][1] c_mygrid[75][1] c_mygrid[76][1] c_mygrid[77][1] c_mygrid[78][1] c_mygrid[79][1] &
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c_mygrid[80][1] c_mygrid[81][1] c_mygrid[82][1] c_mygrid[83][1] c_mygrid[84][1] c_mygrid[85][1] c_mygrid[86][1] c_mygrid[87][1] c_mygrid[88][1] c_mygrid[89][1] &
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c_mygrid[90][1] c_mygrid[91][1] c_mygrid[92][1] c_mygrid[93][1] c_mygrid[94][1] c_mygrid[95][1] c_mygrid[96][1] c_mygrid[97][1] c_mygrid[98][1] c_mygrid[99][1] &
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c_mygrid[101][1] c_mygrid[102][1] c_mygrid[103][1] c_mygrid[104][1] c_mygrid[105][1] c_mygrid[106][1] c_mygrid[107][1] c_mygrid[108][1] c_mygrid[109][1] &
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c_mygrid[110][1] c_mygrid[111][1] c_mygrid[112][1] c_mygrid[113][1] c_mygrid[114][1] c_mygrid[115][1] c_mygrid[116][1] c_mygrid[117][1] c_mygrid[118][1] c_mygrid[119][1] &
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c_mygrid[120][1] c_mygrid[121][1] c_mygrid[122][1] c_mygrid[123][1] c_mygrid[124][1] c_mygrid[125][1] c_mygrid[126][1] c_mygrid[127][1] c_mygrid[128][1] c_mygrid[129][1] &
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c_mygrid[130][1] c_mygrid[131][1] c_mygrid[132][1] c_mygrid[133][1] c_mygrid[134][1] c_mygrid[135][1] c_mygrid[136][1] c_mygrid[137][1] c_mygrid[138][1] c_mygrid[139][1] &
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c_mygrid[140][1] c_mygrid[141][1] c_mygrid[142][1] c_mygrid[143][1] c_mygrid[144][1] c_mygrid[145][1] c_mygrid[146][1] c_mygrid[147][1] c_mygrid[148][1] c_mygrid[149][1] &
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c_mygrid[150][1] c_mygrid[151][1] c_mygrid[152][1] c_mygrid[153][1] c_mygrid[154][1] c_mygrid[155][1] c_mygrid[156][1] c_mygrid[157][1] c_mygrid[158][1] c_mygrid[159][1] &
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c_mygrid[160][1] c_mygrid[161][1] c_mygrid[162][1] c_mygrid[163][1] c_mygrid[164][1] c_mygrid[165][1] c_mygrid[166][1] c_mygrid[167][1] c_mygrid[168][1] c_mygrid[169][1] &
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c_mygrid[170][1] c_mygrid[171][1] c_mygrid[172][1] c_mygrid[173][1] c_mygrid[174][1] c_mygrid[175][1] c_mygrid[176][1] c_mygrid[177][1] c_mygrid[178][1] c_mygrid[179][1] &
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c_mygrid[180][1] c_mygrid[181][1] c_mygrid[182][1] c_mygrid[183][1] c_mygrid[184][1] c_mygrid[185][1] c_mygrid[186][1] c_mygrid[187][1] c_mygrid[188][1] c_mygrid[189][1] &
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c_mygrid[190][1] c_mygrid[191][1] c_mygrid[192][1] c_mygrid[193][1] c_mygrid[194][1] c_mygrid[195][1] c_mygrid[196][1] c_mygrid[197][1] c_mygrid[198][1] c_mygrid[199][1] &
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c_mygrid[201][1] c_mygrid[202][1] c_mygrid[203][1] c_mygrid[204][1] c_mygrid[205][1] c_mygrid[206][1] c_mygrid[207][1] c_mygrid[208][1] c_mygrid[209][1] &
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c_mygrid[210][1] c_mygrid[211][1] c_mygrid[212][1] c_mygrid[213][1] c_mygrid[214][1] c_mygrid[215][1] c_mygrid[216][1] c_mygrid[217][1] c_mygrid[218][1] c_mygrid[219][1] &
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c_mygrid[220][1] c_mygrid[221][1] c_mygrid[222][1] c_mygrid[223][1] c_mygrid[224][1] c_mygrid[225][1] c_mygrid[226][1] c_mygrid[227][1] c_mygrid[228][1] c_mygrid[229][1] &
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c_mygrid[230][1] c_mygrid[231][1] c_mygrid[232][1] c_mygrid[233][1] c_mygrid[234][1] c_mygrid[235][1] c_mygrid[236][1] c_mygrid[237][1] c_mygrid[238][1] c_mygrid[239][1] &
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c_mygrid[240][1] c_mygrid[241][1] c_mygrid[242][1] c_mygrid[243][1] c_mygrid[244][1] c_mygrid[245][1] c_mygrid[246][1] c_mygrid[247][1] c_mygrid[248][1] c_mygrid[249][1] &
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c_mygrid[250][1] c_mygrid[251][1] c_mygrid[252][1] c_mygrid[253][1] c_mygrid[254][1] c_mygrid[255][1] c_mygrid[256][1] c_mygrid[257][1] c_mygrid[258][1] c_mygrid[259][1] &
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c_mygrid[260][1] c_mygrid[261][1] c_mygrid[262][1] c_mygrid[263][1] c_mygrid[264][1] c_mygrid[265][1] c_mygrid[266][1] c_mygrid[267][1] c_mygrid[268][1] c_mygrid[269][1] &
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c_mygrid[270][1] c_mygrid[271][1] c_mygrid[272][1] c_mygrid[273][1] c_mygrid[274][1] c_mygrid[275][1] c_mygrid[276][1] c_mygrid[277][1] c_mygrid[278][1] c_mygrid[279][1] &
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c_mygrid[280][1] c_mygrid[281][1] c_mygrid[282][1] c_mygrid[283][1] c_mygrid[284][1] c_mygrid[285][1] c_mygrid[286][1] c_mygrid[287][1] c_mygrid[288][1] c_mygrid[289][1] &
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c_mygrid[290][1] c_mygrid[291][1] c_mygrid[292][1] c_mygrid[293][1] c_mygrid[294][1] c_mygrid[295][1] c_mygrid[296][1] c_mygrid[297][1] c_mygrid[298][1] c_mygrid[299][1] &
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c_mygrid[301][1] c_mygrid[302][1] c_mygrid[303][1] c_mygrid[304][1] c_mygrid[305][1] c_mygrid[306][1] c_mygrid[307][1] c_mygrid[308][1] c_mygrid[309][1] &
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c_mygrid[310][1] c_mygrid[311][1] c_mygrid[312][1] c_mygrid[313][1] c_mygrid[314][1] c_mygrid[315][1] c_mygrid[316][1] c_mygrid[317][1] c_mygrid[318][1] c_mygrid[319][1] &
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c_mygrid[320][1] c_mygrid[321][1] c_mygrid[322][1] c_mygrid[323][1] c_mygrid[324][1] c_mygrid[325][1] c_mygrid[326][1] c_mygrid[327][1] c_mygrid[328][1] c_mygrid[329][1] &
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c_mygrid[330][1] c_mygrid[331][1] c_mygrid[332][1] c_mygrid[333][1] c_mygrid[334][1] c_mygrid[335][1] c_mygrid[336][1] c_mygrid[337][1] c_mygrid[338][1] c_mygrid[339][1] &
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c_mygrid[340][1] c_mygrid[341][1] c_mygrid[342][1] c_mygrid[343][1] c_mygrid[344][1] c_mygrid[345][1] c_mygrid[346][1] c_mygrid[347][1] c_mygrid[348][1] c_mygrid[349][1] &
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c_mygrid[350][1] c_mygrid[351][1] c_mygrid[352][1] c_mygrid[353][1] c_mygrid[354][1] c_mygrid[355][1] c_mygrid[356][1] c_mygrid[357][1] c_mygrid[358][1] c_mygrid[359][1] &
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c_mygrid[360][1] c_mygrid[361][1] c_mygrid[362][1] c_mygrid[363][1] c_mygrid[364][1] c_mygrid[365][1] c_mygrid[366][1] c_mygrid[367][1] c_mygrid[368][1] c_mygrid[369][1] &
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c_mygrid[370][1] c_mygrid[371][1] c_mygrid[372][1] c_mygrid[373][1] c_mygrid[374][1] c_mygrid[375][1] c_mygrid[376][1] c_mygrid[377][1] c_mygrid[378][1] c_mygrid[379][1] &
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c_mygrid[380][1] c_mygrid[381][1] c_mygrid[382][1] c_mygrid[383][1] c_mygrid[384][1]
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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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@ -34,7 +34,7 @@ ComputeGrid::ComputeGrid(LAMMPS *lmp, int narg, char **arg) :
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array_flag = 1;
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size_array_cols = 0;
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size_array_rows = 0;
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extarray = 1;
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extarray = 0;
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int iarg0 = 3;
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int iarg = iarg0;
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@ -119,10 +119,6 @@ void ComputeGrid::setup()
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+ pow(delxy*my,2))*delxinvtmp + 1;
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}
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printf("mx = %d\n",mx);
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printf("my = %d\n",my);
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printf("mz = %d\n",mz);
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// size global grid to accomodate periodic interactions
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nxfull = nx + 2*mx;
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@ -130,10 +126,6 @@ void ComputeGrid::setup()
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nzfull = nz + 2*mz;
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nxyfull = nxfull * nyfull;
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printf("nxfull = %d\n",nxfull);
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printf("nyfull = %d\n",nyfull);
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printf("nzfull = %d\n",nzfull);
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x0full = boxlo[0] - mx*delx;
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y0full = boxlo[1] - my*dely;
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z0full = boxlo[2] - mz*delz;
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@ -148,9 +140,9 @@ void ComputeGrid::setup()
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void ComputeGrid::igridfull2x(int igrid, double *x)
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{
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int iz = igrid / nxyfull;
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igrid -= iz*nxyfull;
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igrid -= iz * nxyfull;
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int iy = igrid / nxfull;
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igrid -= igrid*nxfull;
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igrid -= iy * nxfull;
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int ix = igrid;
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x[0] = x0full+ix*delx;
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@ -161,14 +153,28 @@ void ComputeGrid::igridfull2x(int igrid, double *x)
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}
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/* ----------------------------------------------------------------------
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copy local grid to global array
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------------------------------------------------------------------------- */
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void ComputeGrid::copy_local_grid()
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{
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int igridfull;
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for (int iarray = 0; iarray < size_array_rows; iarray++) {
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igridfull = iarray2igridfull(iarray);
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for (int icol = 0; icol < size_array_cols; icol++)
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array[iarray][icol] = gridfull[igridfull][icol];
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}
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}
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/* ----------------------------------------------------------------------
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gather global array from full grid
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------------------------------------------------------------------------- */
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void ComputeGrid::gather_global_array()
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{
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int iarray;
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memset(&array[0][0],0,size_array_rows*size_array_cols*sizeof(double));
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int iarray;
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memset(&array[0][0],0,size_array_rows*size_array_cols*sizeof(double));
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for (int igrid = 0; igrid < ngridfull; igrid++) {
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@ -190,7 +196,7 @@ int ComputeGrid::igridfull2iarray(int igrid)
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int iz = igrid / nxyfull;
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igrid -= iz*nxyfull;
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int iy = igrid / nxfull;
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igrid -= igrid*nxfull;
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igrid -= iy*nxfull;
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int ix = igrid;
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ix -= mx;
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@ -210,6 +216,28 @@ int ComputeGrid::igridfull2iarray(int igrid)
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return iarray;
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}
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/* ----------------------------------------------------------------------
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convert compute array index to full grid index
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inefficient, should exploit shared ix structure
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------------------------------------------------------------------------- */
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int ComputeGrid::iarray2igridfull(int iarray)
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{
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int iz = iarray / (nx*ny);
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iarray -= iz*(nx*ny);
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int iy = iarray / nx;
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iarray -= iy*nx;
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int ix = iarray;
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ix += mx;
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iy += my;
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iz += mz;
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int igrid = (iz * nyfull + iy) * nxfull + ix;
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return igrid;
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}
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/* ----------------------------------------------------------------------
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free and reallocate arrays
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------------------------------------------------------------------------- */
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@ -46,7 +46,9 @@ class ComputeGrid : public Compute {
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virtual void allocate();
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void igridfull2x(int, double*); // convert full grid point to coord
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void gather_global_array(); // gather global array from full grid
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void copy_local_grid(); // copy local grid to global array
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int igridfull2iarray(int); // convert full grid index to compute array index
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int iarray2igridfull(int); // convert compute array index to full grid index
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private:
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};
|
||||
|
||||
Reference in New Issue
Block a user