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Added cols for coords

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This commit is contained in:
Aidan Thompson
2019-10-23 21:51:36 -06:00
parent 0fc325c98b
commit 5956908cfd
5 changed files with 90 additions and 46 deletions
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6
examples/snap/in.grid
View File

@ -60,7 +60,11 @@ compute mygrid all sna/grid grid ${ngrid} ${ngrid} ${ngrid} &
# define output # define output
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] 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] &
c_mygrid[1][2] c_mygrid[2][2] c_mygrid[3][2] c_mygrid[4][2] c_mygrid[5][2] c_mygrid[6][2] c_mygrid[7][2] c_mygrid[8][2] &
c_mygrid[1][3] c_mygrid[2][3] c_mygrid[3][3] c_mygrid[4][3] c_mygrid[5][3] c_mygrid[6][3] c_mygrid[7][3] c_mygrid[8][3] &
c_mygrid[1][4] c_mygrid[2][4] c_mygrid[3][4] c_mygrid[4][4] c_mygrid[5][4] c_mygrid[6][4] c_mygrid[7][4] c_mygrid[8][4]
thermo_modify norm yes thermo_modify norm yes
dump mydump_b all custom 1000 dump_b id c_b[*] dump mydump_b all custom 1000 dump_b id c_b[*]

78
examples/snap/in.grid.tri
View File

@ -66,45 +66,45 @@ compute mygrid all sna/grid grid ${ngridx} ${ngridy} ${ngridz} &
# define output # define output
thermo_style custom step temp ke pe vol & 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] c_mygrid[9][1] & c_mygrid[1][4] c_mygrid[2][4] c_mygrid[3][4] c_mygrid[4][4] c_mygrid[5][4] c_mygrid[6][4] c_mygrid[7][4] c_mygrid[8][4] c_mygrid[9][4] &
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] & c_mygrid[10][4] c_mygrid[11][4] c_mygrid[12][4] c_mygrid[13][4] c_mygrid[14][4] c_mygrid[15][4] c_mygrid[16][4] c_mygrid[17][4] c_mygrid[18][4] c_mygrid[19][4] &
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] & c_mygrid[20][4] c_mygrid[21][4] c_mygrid[22][4] c_mygrid[23][4] c_mygrid[24][4] c_mygrid[25][4] c_mygrid[26][4] c_mygrid[27][4] c_mygrid[28][4] c_mygrid[29][4] &
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] & c_mygrid[30][4] c_mygrid[31][4] c_mygrid[32][4] c_mygrid[33][4] c_mygrid[34][4] c_mygrid[35][4] c_mygrid[36][4] c_mygrid[37][4] c_mygrid[38][4] c_mygrid[39][4] &
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] & c_mygrid[40][4] c_mygrid[41][4] c_mygrid[42][4] c_mygrid[43][4] c_mygrid[44][4] c_mygrid[45][4] c_mygrid[46][4] c_mygrid[47][4] c_mygrid[48][4] c_mygrid[49][4] &
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] & c_mygrid[50][4] c_mygrid[51][4] c_mygrid[52][4] c_mygrid[53][4] c_mygrid[54][4] c_mygrid[55][4] c_mygrid[56][4] c_mygrid[57][4] c_mygrid[58][4] c_mygrid[59][4] &
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] & c_mygrid[60][4] c_mygrid[61][4] c_mygrid[62][4] c_mygrid[63][4] c_mygrid[64][4] c_mygrid[65][4] c_mygrid[66][4] c_mygrid[67][4] c_mygrid[68][4] c_mygrid[69][4] &
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] & c_mygrid[70][4] c_mygrid[71][4] c_mygrid[72][4] c_mygrid[73][4] c_mygrid[74][4] c_mygrid[75][4] c_mygrid[76][4] c_mygrid[77][4] c_mygrid[78][4] c_mygrid[79][4] &
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] & c_mygrid[80][4] c_mygrid[81][4] c_mygrid[82][4] c_mygrid[83][4] c_mygrid[84][4] c_mygrid[85][4] c_mygrid[86][4] c_mygrid[87][4] c_mygrid[88][4] c_mygrid[89][4] &
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] & c_mygrid[90][4] c_mygrid[91][4] c_mygrid[92][4] c_mygrid[93][4] c_mygrid[94][4] c_mygrid[95][4] c_mygrid[96][4] c_mygrid[97][4] c_mygrid[98][4] c_mygrid[99][4] &
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] & c_mygrid[101][4] c_mygrid[102][4] c_mygrid[103][4] c_mygrid[104][4] c_mygrid[105][4] c_mygrid[106][4] c_mygrid[107][4] c_mygrid[108][4] c_mygrid[109][4] &
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] & c_mygrid[110][4] c_mygrid[111][4] c_mygrid[112][4] c_mygrid[113][4] c_mygrid[114][4] c_mygrid[115][4] c_mygrid[116][4] c_mygrid[117][4] c_mygrid[118][4] c_mygrid[119][4] &
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] & c_mygrid[120][4] c_mygrid[121][4] c_mygrid[122][4] c_mygrid[123][4] c_mygrid[124][4] c_mygrid[125][4] c_mygrid[126][4] c_mygrid[127][4] c_mygrid[128][4] c_mygrid[129][4] &
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] & c_mygrid[130][4] c_mygrid[131][4] c_mygrid[132][4] c_mygrid[133][4] c_mygrid[134][4] c_mygrid[135][4] c_mygrid[136][4] c_mygrid[137][4] c_mygrid[138][4] c_mygrid[139][4] &
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] & c_mygrid[140][4] c_mygrid[141][4] c_mygrid[142][4] c_mygrid[143][4] c_mygrid[144][4] c_mygrid[145][4] c_mygrid[146][4] c_mygrid[147][4] c_mygrid[148][4] c_mygrid[149][4] &
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] & c_mygrid[150][4] c_mygrid[151][4] c_mygrid[152][4] c_mygrid[153][4] c_mygrid[154][4] c_mygrid[155][4] c_mygrid[156][4] c_mygrid[157][4] c_mygrid[158][4] c_mygrid[159][4] &
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] & c_mygrid[160][4] c_mygrid[161][4] c_mygrid[162][4] c_mygrid[163][4] c_mygrid[164][4] c_mygrid[165][4] c_mygrid[166][4] c_mygrid[167][4] c_mygrid[168][4] c_mygrid[169][4] &
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] & c_mygrid[170][4] c_mygrid[171][4] c_mygrid[172][4] c_mygrid[173][4] c_mygrid[174][4] c_mygrid[175][4] c_mygrid[176][4] c_mygrid[177][4] c_mygrid[178][4] c_mygrid[179][4] &
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] & c_mygrid[180][4] c_mygrid[181][4] c_mygrid[182][4] c_mygrid[183][4] c_mygrid[184][4] c_mygrid[185][4] c_mygrid[186][4] c_mygrid[187][4] c_mygrid[188][4] c_mygrid[189][4] &
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] & c_mygrid[190][4] c_mygrid[191][4] c_mygrid[192][4] c_mygrid[193][4] c_mygrid[194][4] c_mygrid[195][4] c_mygrid[196][4] c_mygrid[197][4] c_mygrid[198][4] c_mygrid[199][4] &
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] & c_mygrid[201][4] c_mygrid[202][4] c_mygrid[203][4] c_mygrid[204][4] c_mygrid[205][4] c_mygrid[206][4] c_mygrid[207][4] c_mygrid[208][4] c_mygrid[209][4] &
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] & c_mygrid[210][4] c_mygrid[211][4] c_mygrid[212][4] c_mygrid[213][4] c_mygrid[214][4] c_mygrid[215][4] c_mygrid[216][4] c_mygrid[217][4] c_mygrid[218][4] c_mygrid[219][4] &
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] & c_mygrid[220][4] c_mygrid[221][4] c_mygrid[222][4] c_mygrid[223][4] c_mygrid[224][4] c_mygrid[225][4] c_mygrid[226][4] c_mygrid[227][4] c_mygrid[228][4] c_mygrid[229][4] &
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] & c_mygrid[230][4] c_mygrid[231][4] c_mygrid[232][4] c_mygrid[233][4] c_mygrid[234][4] c_mygrid[235][4] c_mygrid[236][4] c_mygrid[237][4] c_mygrid[238][4] c_mygrid[239][4] &
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] & c_mygrid[240][4] c_mygrid[241][4] c_mygrid[242][4] c_mygrid[243][4] c_mygrid[244][4] c_mygrid[245][4] c_mygrid[246][4] c_mygrid[247][4] c_mygrid[248][4] c_mygrid[249][4] &
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] & c_mygrid[250][4] c_mygrid[251][4] c_mygrid[252][4] c_mygrid[253][4] c_mygrid[254][4] c_mygrid[255][4] c_mygrid[256][4] c_mygrid[257][4] c_mygrid[258][4] c_mygrid[259][4] &
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] & c_mygrid[260][4] c_mygrid[261][4] c_mygrid[262][4] c_mygrid[263][4] c_mygrid[264][4] c_mygrid[265][4] c_mygrid[266][4] c_mygrid[267][4] c_mygrid[268][4] c_mygrid[269][4] &
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] & c_mygrid[270][4] c_mygrid[271][4] c_mygrid[272][4] c_mygrid[273][4] c_mygrid[274][4] c_mygrid[275][4] c_mygrid[276][4] c_mygrid[277][4] c_mygrid[278][4] c_mygrid[279][4] &
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] & c_mygrid[280][4] c_mygrid[281][4] c_mygrid[282][4] c_mygrid[283][4] c_mygrid[284][4] c_mygrid[285][4] c_mygrid[286][4] c_mygrid[287][4] c_mygrid[288][4] c_mygrid[289][4] &
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] & c_mygrid[290][4] c_mygrid[291][4] c_mygrid[292][4] c_mygrid[293][4] c_mygrid[294][4] c_mygrid[295][4] c_mygrid[296][4] c_mygrid[297][4] c_mygrid[298][4] c_mygrid[299][4] &
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] & c_mygrid[301][4] c_mygrid[302][4] c_mygrid[303][4] c_mygrid[304][4] c_mygrid[305][4] c_mygrid[306][4] c_mygrid[307][4] c_mygrid[308][4] c_mygrid[309][4] &
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] & c_mygrid[310][4] c_mygrid[311][4] c_mygrid[312][4] c_mygrid[313][4] c_mygrid[314][4] c_mygrid[315][4] c_mygrid[316][4] c_mygrid[317][4] c_mygrid[318][4] c_mygrid[319][4] &
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] & c_mygrid[320][4] c_mygrid[321][4] c_mygrid[322][4] c_mygrid[323][4] c_mygrid[324][4] c_mygrid[325][4] c_mygrid[326][4] c_mygrid[327][4] c_mygrid[328][4] c_mygrid[329][4] &
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] & c_mygrid[330][4] c_mygrid[331][4] c_mygrid[332][4] c_mygrid[333][4] c_mygrid[334][4] c_mygrid[335][4] c_mygrid[336][4] c_mygrid[337][4] c_mygrid[338][4] c_mygrid[339][4] &
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] & c_mygrid[340][4] c_mygrid[341][4] c_mygrid[342][4] c_mygrid[343][4] c_mygrid[344][4] c_mygrid[345][4] c_mygrid[346][4] c_mygrid[347][4] c_mygrid[348][4] c_mygrid[349][4] &
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] & c_mygrid[350][4] c_mygrid[351][4] c_mygrid[352][4] c_mygrid[353][4] c_mygrid[354][4] c_mygrid[355][4] c_mygrid[356][4] c_mygrid[357][4] c_mygrid[358][4] c_mygrid[359][4] &
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] & c_mygrid[360][4] c_mygrid[361][4] c_mygrid[362][4] c_mygrid[363][4] c_mygrid[364][4] c_mygrid[365][4] c_mygrid[366][4] c_mygrid[367][4] c_mygrid[368][4] c_mygrid[369][4] &
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] & c_mygrid[370][4] c_mygrid[371][4] c_mygrid[372][4] c_mygrid[373][4] c_mygrid[374][4] c_mygrid[375][4] c_mygrid[376][4] c_mygrid[377][4] c_mygrid[378][4] c_mygrid[379][4] &
c_mygrid[380][1] c_mygrid[381][1] c_mygrid[382][1] c_mygrid[383][1] c_mygrid[384][1] c_mygrid[380][4] c_mygrid[381][4] c_mygrid[382][4] c_mygrid[383][4] c_mygrid[384][4]
thermo_modify norm yes thermo_modify norm yes

6
src/SNAP/compute_sna_grid.cpp
View File

@ -120,7 +120,7 @@ ComputeSNAGrid::ComputeSNAGrid(LAMMPS *lmp, int narg, char **arg) :
rmin0,switchflag,bzeroflag); rmin0,switchflag,bzeroflag);
ncoeff = snaptr->ncoeff; ncoeff = snaptr->ncoeff;
size_array_cols = ncoeff; size_array_cols = size_array_cols_base + ncoeff;
if (quadraticflag) size_array_cols += (ncoeff*(ncoeff+1))/2; if (quadraticflag) size_array_cols += (ncoeff*(ncoeff+1))/2;
array_flag = 1; array_flag = 1;
} }
@ -237,8 +237,8 @@ void ComputeSNAGrid::compute_array()
snaptr->compute_zi(); snaptr->compute_zi();
snaptr->compute_bi(); snaptr->compute_bi();
for (int icoeff = 0; icoeff < ncoeff; icoeff++) for (int icoeff = 0; icoeff < ncoeff; icoeff++)
sna[igrid][icoeff] = snaptr->blist[icoeff]; sna[igrid][size_array_cols_base+icoeff] = snaptr->blist[icoeff];
// printf("igrid = %d %g %g %g %d B0 = %g\n",igrid,xtmp,ytmp,ztmp,ninside,sna[igrid][0]); // printf("igrid = %d %g %g %g %d B0 = %g\n",igrid,xtmp,ytmp,ztmp,ninside,sna[igrid][size_array_cols_base+0]);
if (quadraticflag) { if (quadraticflag) {
int ncount = ncoeff; int ncount = ncoeff;
for (int icoeff = 0; icoeff < ncoeff; icoeff++) { for (int icoeff = 0; icoeff < ncoeff; icoeff++) {

41
src/compute_grid.cpp
View File

@ -51,6 +51,7 @@ ComputeGrid::ComputeGrid(LAMMPS *lmp, int narg, char **arg) :
nargbase = iarg - iarg0; nargbase = iarg - iarg0;
size_array_rows = nx*ny*nz; size_array_rows = nx*ny*nz;
size_array_cols_base = 3;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -131,6 +132,7 @@ void ComputeGrid::setup()
z0full = boxlo[2] - mz*delz; z0full = boxlo[2] - mz*delz;
allocate(); allocate();
assign_coords_array();
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -153,6 +155,26 @@ void ComputeGrid::igridfull2x(int igrid, double *x)
} }
/* ----------------------------------------------------------------------
convert array index to box coords
------------------------------------------------------------------------- */
void ComputeGrid::iarray2x(int iarray, double *x)
{
int iz = iarray / (nx*ny);
iarray -= iz * (nx*ny);
int iy = iarray / nx;
iarray -= iy * nx;
int ix = iarray;
x[0] = ix*delx;
x[1] = iy*dely;
x[2] = iz*delz;
if (triclinic) domain->lamda2x(x, x);
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
copy local grid to global array copy local grid to global array
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -162,11 +184,26 @@ void ComputeGrid::copy_local_grid()
int igridfull; int igridfull;
for (int iarray = 0; iarray < size_array_rows; iarray++) { for (int iarray = 0; iarray < size_array_rows; iarray++) {
igridfull = iarray2igridfull(iarray); igridfull = iarray2igridfull(iarray);
for (int icol = 0; icol < size_array_cols; icol++) for (int icol = size_array_cols_base; icol < size_array_cols; icol++)
array[iarray][icol] = gridfull[igridfull][icol]; array[iarray][icol] = gridfull[igridfull][icol];
} }
} }
/* ----------------------------------------------------------------------
copy coords to global array
------------------------------------------------------------------------- */
void ComputeGrid::assign_coords_array()
{
double x[3];
for (int iarray = 0; iarray < size_array_rows; iarray++) {
iarray2x(iarray,x);
array[iarray][0] = x[0];
array[iarray][1] = x[1];
array[iarray][2] = x[2];
}
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
gather global array from full grid gather global array from full grid
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
@ -181,7 +218,7 @@ void ComputeGrid::gather_global_array()
// inefficient, should exploit shared ix structure // inefficient, should exploit shared ix structure
iarray = igridfull2iarray(igrid); iarray = igridfull2iarray(igrid);
for (int icol = 0; icol < size_array_cols; icol++) for (int icol = size_array_cols_base; icol < size_array_cols; icol++)
array[iarray][icol] += gridfull[igrid][icol]; array[iarray][icol] += gridfull[igrid][icol];
} }
} }

5
src/compute_grid.h
View File

@ -33,7 +33,7 @@ class ComputeGrid : public Compute {
int nx, ny, nz; // grid dimensions int nx, ny, nz; // grid dimensions
int nxfull, nyfull, nzfull; // grid dimensions with ghost points int nxfull, nyfull, nzfull; // grid dimensions with ghost points
int nxyfull; // nx_full*ny_full int nxyfull; // nx_full*ny_full
int ngridfull; // number of full grid points int ngridfull; // number of full grid points
double **gridfull; // full grid points double **gridfull; // full grid points
int mx, my, mz; // cutmax stencil dimensions int mx, my, mz; // cutmax stencil dimensions
int triclinic; // triclinic flag int triclinic; // triclinic flag
@ -43,10 +43,13 @@ class ComputeGrid : public Compute {
double x0full, y0full, z0full; // origin of full grid double x0full, y0full, z0full; // origin of full grid
int nargbase; // number of base class args int nargbase; // number of base class args
double cutmax; // largest cutoff distance double cutmax; // largest cutoff distance
int size_array_cols_base; // number of columns used for coords, etc.
virtual void allocate(); virtual void allocate();
void igridfull2x(int, double*); // convert full grid point to coord void igridfull2x(int, double*); // convert full grid point to coord
void iarray2x(int, double*); // convert array point to coord
void gather_global_array(); // gather global array from full grid void gather_global_array(); // gather global array from full grid
void copy_local_grid(); // copy local grid to global array void copy_local_grid(); // copy local grid to global array
void assign_coords_array(); // assign coords to global array
int igridfull2iarray(int); // convert full grid index to compute array index int igridfull2iarray(int); // convert full grid index to compute array index
int iarray2igridfull(int); // convert compute array index to full grid index int iarray2igridfull(int); // convert compute array index to full grid index