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!! |
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!! Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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!! |
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!! The University of Notre Dame grants you ("Licensee") a |
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!! non-exclusive, royalty free, license to use, modify and |
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!! redistribute this software in source and binary code form, provided |
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!! that the following conditions are met: |
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!! |
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!! 1. Acknowledgement of the program authors must be made in any |
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!! publication of scientific results based in part on use of the |
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!! program. An acceptable form of acknowledgement is citation of |
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!! the article in which the program was described (Matthew |
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!! A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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!! J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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!! Parallel Simulation Engine for Molecular Dynamics," |
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!! J. Comput. Chem. 26, pp. 252-271 (2005)) |
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!! |
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!! 2. Redistributions of source code must retain the above copyright |
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!! notice, this list of conditions and the following disclaimer. |
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!! |
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!! 3. Redistributions in binary form must reproduce the above copyright |
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!! notice, this list of conditions and the following disclaimer in the |
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!! documentation and/or other materials provided with the |
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!! distribution. |
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!! |
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!! This software is provided "AS IS," without a warranty of any |
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!! kind. All express or implied conditions, representations and |
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!! warranties, including any implied warranty of merchantability, |
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!! fitness for a particular purpose or non-infringement, are hereby |
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!! excluded. The University of Notre Dame and its licensors shall not |
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!! be liable for any damages suffered by licensee as a result of |
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!! using, modifying or distributing the software or its |
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!! derivatives. In no event will the University of Notre Dame or its |
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!! licensors be liable for any lost revenue, profit or data, or for |
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!! direct, indirect, special, consequential, incidental or punitive |
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!! damages, however caused and regardless of the theory of liability, |
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!! arising out of the use of or inability to use software, even if the |
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!! University of Notre Dame has been advised of the possibility of |
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!! such damages. |
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!! |
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|
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|
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module shapes |
44 |
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|
45 |
|
use force_globals |
390 |
|
real (kind=dp), intent(inout) :: rij, r2 |
391 |
|
real (kind=dp), dimension(3), intent(in) :: d |
392 |
|
real (kind=dp), dimension(3), intent(inout) :: fpair |
393 |
< |
real (kind=dp) :: pot, vpair, sw |
393 |
> |
real (kind=dp) :: pot, vpair, sw, dswdr |
394 |
|
real (kind=dp), dimension(9,nLocal) :: A |
395 |
|
real (kind=dp), dimension(3,nLocal) :: f |
396 |
|
real (kind=dp), dimension(3,nLocal) :: t |
401 |
|
integer :: l, m, lm, id1, id2, localError, function_type |
402 |
|
real (kind=dp) :: sigma_i, s_i, eps_i, sigma_j, s_j, eps_j |
403 |
|
real (kind=dp) :: coeff |
404 |
+ |
real (kind=dp) :: pot_temp |
405 |
|
|
406 |
|
real (kind=dp) :: dsigmaidx, dsigmaidy, dsigmaidz |
407 |
|
real (kind=dp) :: dsigmaidux, dsigmaiduy, dsigmaiduz |
420 |
|
|
421 |
|
real (kind=dp) :: xi, yi, zi, xj, yj, zj, xi2, yi2, zi2, xj2, yj2, zj2 |
422 |
|
|
423 |
+ |
real (kind=dp) :: sti2, stj2 |
424 |
+ |
|
425 |
|
real (kind=dp) :: proji, proji3, projj, projj3 |
426 |
|
real (kind=dp) :: cti, ctj, cpi, cpj, spi, spj |
427 |
|
real (kind=dp) :: Phunc, sigma, s, eps, rtdenom, rt |
562 |
|
|
563 |
|
xi2 = xi*xi |
564 |
|
yi2 = yi*yi |
565 |
< |
zi2 = zi*zi |
521 |
< |
|
522 |
< |
proji = sqrt(xi2 + yi2) |
523 |
< |
proji3 = proji*proji*proji |
524 |
< |
|
565 |
> |
zi2 = zi*zi |
566 |
|
cti = zi / rij |
567 |
|
|
568 |
+ |
if (cti .gt. 1.0_dp) cti = 1.0_dp |
569 |
+ |
if (cti .lt. -1.0_dp) cti = -1.0_dp |
570 |
+ |
|
571 |
|
dctidx = - zi * xi / r3 |
572 |
|
dctidy = - zi * yi / r3 |
573 |
|
dctidz = 1.0d0 / rij - zi2 / r3 |
574 |
< |
dctidux = yi / rij |
575 |
< |
dctiduy = -xi / rij |
576 |
< |
dctiduz = 0.0d0 |
574 |
> |
dctidux = - (zi * xi2) / r3 |
575 |
> |
dctiduy = - (zi * yi2) / r3 |
576 |
> |
dctiduz = zi / rij - (zi2 * zi) / r3 |
577 |
> |
|
578 |
> |
! this is an attempt to try to truncate the singularity when |
579 |
> |
! sin(theta) is near 0.0: |
580 |
> |
|
581 |
> |
sti2 = 1.0_dp - cti*cti |
582 |
> |
if (dabs(sti2) .lt. 1.0d-12) then |
583 |
> |
proji = sqrt(rij * 1.0d-12) |
584 |
> |
dcpidx = 1.0d0 / proji |
585 |
> |
dcpidy = 0.0d0 |
586 |
> |
dcpidux = xi / proji |
587 |
> |
dcpiduy = 0.0d0 |
588 |
> |
dspidx = 0.0d0 |
589 |
> |
dspidy = 1.0d0 / proji |
590 |
> |
dspidux = 0.0d0 |
591 |
> |
dspiduy = yi / proji |
592 |
> |
else |
593 |
> |
proji = sqrt(xi2 + yi2) |
594 |
> |
proji3 = proji*proji*proji |
595 |
> |
dcpidx = 1.0d0 / proji - xi2 / proji3 |
596 |
> |
dcpidy = - xi * yi / proji3 |
597 |
> |
dcpidux = xi / proji - (xi2 * xi) / proji3 |
598 |
> |
dcpiduy = - (xi * yi2) / proji3 |
599 |
> |
dspidx = - xi * yi / proji3 |
600 |
> |
dspidy = 1.0d0 / proji - yi2 / proji3 |
601 |
> |
dspidux = - (yi * xi2) / proji3 |
602 |
> |
dspiduy = yi / proji - (yi2 * yi) / proji3 |
603 |
> |
endif |
604 |
|
|
605 |
|
cpi = xi / proji |
535 |
– |
dcpidx = 1.0d0 / proji - xi2 / proji3 |
536 |
– |
dcpidy = - xi * yi / proji3 |
606 |
|
dcpidz = 0.0d0 |
607 |
< |
dcpidux = xi * yi * zi / proji3 |
539 |
< |
dcpiduy = -zi * (1.0d0 / proji - xi2 / proji3) |
540 |
< |
dcpiduz = -yi * (1.0d0 / proji - xi2 / proji3) - (xi2 * yi / proji3) |
607 |
> |
dcpiduz = 0.0d0 |
608 |
|
|
609 |
|
spi = yi / proji |
543 |
– |
dspidx = - xi * yi / proji3 |
544 |
– |
dspidy = 1.0d0 / proji - yi2 / proji3 |
610 |
|
dspidz = 0.0d0 |
611 |
< |
dspidux = -zi * (1.0d0 / proji - yi2 / proji3) |
547 |
< |
dspiduy = xi * yi * zi / proji3 |
548 |
< |
dspiduz = xi * (1.0d0 / proji - yi2 / proji3) + (xi * yi2 / proji3) |
611 |
> |
dspiduz = 0.0d0 |
612 |
|
|
613 |
|
call Associated_Legendre(cti, ShapeMap%Shapes(st1)%bigM, & |
614 |
|
ShapeMap%Shapes(st1)%bigL, LMAX, & |
816 |
|
xj2 = xj*xj |
817 |
|
yj2 = yj*yj |
818 |
|
zj2 = zj*zj |
756 |
– |
|
757 |
– |
projj = sqrt(xj2 + yj2) |
758 |
– |
projj3 = projj*projj*projj |
759 |
– |
|
819 |
|
ctj = zj / rij |
820 |
+ |
|
821 |
+ |
if (ctj .gt. 1.0_dp) ctj = 1.0_dp |
822 |
+ |
if (ctj .lt. -1.0_dp) ctj = -1.0_dp |
823 |
+ |
|
824 |
|
dctjdx = - zj * xj / r3 |
825 |
|
dctjdy = - zj * yj / r3 |
826 |
|
dctjdz = 1.0d0 / rij - zj2 / r3 |
827 |
< |
dctjdux = yj / rij |
828 |
< |
dctjduy = -xj / rij |
829 |
< |
dctjduz = 0.0d0 |
827 |
> |
dctjdux = - (zi * xj2) / r3 |
828 |
> |
dctjduy = - (zj * yj2) / r3 |
829 |
> |
dctjduz = zj / rij - (zj2 * zj) / r3 |
830 |
|
|
831 |
< |
cpj = xj / projj |
832 |
< |
dcpjdx = 1.0d0 / projj - xj2 / projj3 |
833 |
< |
dcpjdy = - xj * yj / projj3 |
831 |
> |
! this is an attempt to try to truncate the singularity when |
832 |
> |
! sin(theta) is near 0.0: |
833 |
> |
|
834 |
> |
stj2 = 1.0_dp - ctj*ctj |
835 |
> |
if (dabs(stj2) .lt. 1.0d-12) then |
836 |
> |
projj = sqrt(rij * 1.0d-12) |
837 |
> |
dcpjdx = 1.0d0 / projj |
838 |
> |
dcpjdy = 0.0d0 |
839 |
> |
dcpjdux = xj / projj |
840 |
> |
dcpjduy = 0.0d0 |
841 |
> |
dspjdx = 0.0d0 |
842 |
> |
dspjdy = 1.0d0 / projj |
843 |
> |
dspjdux = 0.0d0 |
844 |
> |
dspjduy = yj / projj |
845 |
> |
else |
846 |
> |
projj = sqrt(xj2 + yj2) |
847 |
> |
projj3 = projj*projj*projj |
848 |
> |
dcpjdx = 1.0d0 / projj - xj2 / projj3 |
849 |
> |
dcpjdy = - xj * yj / projj3 |
850 |
> |
dcpjdux = xj / projj - (xj2 * xj) / projj3 |
851 |
> |
dcpjduy = - (xj * yj2) / projj3 |
852 |
> |
dspjdx = - xj * yj / projj3 |
853 |
> |
dspjdy = 1.0d0 / projj - yj2 / projj3 |
854 |
> |
dspjdux = - (yj * xj2) / projj3 |
855 |
> |
dspjduy = yj / projj - (yj2 * yj) / projj3 |
856 |
> |
endif |
857 |
> |
|
858 |
> |
cpj = xj / projj |
859 |
|
dcpjdz = 0.0d0 |
860 |
< |
dcpjdux = xj * yj * zj / projj3 |
773 |
< |
dcpjduy = -zj * (1.0d0 / projj - xj2 / projj3) |
774 |
< |
dcpjduz = -yj * (1.0d0 / projj - xj2 / projj3) - (xj2 * yj / projj3) |
860 |
> |
dcpjduz = 0.0d0 |
861 |
|
|
862 |
|
spj = yj / projj |
777 |
– |
dspjdx = - xj * yj / projj3 |
778 |
– |
dspjdy = 1.0d0 / projj - yj2 / projj3 |
863 |
|
dspjdz = 0.0d0 |
864 |
< |
dspjdux = -zj * (1.0d0 / projj - yj2 / projj3) |
865 |
< |
dspjduy = xj * yj * zj / projj3 |
866 |
< |
dspjduz = xj * (1.0d0 / projj - yi2 / projj3) + (xj * yj2 / projj3) |
867 |
< |
|
864 |
> |
dspjduz = 0.0d0 |
865 |
> |
|
866 |
> |
|
867 |
> |
write(*,*) 'dcpdu = ' ,dcpidux, dcpiduy, dcpiduz |
868 |
> |
write(*,*) 'dcpdu = ' ,dcpjdux, dcpjduy, dcpjduz |
869 |
|
call Associated_Legendre(ctj, ShapeMap%Shapes(st2)%bigM, & |
870 |
|
ShapeMap%Shapes(st2)%bigL, LMAX, & |
871 |
|
plm_j, dlm_j) |
1005 |
|
dPhuncdUz = coeff*(spj * dum_j(m-1)*dcpjduz + dspjduz *um_j(m-1)) |
1006 |
|
endif |
1007 |
|
|
1008 |
+ |
write(*,*) 'l,m = ', l, m, coeff, dPhuncdUx, dPhuncdUy, dPhuncdUz |
1009 |
+ |
|
1010 |
|
eps_j = eps_j + plm_j(m,l)*Phunc |
1011 |
|
|
1012 |
|
depsjdx = depsjdx + plm_j(m,l)*dPhuncdX + & |
1077 |
|
depsduyj = eps_i * depsjduy / (2.0d0 * eps) |
1078 |
|
depsduzj = eps_i * depsjduz / (2.0d0 * eps) |
1079 |
|
|
1080 |
+ |
!!$ write(*,*) 'depsidu = ', depsidux, depsiduy, depsiduz |
1081 |
+ |
!!$ write(*,*) 'depsjdu = ', depsjdux, depsjduy, depsjduz |
1082 |
+ |
!!$ |
1083 |
+ |
!!$ write(*,*) 'depsdui = ', depsduxi, depsduyi, depsduzi |
1084 |
+ |
!!$ write(*,*) 'depsduj = ', depsduxj, depsduyj, depsduzj |
1085 |
+ |
!!$ |
1086 |
+ |
!!$ write(*,*) 's, sig, eps = ', s, sigma, eps |
1087 |
+ |
|
1088 |
|
rtdenom = rij-sigma+s |
1089 |
|
rt = s / rtdenom |
1090 |
|
|
1109 |
|
rt12 = rt6*rt6 |
1110 |
|
rt126 = rt12 - rt6 |
1111 |
|
|
1112 |
+ |
pot_temp = 4.0d0 * eps * rt126 |
1113 |
+ |
|
1114 |
+ |
vpair = vpair + pot_temp |
1115 |
|
if (do_pot) then |
1116 |
|
#ifdef IS_MPI |
1117 |
< |
pot_row(atom1) = pot_row(atom1) + 2.0d0*eps*rt126*sw |
1118 |
< |
pot_col(atom2) = pot_col(atom2) + 2.0d0*eps*rt126*sw |
1117 |
> |
pot_row(atom1) = pot_row(atom1) + 0.5d0*pot_temp*sw |
1118 |
> |
pot_col(atom2) = pot_col(atom2) + 0.5d0*pot_temp*sw |
1119 |
|
#else |
1120 |
< |
pot = pot + 4.0d0*eps*rt126*sw |
1120 |
> |
pot = pot + pot_temp*sw |
1121 |
|
#endif |
1122 |
|
endif |
1123 |
+ |
|
1124 |
+ |
!!$ write(*,*) 'drtdu, depsdu = ', drtduxi, depsduxi |
1125 |
|
|
1126 |
|
dvdxi = 24.0d0*eps*(2.0d0*rt11 - rt5)*drtdxi + 4.0d0*depsdxi*rt126 |
1127 |
|
dvdyi = 24.0d0*eps*(2.0d0*rt11 - rt5)*drtdyi + 4.0d0*depsdyi*rt126 |
1140 |
|
! do the torques first since they are easy: |
1141 |
|
! remember that these are still in the body fixed axes |
1142 |
|
|
1043 |
– |
txi = dvduxi * sw |
1044 |
– |
tyi = dvduyi * sw |
1045 |
– |
tzi = dvduzi * sw |
1143 |
|
|
1144 |
< |
txj = dvduxj * sw |
1145 |
< |
tyj = dvduyj * sw |
1146 |
< |
tzj = dvduzj * sw |
1144 |
> |
!!$ write(*,*) 'sw = ', sw |
1145 |
> |
!!$ write(*,*) 'dvdu1 = ', dvduxi, dvduyi, dvduzi |
1146 |
> |
!!$ write(*,*) 'dvdu2 = ', dvduxj, dvduyj, dvduzj |
1147 |
> |
!!$ |
1148 |
> |
txi = (dvduzi - dvduyi) * sw |
1149 |
> |
tyi = (dvduxi - dvduzi) * sw |
1150 |
> |
tzi = (dvduyi - dvduxi) * sw |
1151 |
|
|
1152 |
+ |
txj = (dvduzj - dvduyj) * sw |
1153 |
+ |
tyj = (dvduxj - dvduzj) * sw |
1154 |
+ |
tzj = (dvduyj - dvduxj) * sw |
1155 |
+ |
|
1156 |
+ |
!!$ txi = -dvduxi * sw |
1157 |
+ |
!!$ tyi = -dvduyi * sw |
1158 |
+ |
!!$ tzi = -dvduzi * sw |
1159 |
+ |
!!$ |
1160 |
+ |
!!$ txj = dvduxj * sw |
1161 |
+ |
!!$ tyj = dvduyj * sw |
1162 |
+ |
!!$ tzj = dvduzj * sw |
1163 |
+ |
|
1164 |
+ |
write(*,*) 't1 = ', txi, tyi, tzi |
1165 |
+ |
write(*,*) 't2 = ', txj, tyj, tzj |
1166 |
+ |
|
1167 |
|
! go back to lab frame using transpose of rotation matrix: |
1168 |
|
|
1169 |
|
#ifdef IS_MPI |
1227 |
|
fyji = -fyjj |
1228 |
|
fzji = -fzjj |
1229 |
|
|
1230 |
< |
fxradial = fxii + fxji |
1231 |
< |
fyradial = fyii + fyji |
1232 |
< |
fzradial = fzii + fzji |
1230 |
> |
fxradial = 0.5_dp * (fxii + fxji) |
1231 |
> |
fyradial = 0.5_dp * (fyii + fyji) |
1232 |
> |
fzradial = 0.5_dp * (fzii + fzji) |
1233 |
|
|
1234 |
|
#ifdef IS_MPI |
1235 |
|
f_Row(1,atom1) = f_Row(1,atom1) + fxradial |
1264 |
|
fpair(3) = fpair(3) + fzradial |
1265 |
|
|
1266 |
|
endif |
1267 |
< |
|
1267 |
> |
|
1268 |
|
end subroutine do_shape_pair |
1269 |
|
|
1270 |
|
SUBROUTINE Associated_Legendre(x, l, m, lmax, plm, dlm) |
1430 |
|
end subroutine Orthogonal_Polynomial |
1431 |
|
|
1432 |
|
end module shapes |
1317 |
– |
|
1318 |
– |
subroutine makeShape(nContactFuncs, ContactFuncLValue, & |
1319 |
– |
ContactFuncMValue, ContactFunctionType, ContactFuncCoefficient, & |
1320 |
– |
nRangeFuncs, RangeFuncLValue, RangeFuncMValue, RangeFunctionType, & |
1321 |
– |
RangeFuncCoefficient, nStrengthFuncs, StrengthFuncLValue, & |
1322 |
– |
StrengthFuncMValue, StrengthFunctionType, StrengthFuncCoefficient, & |
1323 |
– |
myATID, status) |
1324 |
– |
|
1325 |
– |
use definitions |
1326 |
– |
use shapes, only: newShapeType |
1327 |
– |
|
1328 |
– |
integer :: nContactFuncs |
1329 |
– |
integer :: nRangeFuncs |
1330 |
– |
integer :: nStrengthFuncs |
1331 |
– |
integer :: status |
1332 |
– |
integer :: myATID |
1333 |
– |
|
1334 |
– |
integer, dimension(nContactFuncs) :: ContactFuncLValue |
1335 |
– |
integer, dimension(nContactFuncs) :: ContactFuncMValue |
1336 |
– |
integer, dimension(nContactFuncs) :: ContactFunctionType |
1337 |
– |
real(kind=dp), dimension(nContactFuncs) :: ContactFuncCoefficient |
1338 |
– |
integer, dimension(nRangeFuncs) :: RangeFuncLValue |
1339 |
– |
integer, dimension(nRangeFuncs) :: RangeFuncMValue |
1340 |
– |
integer, dimension(nRangeFuncs) :: RangeFunctionType |
1341 |
– |
real(kind=dp), dimension(nRangeFuncs) :: RangeFuncCoefficient |
1342 |
– |
integer, dimension(nStrengthFuncs) :: StrengthFuncLValue |
1343 |
– |
integer, dimension(nStrengthFuncs) :: StrengthFuncMValue |
1344 |
– |
integer, dimension(nStrengthFuncs) :: StrengthFunctionType |
1345 |
– |
real(kind=dp), dimension(nStrengthFuncs) :: StrengthFuncCoefficient |
1346 |
– |
|
1347 |
– |
call newShapeType(nContactFuncs, ContactFuncLValue, & |
1348 |
– |
ContactFuncMValue, ContactFunctionType, ContactFuncCoefficient, & |
1349 |
– |
nRangeFuncs, RangeFuncLValue, RangeFuncMValue, RangeFunctionType, & |
1350 |
– |
RangeFuncCoefficient, nStrengthFuncs, StrengthFuncLValue, & |
1351 |
– |
StrengthFuncMValue, StrengthFunctionType, StrengthFuncCoefficient, & |
1352 |
– |
myATID, status) |
1353 |
– |
|
1354 |
– |
return |
1355 |
– |
end subroutine makeShape |
1356 |
– |
|
1357 |
– |
subroutine completeShapeFF(status) |
1358 |
– |
|
1359 |
– |
use shapes, only: complete_Shape_FF |
1360 |
– |
|
1361 |
– |
integer, intent(out) :: status |
1362 |
– |
integer :: myStatus |
1363 |
– |
|
1364 |
– |
myStatus = 0 |
1365 |
– |
|
1366 |
– |
call complete_Shape_FF(myStatus) |
1367 |
– |
|
1368 |
– |
status = myStatus |
1369 |
– |
|
1370 |
– |
return |
1371 |
– |
end subroutine completeShapeFF |
1372 |
– |
|