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  1. #!/bin/bash
  2. file1='...
  3.      bfgs converged in   9 scf cycles and   8 bfgs steps
  4.      (criteria: energy <  6.0E-05 Ry, force <  1.0E-04 Ry/Bohr)
  5.  
  6.      End of BFGS Geometry Optimization
  7.  
  8.      Final energy   =   -1343.8825757257 Ry
  9. Begin final coordinates
  10.  
  11. ATOMIC_POSITIONS (angstrom)
  12. Fe            1.0730540812        3.7648438571        1.4484500000
  13. Fe            3.2976459188        0.6816561429        1.4484500000
  14. Fe            3.2584040812        2.9049061429        0.0000000000
  15. Fe            1.1122959188        1.5415938571        0.0000000000
  16. C             2.1853500000        2.2232500000        1.4484500000
  17. C             0.0000000000        0.0000000000       -0.0000000000
  18. End final coordinates
  19.  
  20.  
  21.  
  22.      Writing output data file ./out/100Co2C.save/
  23.  
  24.      init_run     :    486.03s CPU    493.55s WALL (       1 calls)
  25. ...'
  26. file2='...
  27. ATOMIC_SPECIES
  28. C      12.0107 C.pbesol-n-kjpaw_psl.1.0.0.UPF
  29. Co     58.933195 co_pbesol_v1.2.uspp.F.UPF
  30. Fe     55.845 Fe.pbesol-spn-kjpaw_psl.0.2.1.UPF
  31. ATOMIC_POSITIONS angstrom
  32. Co            1.0085465598        3.7287218832        1.4484500000
  33. Co            3.3775861828        0.7084455291        1.4484500000
  34. Fe            3.2243420022        2.9272726906        0.0000000000
  35. Co            1.1549449803        1.5394425244        0.0000000000
  36. C             2.1517221305        2.1838545768        1.4484500000
  37. C             0.0096081444        0.0285127960        0.0000000000
  38. K_POINTS crystal
  39. 388
  40.     0.0000000000     0.0000000000     0.0000000000 1
  41. ...'
  42. new_coords=$(sed -n '/Begin/,/End/{//b;p}' <<< "$file1")
  43. new_coords=$(echo "${new_coords//ATOMIC_POSITIONS (angstrom)}" | sed '/^$/d')
  44. old_coords=$(sed -n '/ATOMIC_POSITIONS/,/K_POINTS/{//b;p}' <<< "$file2")
  45.  
  46. quoteRe() { sed -e 's/[^^]/[&]/g; s/\^/\\^/g; $!a\'$'\n''\\n' <<<"$1" | tr -d '\n'; }
  47. quoteSubst() {
  48.   IFS= read -d '' -r < <(sed -e ':a' -e '$!{N;ba' -e '}' -e 's/[&/\]/\\&/g; s/\n/\\&/g' <<<"$1")
  49.   printf %s "${REPLY%$'\n'}"
  50. }
  51.  
  52. sed -e ':a' -e '$!{N;ba' -e '}' -e "s/$(quoteRe "$old_coords")/$(quoteSubst "$new_coords")/" <<< "$file2"
Success #stdin #stdout 0.02s 5560KB
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...
ATOMIC_SPECIES
C      12.0107 C.pbesol-n-kjpaw_psl.1.0.0.UPF
Co     58.933195 co_pbesol_v1.2.uspp.F.UPF
Fe     55.845 Fe.pbesol-spn-kjpaw_psl.0.2.1.UPF
ATOMIC_POSITIONS angstrom
Fe            1.0730540812        3.7648438571        1.4484500000
Fe            3.2976459188        0.6816561429        1.4484500000
Fe            3.2584040812        2.9049061429        0.0000000000
Fe            1.1122959188        1.5415938571        0.0000000000
C             2.1853500000        2.2232500000        1.4484500000
C             0.0000000000        0.0000000000       -0.0000000000
K_POINTS crystal
388
    0.0000000000     0.0000000000     0.0000000000 1
...
https://ideone.com/x3CXQQ
language:
Bash (bash 5.0.3)
created:
3 years ago
visibility:
secret

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