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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| #! FIELDS time r1 r2 r3 r4 r5 r6 | ||
| 0.000000 12.624019 0.000000 12.624019 12.624019 12.624019 0.000000 | ||
| 1.000000 12.624019 8.981462 12.624019 12.624019 12.624019 0.000000 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| include ../../scripts/test.make |
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| @@ -0,0 +1,3 @@ | ||
| type=driver | ||
| # we use A so as to make the comparison with pdb easier | ||
| arg="--ixyz traj.xyz --length-units A" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| import random | ||
| def print_pdb(coords,file): | ||
| i=0 | ||
| for coord in coords: | ||
| i+=1 | ||
| print("{:6s}{:5d} {:^4s}{:1s}{:3s} {:1s}{:4d}{:1s} {:8.3f}{:8.3f}{:8.3f}{:6.2f}{:6.2f} {:>2s}{:2s}".format( | ||
| "ATOM",i,"type","","","",1,"",coord[0],coord[1],coord[2],1.0,1.0,"",""),file=f) | ||
|
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| def print_xyz(box,coords,file): | ||
| print(len(coords),file=f) | ||
| print(box[0],box[1],box[2],file=f) | ||
| for coord in coords: | ||
| print("type ",coord[0],coord[1],coord[2],file=f) | ||
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| coords=[] | ||
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| box=[11,11,11] | ||
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| for i in range(-20,21): | ||
| if i%2==0: j=i | ||
| else: j=-i | ||
| coords.append([j,0.0,0.0]) | ||
| for i in range(-20,21): | ||
| if i%2==0: j=i | ||
| else: j=-i | ||
| coords.append([0.0,j,0.0]) | ||
| for i in range(-20,21): | ||
| if i%2==0: j=i | ||
| else: j=-i | ||
| coords.append([0.0,0.0,j]) | ||
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| with open("ref.pdb","w") as f: | ||
| print_pdb(coords,f) | ||
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| with open("traj.xyz","w") as f: | ||
| print_xyz(box,coords,f) | ||
| for i in range(len(coords)): | ||
| coords[i][0]+=box[0]*(i%3) | ||
| print_xyz(box,coords,f) | ||
|
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||
|
|
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,24 @@ | ||
| UNITS LENGTH=A | ||
|
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| # this will incorrectly reconstruct PBC, and return !=0 | ||
| r1: RMSD REFERENCE=ref.pdb | ||
|
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| # this is zero in first frame, but non zero in subsequent (shifted) frames | ||
| r2: RMSD REFERENCE=ref.pdb NOPBC | ||
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| WHOLEMOLECULES ENTITY0=1-123 | ||
| DUMPATOMS ATOMS=1-123 FILE=wrong.xyz PRECISION=3 | ||
| # these are always non zero, as PBC are wrong here | ||
| r3: RMSD REFERENCE=ref.pdb | ||
| r4: RMSD REFERENCE=ref.pdb NOPBC | ||
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| MOLINFO STRUCTURE=ref.pdb WHOLE | ||
| WHOLEMOLECULES ENTITY0=1-123 EMST | ||
| DUMPATOMS ATOMS=1-123 FILE=right.xyz PRECISION=3 | ||
| # this is non zero (incorrectly reconstructed) | ||
| r5: RMSD REFERENCE=ref.pdb | ||
| # finally, this is always zero | ||
| r6: RMSD REFERENCE=ref.pdb NOPBC | ||
|
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| PRINT ARG=(r.) FILE=COLVAR |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,123 @@ | ||
| ATOM 1 type 1 -20.000 0.000 0.000 1.00 1.00 | ||
| ATOM 2 type 1 19.000 0.000 0.000 1.00 1.00 | ||
| ATOM 3 type 1 -18.000 0.000 0.000 1.00 1.00 | ||
| ATOM 4 type 1 17.000 0.000 0.000 1.00 1.00 | ||
| ATOM 5 type 1 -16.000 0.000 0.000 1.00 1.00 | ||
| ATOM 6 type 1 15.000 0.000 0.000 1.00 1.00 | ||
| ATOM 7 type 1 -14.000 0.000 0.000 1.00 1.00 | ||
| ATOM 8 type 1 13.000 0.000 0.000 1.00 1.00 | ||
| ATOM 9 type 1 -12.000 0.000 0.000 1.00 1.00 | ||
| ATOM 10 type 1 11.000 0.000 0.000 1.00 1.00 | ||
| ATOM 11 type 1 -10.000 0.000 0.000 1.00 1.00 | ||
| ATOM 12 type 1 9.000 0.000 0.000 1.00 1.00 | ||
| ATOM 13 type 1 -8.000 0.000 0.000 1.00 1.00 | ||
| ATOM 14 type 1 7.000 0.000 0.000 1.00 1.00 | ||
| ATOM 15 type 1 -6.000 0.000 0.000 1.00 1.00 | ||
| ATOM 16 type 1 5.000 0.000 0.000 1.00 1.00 | ||
| ATOM 17 type 1 -4.000 0.000 0.000 1.00 1.00 | ||
| ATOM 18 type 1 3.000 0.000 0.000 1.00 1.00 | ||
| ATOM 19 type 1 -2.000 0.000 0.000 1.00 1.00 | ||
| ATOM 20 type 1 1.000 0.000 0.000 1.00 1.00 | ||
| ATOM 21 type 1 0.000 0.000 0.000 1.00 1.00 | ||
| ATOM 22 type 1 -1.000 0.000 0.000 1.00 1.00 | ||
| ATOM 23 type 1 2.000 0.000 0.000 1.00 1.00 | ||
| ATOM 24 type 1 -3.000 0.000 0.000 1.00 1.00 | ||
| ATOM 25 type 1 4.000 0.000 0.000 1.00 1.00 | ||
| ATOM 26 type 1 -5.000 0.000 0.000 1.00 1.00 | ||
| ATOM 27 type 1 6.000 0.000 0.000 1.00 1.00 | ||
| ATOM 28 type 1 -7.000 0.000 0.000 1.00 1.00 | ||
| ATOM 29 type 1 8.000 0.000 0.000 1.00 1.00 | ||
| ATOM 30 type 1 -9.000 0.000 0.000 1.00 1.00 | ||
| ATOM 31 type 1 10.000 0.000 0.000 1.00 1.00 | ||
| ATOM 32 type 1 -11.000 0.000 0.000 1.00 1.00 | ||
| ATOM 33 type 1 12.000 0.000 0.000 1.00 1.00 | ||
| ATOM 34 type 1 -13.000 0.000 0.000 1.00 1.00 | ||
| ATOM 35 type 1 14.000 0.000 0.000 1.00 1.00 | ||
| ATOM 36 type 1 -15.000 0.000 0.000 1.00 1.00 | ||
| ATOM 37 type 1 16.000 0.000 0.000 1.00 1.00 | ||
| ATOM 38 type 1 -17.000 0.000 0.000 1.00 1.00 | ||
| ATOM 39 type 1 18.000 0.000 0.000 1.00 1.00 | ||
| ATOM 40 type 1 -19.000 0.000 0.000 1.00 1.00 | ||
| ATOM 41 type 1 20.000 0.000 0.000 1.00 1.00 | ||
| ATOM 42 type 1 0.000 -20.000 0.000 1.00 1.00 | ||
| ATOM 43 type 1 0.000 19.000 0.000 1.00 1.00 | ||
| ATOM 44 type 1 0.000 -18.000 0.000 1.00 1.00 | ||
| ATOM 45 type 1 0.000 17.000 0.000 1.00 1.00 | ||
| ATOM 46 type 1 0.000 -16.000 0.000 1.00 1.00 | ||
| ATOM 47 type 1 0.000 15.000 0.000 1.00 1.00 | ||
| ATOM 48 type 1 0.000 -14.000 0.000 1.00 1.00 | ||
| ATOM 49 type 1 0.000 13.000 0.000 1.00 1.00 | ||
| ATOM 50 type 1 0.000 -12.000 0.000 1.00 1.00 | ||
| ATOM 51 type 1 0.000 11.000 0.000 1.00 1.00 | ||
| ATOM 52 type 1 0.000 -10.000 0.000 1.00 1.00 | ||
| ATOM 53 type 1 0.000 9.000 0.000 1.00 1.00 | ||
| ATOM 54 type 1 0.000 -8.000 0.000 1.00 1.00 | ||
| ATOM 55 type 1 0.000 7.000 0.000 1.00 1.00 | ||
| ATOM 56 type 1 0.000 -6.000 0.000 1.00 1.00 | ||
| ATOM 57 type 1 0.000 5.000 0.000 1.00 1.00 | ||
| ATOM 58 type 1 0.000 -4.000 0.000 1.00 1.00 | ||
| ATOM 59 type 1 0.000 3.000 0.000 1.00 1.00 | ||
| ATOM 60 type 1 0.000 -2.000 0.000 1.00 1.00 | ||
| ATOM 61 type 1 0.000 1.000 0.000 1.00 1.00 | ||
| ATOM 62 type 1 0.000 0.000 0.000 1.00 1.00 | ||
| ATOM 63 type 1 0.000 -1.000 0.000 1.00 1.00 | ||
| ATOM 64 type 1 0.000 2.000 0.000 1.00 1.00 | ||
| ATOM 65 type 1 0.000 -3.000 0.000 1.00 1.00 | ||
| ATOM 66 type 1 0.000 4.000 0.000 1.00 1.00 | ||
| ATOM 67 type 1 0.000 -5.000 0.000 1.00 1.00 | ||
| ATOM 68 type 1 0.000 6.000 0.000 1.00 1.00 | ||
| ATOM 69 type 1 0.000 -7.000 0.000 1.00 1.00 | ||
| ATOM 70 type 1 0.000 8.000 0.000 1.00 1.00 | ||
| ATOM 71 type 1 0.000 -9.000 0.000 1.00 1.00 | ||
| ATOM 72 type 1 0.000 10.000 0.000 1.00 1.00 | ||
| ATOM 73 type 1 0.000 -11.000 0.000 1.00 1.00 | ||
| ATOM 74 type 1 0.000 12.000 0.000 1.00 1.00 | ||
| ATOM 75 type 1 0.000 -13.000 0.000 1.00 1.00 | ||
| ATOM 76 type 1 0.000 14.000 0.000 1.00 1.00 | ||
| ATOM 77 type 1 0.000 -15.000 0.000 1.00 1.00 | ||
| ATOM 78 type 1 0.000 16.000 0.000 1.00 1.00 | ||
| ATOM 79 type 1 0.000 -17.000 0.000 1.00 1.00 | ||
| ATOM 80 type 1 0.000 18.000 0.000 1.00 1.00 | ||
| ATOM 81 type 1 0.000 -19.000 0.000 1.00 1.00 | ||
| ATOM 82 type 1 0.000 20.000 0.000 1.00 1.00 | ||
| ATOM 83 type 1 0.000 0.000 -20.000 1.00 1.00 | ||
| ATOM 84 type 1 0.000 0.000 19.000 1.00 1.00 | ||
| ATOM 85 type 1 0.000 0.000 -18.000 1.00 1.00 | ||
| ATOM 86 type 1 0.000 0.000 17.000 1.00 1.00 | ||
| ATOM 87 type 1 0.000 0.000 -16.000 1.00 1.00 | ||
| ATOM 88 type 1 0.000 0.000 15.000 1.00 1.00 | ||
| ATOM 89 type 1 0.000 0.000 -14.000 1.00 1.00 | ||
| ATOM 90 type 1 0.000 0.000 13.000 1.00 1.00 | ||
| ATOM 91 type 1 0.000 0.000 -12.000 1.00 1.00 | ||
| ATOM 92 type 1 0.000 0.000 11.000 1.00 1.00 | ||
| ATOM 93 type 1 0.000 0.000 -10.000 1.00 1.00 | ||
| ATOM 94 type 1 0.000 0.000 9.000 1.00 1.00 | ||
| ATOM 95 type 1 0.000 0.000 -8.000 1.00 1.00 | ||
| ATOM 96 type 1 0.000 0.000 7.000 1.00 1.00 | ||
| ATOM 97 type 1 0.000 0.000 -6.000 1.00 1.00 | ||
| ATOM 98 type 1 0.000 0.000 5.000 1.00 1.00 | ||
| ATOM 99 type 1 0.000 0.000 -4.000 1.00 1.00 | ||
| ATOM 100 type 1 0.000 0.000 3.000 1.00 1.00 | ||
| ATOM 101 type 1 0.000 0.000 -2.000 1.00 1.00 | ||
| ATOM 102 type 1 0.000 0.000 1.000 1.00 1.00 | ||
| ATOM 103 type 1 0.000 0.000 0.000 1.00 1.00 | ||
| ATOM 104 type 1 0.000 0.000 -1.000 1.00 1.00 | ||
| ATOM 105 type 1 0.000 0.000 2.000 1.00 1.00 | ||
| ATOM 106 type 1 0.000 0.000 -3.000 1.00 1.00 | ||
| ATOM 107 type 1 0.000 0.000 4.000 1.00 1.00 | ||
| ATOM 108 type 1 0.000 0.000 -5.000 1.00 1.00 | ||
| ATOM 109 type 1 0.000 0.000 6.000 1.00 1.00 | ||
| ATOM 110 type 1 0.000 0.000 -7.000 1.00 1.00 | ||
| ATOM 111 type 1 0.000 0.000 8.000 1.00 1.00 | ||
| ATOM 112 type 1 0.000 0.000 -9.000 1.00 1.00 | ||
| ATOM 113 type 1 0.000 0.000 10.000 1.00 1.00 | ||
| ATOM 114 type 1 0.000 0.000 -11.000 1.00 1.00 | ||
| ATOM 115 type 1 0.000 0.000 12.000 1.00 1.00 | ||
| ATOM 116 type 1 0.000 0.000 -13.000 1.00 1.00 | ||
| ATOM 117 type 1 0.000 0.000 14.000 1.00 1.00 | ||
| ATOM 118 type 1 0.000 0.000 -15.000 1.00 1.00 | ||
| ATOM 119 type 1 0.000 0.000 16.000 1.00 1.00 | ||
| ATOM 120 type 1 0.000 0.000 -17.000 1.00 1.00 | ||
| ATOM 121 type 1 0.000 0.000 18.000 1.00 1.00 | ||
| ATOM 122 type 1 0.000 0.000 -19.000 1.00 1.00 | ||
| ATOM 123 type 1 0.000 0.000 20.000 1.00 1.00 |
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Found broken examples in automatic/a-masterclass-22-09.txt
Found broken examples in automatic/a-masterclass-22-11.txt
Found broken examples in automatic/a-masterclass-22-12.txt
Found broken examples in automatic/performance-optimization.txt
Found broken examples in automatic/a-trieste-6.txt
Found broken examples in automatic/munster.txt
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in MiscelaneousPP.md