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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| import os | ||
| from pyxtal.db import database | ||
| from pyxtal.optimize.common import optimizer | ||
| from pyxtal.representation import representation | ||
|
|
||
| db = database("pyxtal/database/test.db") | ||
| row = db.get_row("ACSALA") | ||
| xtal1 = db.get_pyxtal("ACSALA") | ||
| smile = row.mol_smi | ||
|
|
||
| # Prepare prm | ||
| w_dir = "tmp" | ||
| os.makedirs(w_dir, exist_ok=True) | ||
|
|
||
| c_info = row.data["charmm_info"] | ||
| with open(w_dir + "/pyxtal.prm", "w") as prm: | ||
| prm.write(c_info["prm"]) | ||
| with open(w_dir + "/pyxtal.rtf", "w") as rtf: | ||
| rtf.write(c_info["rtf"]) | ||
|
|
||
| res = optimizer(xtal1, c_info, w_dir, skip_ani=True) | ||
| xtal1, eng = res["xtal"], res["energy"] | ||
| rep0 = xtal1.get_1D_representation() | ||
| print(rep0.to_string(eng)) | ||
|
|
||
| data=""" | ||
| 82 7.48 14.98 8.83 89.3 1 0 0.63 0.99 0.72 119.2 -43.2 -162.6 -104.9 1.4 -162.2 0 # -20.229 | ||
| 83 11.93 8.09 10.32 114.1 1 0 0.69 0.24 0.16 177.8 6.9 -50.4 -78.0 10.7 -179.0 0 # -21.083 | ||
| 82 15.73 7.54 7.11 91.0 1 0 0.36 0.19 0.23 49.9 27.0 -60.6 72.5 15.9 4.6 0 # -21.806 | ||
| 83 10.09 8.11 10.50 95.4 1 0 0.22 0.02 0.28 14.1 57.4 -97.6 68.8 3.7 -154.6 0 # -21.054 | ||
| 81 10.09 9.68 8.95 101.9 1 0 0.22 0.47 0.24 -66.8 58.1 45.1 -119.2 -16.7 -158.4 0 # -21.673 | ||
| 83 11.43 8.72 17.41 93.4 1 0 0.46 0.62 0.89 162.8 19.1 -30.6 -97.3 -10.0 173.3 0 # -20.371 | ||
| 83 7.23 12.62 24.83 92.1 1 0 0.16 0.28 0.90 -17.9 0.9 -102.1 -139.0 10.5 4.1 0 # -20.165 | ||
| 82 8.55 8.08 12.75 99.7 1 0 0.93 0.12 0.19 65.8 -20.1 -64.9 146.5 1.7 2.8 0 # -21.595 | ||
| 82 21.78 6.34 6.37 89.1 1 0 0.87 0.07 0.17 -15.1 14.3 53.3 87.8 6.7 23.9 0 # -21.703 | ||
| 81 10.64 24.45 6.54 105.8 1 0 0.75 0.99 1.00 26.7 2.6 58.9 -95.8 -8.9 -22.0 0 # -18.588 | ||
| 81 17.91 11.03 8.54 77.7 1 0 0.60 0.19 0.65 -154.8 -0.5 153.4 -68.2 -11.6 160.8 0 # -19.887 | ||
| 83 17.33 7.11 6.94 89.5 1 0 0.59 0.11 0.25 44.6 -18.0 -12.7 85.2 5.5 6.2 0 # -22.601 | ||
| 83 7.38 9.45 12.02 85.0 1 0 0.75 0.29 0.73 -33.7 2.8 65.4 -139.0 1.4 -3.0 0 # -22.578 | ||
| 81 7.62 7.19 16.62 78.4 1 0 0.72 0.14 0.36 -24.3 23.4 -100.0 79.2 5.4 -146.2 0 # -21.578 | ||
| 81 20.29 6.30 11.11 82.9 1 0 0.36 0.58 0.52 43.6 -28.4 -151.6 84.9 6.1 -171.1 0 # -21.478 | ||
| 83 13.60 10.68 5.91 89.5 1 0 0.61 0.79 0.01 -92.9 -8.4 -112.3 67.2 10.3 20.1 0 # -22.065 | ||
| 83 12.90 7.43 9.82 68.4 1 0 0.46 0.40 0.31 -154.9 4.7 -127.4 -79.0 4.8 -178.9 0 # -21.339 | ||
| 82 14.16 7.19 8.59 89.4 1 0 0.99 0.40 0.76 144.0 23.3 5.4 -131.3 1.8 -131.6 0 # -21.648 | ||
| 82 10.69 8.58 9.58 92.7 1 0 0.40 0.91 0.70 -137.3 -14.1 102.0 -56.2 2.9 -26.2 0 # -21.350 | ||
| 82 7.14 9.93 12.66 99.4 1 0 0.57 0.71 0.37 174.2 29.5 -82.0 -68.2 -3.7 -25.4 0 # -21.642 | ||
| 82 12.81 9.29 7.47 106.4 1 0 0.51 0.76 0.08 -72.1 -53.4 -58.6 94.1 -5.0 -152.4 0 # -21.591 | ||
| 83 15.45 5.42 10.42 74.5 1 0 0.58 0.88 0.25 114.9 -40.3 139.5 -131.8 14.4 -5.8 0 # -21.126 | ||
| 83 7.17 8.80 14.96 76.6 1 0 0.70 0.52 0.78 98.0 7.9 -97.4 -140.3 1.0 6.0 0 # -20.570 | ||
| 81 8.51 9.72 10.95 80.4 1 0 0.15 0.03 0.66 -105.6 48.1 -165.5 79.0 9.8 -164.2 0 # -20.798 | ||
| 81 10.80 6.21 13.22 105.8 1 0 0.26 0.50 0.98 -7.0 16.5 -121.9 76.4 10.7 23.2 0 # -21.623 | ||
| 83 9.75 17.07 5.49 79.8 1 0 0.79 0.40 0.34 -89.9 -31.1 131.5 124.1 -3.7 -164.8 0 # -21.549 | ||
| 83 8.79 14.19 7.55 114.4 1 0 0.19 0.90 0.11 -14.5 -35.7 -41.2 -103.5 -1.9 -163.5 0 # -21.481 | ||
| 82 9.50 11.03 8.50 76.8 1 0 0.92 0.26 0.44 -147.4 24.1 174.0 66.9 -5.9 -155.0 0 # -21.454 | ||
| 82 18.63 11.08 4.05 92.5 1 0 0.14 0.68 0.50 -112.3 -30.7 -179.4 -140.1 6.3 7.5 0 # -22.506 | ||
| 81 7.46 17.37 7.12 105.2 1 0 0.54 0.89 0.50 8.2 56.6 151.3 143.0 1.9 143.0 0 # -21.609 | ||
| 82 9.60 9.16 9.92 102.9 1 0 0.46 0.76 0.31 -65.0 -7.7 51.9 -86.0 8.9 -174.2 0 # -21.469 | ||
| 81 8.07 15.16 7.85 116.7 1 0 0.15 0.56 0.78 124.0 -7.5 -161.3 107.1 -4.5 164.5 0 # -20.655 | ||
| 82 9.51 8.48 11.02 100.8 1 0 0.60 0.11 0.39 69.4 -45.4 130.6 116.5 -5.0 -28.0 0 # -21.952 | ||
| 83 8.20 12.36 8.66 90.9 1 0 0.30 0.54 0.18 -73.6 -44.1 -81.7 -73.5 -4.2 -4.6 0 # -21.365 | ||
| 82 9.39 9.43 10.22 65.5 1 0 0.82 0.06 0.41 -15.5 37.7 81.7 107.0 -6.7 166.0 0 # -21.372 | ||
| 82 7.08 17.03 8.16 64.1 1 0 0.79 0.57 0.87 35.5 4.5 80.6 -73.7 -3.2 -5.8 0 # -21.481 | ||
| 81 6.25 8.84 15.75 86.1 1 0 0.26 0.01 0.84 23.5 5.3 83.1 72.6 7.5 -161.0 0 # -21.397 | ||
| 82 5.72 10.11 14.41 100.0 1 0 0.91 0.65 0.34 -80.8 44.0 -52.6 -62.4 -2.2 -40.9 0 # -21.069 | ||
| 81 17.87 9.41 6.88 97.2 1 0 0.82 0.67 0.38 -96.0 -4.2 -164.9 148.0 4.4 -14.3 0 # -19.779 | ||
| 81 7.29 14.97 8.03 101.2 1 0 0.46 0.88 0.98 -53.7 -66.0 138.7 137.1 0.8 -15.4 0 # -22.045 | ||
| 82 6.71 19.21 6.60 76.0 1 0 0.05 0.59 0.73 -39.1 -1.1 -170.6 -122.2 -1.5 27.4 0 # -21.238 | ||
| """ | ||
|
|
||
| # Split the data into lines | ||
| lines = data.strip().splitlines() | ||
|
|
||
| for line in lines: | ||
| strs = line.split("#")[0]; print('Ref', line) | ||
| rep = representation.from_string(strs, [smile]) | ||
| xtal = rep.to_pyxtal() | ||
| res = optimizer(xtal, c_info, w_dir, skip_ani=True) | ||
| xtal2, eng = res["xtal"], res["energy"] | ||
| rep0 = xtal2.get_1D_representation() | ||
| print(rep0.to_string(eng)) |