Changeset 54293d

Timestamp:

May 9, 2017, 12:18:30 PM (8 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

ForceAnnealing_goodresults, ForceAnnealing_tocheck

Children:

02cbf6

Parents:

d2a077a

Message:

tempcommit: Merge with ba7a54788

Location:

tests/Examples/ManyWaysTranslateAtom

Files:

• post/water_translated.xyz (modified) (1 diff)
• pre/water.xyz (modified) (1 diff)
• testsuite-examples-many-ways-translate-atom.at (modified) (1 diff)

tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz

@@ -1 +1 @@
 3
         Created by molecuilder on Mon May  8 15:05:27 2017, time step 0
-O       6       5       4.628
 H       5.72    5       5.186
 H       4.28    5       5.186
+O       6       5       4.628

tests/Examples/ManyWaysTranslateAtom/pre/water.xyz

@@ -1 +1 @@
 3
         Created by molecuilder on Mon May  8 15:05:27 2017, time step 0
-O       5       5       4.628
 H       5.72    5       5.186
 H       4.28    5       5.186
+O       5       5       4.628

tests/Examples/ManyWaysTranslateAtom/testsuite-examples-many-ways-translate-atom.at

@@ -30 +30 @@
 AT_CHECK([diff -I".*olecuilder.*" water_translateatom.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
 
+# 2. use translate-molecule variant a
+AT_CHECK([../../molecuilder --input water_translatemolecule1_stage1.xyz -o xyz --load water.xyz --select-all-molecules --translate-molecules --position "1,0,0"], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder --input water_translatemolecule1.xyz -o xyz --load water_translatemolecule1_stage1.xyz --select-atom-by-element H --translate-atoms --position "-1,0,0"], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_translatemolecule1.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+# 3. use translate-molecule variant b
+AT_CHECK([../../molecuilder --input water_translatemolecule2.xyz -o xyz --load water.xyz --update-molecules --select-molecules-by-formula O --translate-molecules --position "1,0,0"
+], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_translatemolecule2.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+# 4. use random-perturbation
+AT_CHECK([../../molecuilder --input water_randomperturbation.xyz -o xyz --load water.xyz --set-random-number-distribution "uniform_int" --random-number-distribution-parameters "min=0;max=2;" --set-random-number-engine "mt19937" --random-number-engine-parameters "seed=120;" --select-atom-by-element O --random-perturbation 1.], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_randomperturbation.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+## 5. use stretch-bond and change-bond-angle (twice, old 0.910914 A, old angle 104.449 def)
+#AT_CHECK([../../molecuilder --input water_stretchbond_stage1.pdb -o pdb --load water.xyz -I --select-atom-by-id 2 1 --stretch-bond 1.80825], 0, [ignore], [ignore])
+#AT_CHECK([../../molecuilder --input water_stretchbond.xyz -o xyz --load water_stretchbond_stage1.pdb --select-atom-by-id 2 0 --stretch-bond 0.624311 --select-all-atoms --change-bond-angle 45.3788], 0, [ignore], [ignore])
+#AT_CHECK([diff -I".*olecuilder.*" water_stretchbond.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+# 6. use fill-volume
+AT_CHECK([../../molecuilder --input water_fillvolume.xyz -o xyz --load water.xyz --create-shape --shape-name cyl --shape-type cylinder --stretch "1,1,1" --translation "5.28,6,5.628" --select-shape-by-name cyl --select-all-molecules -v 3 --fill-volume --count 12 --clear-molecule-selection --select-molecule-by-order 1 2 3 --remove-molecule --select-atom-by-element H --translate-atoms --position "-1,0,0"], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_fillvolume.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+# 7. use fill-surface
+AT_CHECK([../../molecuilder --input water_fillsurface.xyz -o xyz --load water.xyz --create-shape --shape-name ball --shape-type sphere --stretch "1,1,1" --translation "6,6,5" --select-shape-by-name ball --select-all-molecules --fill-surface --Alignment-Axis "0,1,0" --count 1 --select-atom-by-element H --translate-atoms --position "-1,0,0"], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_fillsurface.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+# 8. use remove-atom and add-atom
+AT_CHECK([../../molecuilder --input water_removeaddatom.xyz -o xyz --load water.xyz --select-atom-by-element O --remove-atom --add-atom O --domain-position "6,5,4.628"], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_removeaddatom.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+# 9. use mirror-atoms
+AT_CHECK([../../molecuilder --input water_mirroratoms.xyz -o xyz --load water.xyz --select-atom-by-element O --mirror-atoms "1,0,0" --plane-offset 5.5], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_mirroratoms.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
+
+# 10. use scale-box
+AT_CHECK([../../molecuilder --input water_scalebox.xyz -o xyz --load water.xyz --change-box "10,0,10,0,0,10" --scale-box "1.2,1,1" --select-atom-by-id 0 --translate-atoms --position "-1.144,0,0" --invert-atoms --unselect-atom-by-element O --mirror-atoms "1,0,0" --plane-offset 4.708], 0, [ignore], [ignore])
+AT_CHECK([diff -I".*olecuilder.*" water_scalebox.xyz ${abs_top_srcdir}/tests/Examples/ManyWaysTranslateAtom/post/water_translated.xyz], 0)
 
 AT_CLEANUP