Merge pull request #46 from KaihangShi/develop

Add an example for Henry's coefficient
snurr-group · Aug 21, 2024 · 0c5b63a · 0c5b63a
2 parents debd7e4 + 659187e
commit 0c5b63a
Show file tree

Hide file tree

Showing 7 changed files with 191 additions and 11 deletions.
diff --git a/Examples/Henrys_coefficient/CO2.def b/Examples/Henrys_coefficient/CO2.def
@@ -0,0 +1,23 @@
+# critical constants: Temperature [T], Pressure [Pa], and Acentric factor [-]
+304.1282
+7377300.0
+0.22394
+#Number Of Atoms
+ 3
+# Number of groups
+1
+# CO2-group
+rigid
+# number of atoms
+3
+# atomic positions
+0 C_co2     0.0           0.0           0.0
+1 O_co2     0.0           0.0           1.16
+2 O_co2     0.0           0.0          -1.16
+# Chiral centers Bond  BondDipoles Bend  UrayBradley InvBend  Torsion Imp. Torsion Bond/Bond Stretch/Bend Bend/Bend Stretch/Torsion Bend/Torsion IntraVDW IntraCoulomb
+               0    2            0    0            0       0        0            0         0            0         0               0            0        0            0
+# Bond stretch: atom n1-n2, type, parameters
+0 1 RIGID_BOND
+0 2 RIGID_BOND
+# Number of config moves
+0
diff --git a/Examples/Henrys_coefficient/MgMOF74_charged.cif b/Examples/Henrys_coefficient/MgMOF74_charged.cif
@@ -0,0 +1,79 @@
+data_image0
+_cell_length_a       6.87407
+_cell_length_b       15.2145
+_cell_length_c       15.2147
+_cell_angle_alpha    117.779
+_cell_angle_beta     98.6603
+_cell_angle_gamma    98.6614
+
+_symmetry_space_group_name_H-M    "P 1"
+_symmetry_int_tables_number       1
+
+loop_
+  _symmetry_equiv_pos_as_xyz
+  'x, y, z'
+
+loop_
+  _atom_site_label
+  _atom_site_occupancy
+  _atom_site_fract_x
+  _atom_site_fract_y
+  _atom_site_fract_z
+  _atom_site_thermal_displace_type
+  _atom_site_B_iso_or_equiv
+  _atom_site_type_symbol
+  _atom_site_charge
+  C1       1.0000 0.30580  0.48194  0.01275  Biso   1.000  C  -0.2104684987306805
+  C2       1.0000 0.17620  0.46921  0.48198  Biso   1.000  C  -0.2104684987306805
+  C3       1.0000 0.11487  0.53380  0.44726  Biso   1.000  C  -0.1438961439497434
+  C4       1.0000 0.29302  0.98723  0.46922  Biso   1.000  C  -0.2104684987306805
+  C5       1.0000 0.82381  0.53079  0.51802  Biso   1.000  C  -0.2104684987306805
+  C6       1.0000 0.14810  0.39109  0.82686  Biso   1.000  C  0.6258360669285988
+  C7       1.0000 0.32122  0.17314  0.56422  Biso   1.000  C  0.6245620773708138
+  C8       1.0000 0.75700  0.43578  0.60891  Biso   1.000  C  0.6245620773708138
+  C9       1.0000 0.85191  0.60891  0.17314  Biso   1.000  C  0.6258360669285988
+  C10      1.0000 0.67878  0.82686  0.43578  Biso   1.000  C  0.6258360669285988
+  C11      1.0000 0.24300  0.56422  0.39109  Biso   1.000  C  0.6245620773708138
+  C12      1.0000 0.53267  0.46544  0.89910  Biso   1.000  C  0.3457498194306733
+  C13      1.0000 0.63355  0.10091  0.56631  Biso   1.000  C  0.3457498194306733
+  C14      1.0000 0.06724  0.43368  0.53458  Biso   1.000  C  0.3457498194306733
+  C15      1.0000 0.46734  0.53456  0.10090  Biso   1.000  C  0.3457498194306733
+  C16      1.0000 0.36646  0.89909  0.43369  Biso   1.000  C  0.3457498194306733
+  C17      1.0000 0.93276  0.56632  0.46542  Biso   1.000  C  0.3457498194306733
+  C18      1.0000 0.58108  0.91345  0.46620  Biso   1.000  C  -0.1415255444240728
+  C19      1.0000 0.66760  0.55276  0.08655  Biso   1.000  C  -0.1415255444240728
+  C20      1.0000 0.88513  0.46620  0.55274  Biso   1.000  C  -0.1438961439497434
+  C21      1.0000 0.41893  0.08655  0.53380  Biso   1.000  C  -0.1415255444240728
+  C22      1.0000 0.33240  0.44724  0.91345  Biso   1.000  C  -0.1415255444240728
+  C23      1.0000 0.70698  0.01277  0.53078  Biso   1.000  C  -0.2104684987306805
+  C24      1.0000 0.69422  0.51806  0.98724  Biso   1.000  C  -0.2104684987306805
+  H1       1.0000 0.84786  0.53293  0.97797  Biso   1.000  H  0.1162825974646878
+  H2       1.0000 0.86991  0.02207  0.55490  Biso   1.000  H  0.1162825974646878
+  H3       1.0000 0.31502  0.44511  0.46715  Biso   1.000  H  0.1162825974646878
+  H4       1.0000 0.15215  0.46707  0.02203  Biso   1.000  H  0.1162825974646878
+  H5       1.0000 0.13009  0.97793  0.44510  Biso   1.000  H  0.1162825974646878
+  H6       1.0000 0.68498  0.55489  0.53285  Biso   1.000  H  0.1162825974646878
+  Mg1      1.0000 0.01746  0.73188  0.40646  Biso   1.000  Mg  1.4261149381623304
+  Mg2      1.0000 0.38898  0.40647  0.67457  Biso   1.000  Mg  1.4261149381623304
+  Mg3      1.0000 0.71443  0.32546  0.73188  Biso   1.000  Mg  1.4261149381623304
+  Mg4      1.0000 0.98254  0.26812  0.59354  Biso   1.000  Mg  1.4261149381623304
+  Mg5      1.0000 0.61101  0.59353  0.32543  Biso   1.000  Mg  1.4261149381623304
+  Mg6      1.0000 0.28557  0.67454  0.26812  Biso   1.000  Mg  1.4261149381623304
+  O1       1.0000 0.60061  0.46926  0.62725  Biso   1.000  O  -0.6597980252910617
+  O2       1.0000 0.02662  0.62725  0.15801  Biso   1.000  O  -0.6597980252910617
+  O3       1.0000 0.86864  0.84201  0.46927  Biso   1.000  O  -0.6597980252910617
+  O4       1.0000 0.39939  0.53074  0.37275  Biso   1.000  O  -0.6597980252910617
+  O5       1.0000 0.17015  0.36185  0.73519  Biso   1.000  O  -0.7279031856225537
+  O6       1.0000 0.43493  0.26482  0.62665  Biso   1.000  O  -0.7279031856225537
+  O7       1.0000 0.80831  0.37336  0.63816  Biso   1.000  O  -0.7279031856225537
+  O8       1.0000 0.82985  0.63815  0.26481  Biso   1.000  O  -0.7279031856225537
+  O9       1.0000 0.19169  0.62664  0.36184  Biso   1.000  O  -0.7279031856225537
+  O10      1.0000 0.13135  0.15800  0.53073  Biso   1.000  O  -0.6597980252910617
+  O11      1.0000 0.57369  0.43506  0.80662  Biso   1.000  O  -0.7728609732971390
+  O12      1.0000 0.76704  0.19339  0.62839  Biso   1.000  O  -0.7728609732971390
+  O13      1.0000 0.13866  0.37160  0.56498  Biso   1.000  O  -0.7728609732971390
+  O14      1.0000 0.42631  0.56494  0.19338  Biso   1.000  O  -0.7728609732971390
+  O15      1.0000 0.23296  0.80661  0.37161  Biso   1.000  O  -0.7728609732971390
+  O16      1.0000 0.86136  0.62839  0.43502  Biso   1.000  O  -0.7728609732971390
+  O17      1.0000 0.56507  0.73518  0.37335  Biso   1.000  O  -0.7279031856225537
+  O18      1.0000 0.97338  0.37275  0.84199  Biso   1.000  O  -0.6597980252910617
diff --git a/Examples/Henrys_coefficient/force_field.def b/Examples/Henrys_coefficient/force_field.def
@@ -0,0 +1,6 @@
+# rules to overwrite
+0
+# number of defined interactions
+0
+# mixing rules to overwrite
+0
diff --git a/Examples/Henrys_coefficient/force_field_mixing_rules.def b/Examples/Henrys_coefficient/force_field_mixing_rules.def
@@ -0,0 +1,15 @@
+# general rule for shifted vs truncated
+truncated
+# general rule tailcorrections
+no
+# number of defined interactions
+6
+# type interaction, parameters.    IMPORTANT: define shortest matches first, so that more specific ones overwrites these
+Mg              lennard-jones         55.85    2.69
+O               lennard-jones         30.19    3.12
+C               lennard-jones         52.83    3.43
+H               lennard-jones         22.14    2.57
+C_co2          lennard-jones    27.0   2.800
+O_co2          lennard-jones    79.0   3.050
+# general mixing rule for Lennard-Jones
+Lorentz-Berthelot
diff --git a/Examples/Henrys_coefficient/pseudo_atoms.def b/Examples/Henrys_coefficient/pseudo_atoms.def
@@ -0,0 +1,9 @@
+#number of pseudo atoms
+6
+#type     print     as     chem     oxi     mass     charge     pol
+Mg     yes     Mg     Mg     0     24.305     0.0     0
+O     yes     O     O     0     15.999     0     0
+C     yes     C     C     0     12.011     0     0
+H     yes     H     H     0     1.008     0.0     0
+C_co2      yes   C  C    0   12.0       0.7   0.0
+O_co2      yes   O  O    0   15.9994   -0.35   0.0
diff --git a/Examples/Henrys_coefficient/simulation.input b/Examples/Henrys_coefficient/simulation.input
@@ -0,0 +1,48 @@
+UseGPUReduction no
+Useflag yes
+
+NumberOfInitializationCycles 0
+NumberOfEquilibrationCycles  0
+NumberOfProductionCycles     10000000
+
+UseMaxStep  yes
+MaxStepPerCycle 1
+
+UseChargesFromCIFFile yes
+
+RestartFile no
+RandomSeed  0
+
+BMCBiasingMethod LJ_Biasing
+
+NumberOfTrialPositions 10
+NumberOfTrialOrientations 10
+
+NumberOfBlocks 1
+AdsorbateAllocateSpace 10240
+NumberOfSimulations 1
+SingleSimulation yes
+
+DifferentFrameworks yes
+InputFileType cif
+FrameworkName MgMOF74_charged
+UnitCells 0 5 3 3
+
+ChargeMethod Ewald
+Temperature 313
+Pressure    1000000
+
+OverlapCriteria 1e20
+CutOffVDW 14.0
+CutOffCoulomb 14.0
+EwaldPrecision 1e-6
+
+UseDNNforHostGuest no
+
+Component 0 MoleculeName             CO2
+            IdealGasRosenbluthWeight 1.0
+            FugacityCoefficient      1.0
+            WidomProbability         1.0
+            CreateNumberOfMolecules  0
+
+
diff --git a/libtorch-patch/Allegro/PATCH_ALLEGRO_DNN_HostGuest_Energy_Functions.h.txt b/libtorch-patch/Allegro/PATCH_ALLEGRO_DNN_HostGuest_Energy_Functions.h.txt
@@ -17,17 +17,17 @@ PATCH_ALLEGRO_INSERTION
       double3* temp_pos; temp_pos = (double3*) malloc(sizeof(double3) * SystemComponents.Moleculesize[SelectedComponent]);
       cudaMemcpy(temp_pos, Sims.Old.pos, sizeof(double3) * SystemComponents.Moleculesize[SelectedComponent], cudaMemcpyDeviceToHost);
       Check_DNNAtom_and_copy_pos_to_UCAtoms(temp_pos, SystemComponents.DNN.UCAtoms[SelectedComponent], SystemComponents.ConsiderThisAdsorbateAtom, SystemComponents.Moleculesize[SelectedComponent]);
-      if(SystemComponents.CURRENTCYCLE <= 30)
-      {
-        printf("DNN INSERTION BEFORE CHECK DNN PseudoAtoms\n");
-        for(size_t i = 0; i < SystemComponents.Moleculesize[SelectedComponent]; i++)
-          printf("pos: %f %f %f\n", temp_pos[i].x, temp_pos[i].y, temp_pos[i].z);
-
-        printf("DNN INSERTION AFTER CHECK DNN PseudoAtoms\n");
-        for(size_t i = 0; i < SystemComponents.DNN.UCAtoms[SelectedComponent].size; i++)
-          printf("pos: %f %f %f\n", SystemComponents.DNN.UCAtoms[SelectedComponent].pos[i].x, SystemComponents.DNN.UCAtoms[SelectedComponent].pos[i].y, SystemComponents.DNN.UCAtoms[SelectedComponent].pos[i].z);
-      }
-        DNN_New = SystemComponents.DNN.MCEnergyWrapper(SelectedComponent, Initialize, SystemComponents.DNNEnergyConversion);
+//      if(SystemComponents.CURRENTCYCLE <= 30)
+//      {
+//        printf("DNN INSERTION BEFORE CHECK DNN PseudoAtoms\n");
+//        for(size_t i = 0; i < SystemComponents.Moleculesize[SelectedComponent]; i++)
+//          printf("pos: %f %f %f\n", temp_pos[i].x, temp_pos[i].y, temp_pos[i].z);
+//
+//        printf("DNN INSERTION AFTER CHECK DNN PseudoAtoms\n");
+//        for(size_t i = 0; i < SystemComponents.DNN.UCAtoms[SelectedComponent].size; i++)
+//          printf("pos: %f %f %f\n", SystemComponents.DNN.UCAtoms[SelectedComponent].pos[i].x, SystemComponents.DNN.UCAtoms[SelectedComponent].pos[i].y, SystemComponents.DNN.UCAtoms[SelectedComponent].pos[i].z);
+//      }
+      DNN_New = SystemComponents.DNN.MCEnergyWrapper(SelectedComponent, Initialize, SystemComponents.DNNEnergyConversion);
       free(temp_pos);
     }