PR: Gibbs Monte Carlo Examples update + output file generation + Inpu…

…t variable container

1. added NPTMC Volume move example
2. updated NVT-Gibbs Move example for TraPPE CO2
3. Source code modifications
    3.1 added input container struct as a buffer storage to convert any form of input to something gRASPA can read (currently works for force field parameters)
    3.2 added variables struct as a bucket for all variables used during the simulation
    3.3 small fix for tail-correction, now it should be okay to use tail_correction in force_field_mixing_rules.def for all pairs of interactions
    3.4 added Keyword "StructureFactor_Multiplier XXX" to allocate more structure factors (multiplies by initial number of structure factors in three dimensions) for Ewald summation, useful for simulations with volume moves, pre-allocate more space to prevent re-allocation during the simulation
4. Add Output option in keywords, use "SaveOutputToFile yes" keyword in simulation.input to save output data file (RASPA-2 style)
5. Add NPT-Gibbs example

Examples/NPT-Gibbs/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 O_co2     0.0 0.0 -1.16
+1 C_co2     0.0 0.0 0.0
+2 O_co2     0.0 0.0 1.16
+# CC S BD B UB IB T ImpT S/S S/B B/B S/T B/T VDW Coulomb
+   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
+1 2 RIGID_BOND
+# Number of config moves
+0

Examples/NPT-Gibbs/Empty-Box.cif

@@ -0,0 +1,36 @@
+data_MFI_SI
+
+_audit_creation_method RASPA-1.0
+_audit_creation_date 2022-11-15
+_audit_author_name 'Zhao Li'
+
+_citation_author_name        'H. van Koningsveld, H. van Bekkum, and J. C. Jansen'
+_citation_title              'On the location and disorder of the tetrapropylammonium (TPA) ion in zeolite ZSM-5 with improved framework accuracy'
+_citation_journal_abbrev     'Acta Cryst.'
+_citation_journal_volume     B43
+_citation_page_first         127
+_citation_page_last          132
+_citation_year               1987
+
+_cell_length_a    1.0
+_cell_length_b    1.0
+_cell_length_c    1.0
+_cell_angle_alpha 90
+_cell_angle_beta  90
+_cell_angle_gamma 90
+_cell_volume      1
+
+_symmetry_cell_setting          orthorhombic
+_symmetry_space_group_name_Hall 'P 1'
+_symmetry_space_group_name_H-M  'P 1'
+_symmetry_Int_Tables_number     1
+
+_symmetry_equiv_pos_as_xyz 'x,y,z'
+
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+_atom_site_charge

Examples/NPT-Gibbs/force_field.def

@@ -0,0 +1,10 @@
+# rules to overwrite
+3
+#
+C_co2 C_co2 truncated yes
+C_co2 O_co2 truncated yes
+O_co2 O_co2 truncated yes
+# number of defined interactions
+0
+# mixing rules to overwrite
+0

Examples/NPT-Gibbs/force_field_mixing_rules.def

@@ -0,0 +1,11 @@
+# general rule for shifted vs truncated
+truncated
+# general rule tailcorrections
+no
+# number of defined interactions
+2
+# type interaction, parameters.    IMPORTANT: define shortest matches first, so that more specific ones overwrites these
+C_co2          lennard-jones    27.0 2.80
+O_co2          lennard-jones    79.0 3.05
+# general mixing rule for Lennard-Jones
+Lorentz-Berthelot

Examples/NPT-Gibbs/pseudo_atoms.def

@@ -0,0 +1,5 @@
+#number of pseudo atoms
+2
+#type      print as chem oxi mass       charge   pol.
+C_co2      yes   C  C    0   12.0       0.70   0.0
+O_co2      yes   O  O    0   15.9994   -0.35   0.0

Examples/NPT-Gibbs/simulation.input

@@ -0,0 +1,49 @@
+NumberOfInitializationCycles 25000
+NumberOfEquilibrationCycles  0
+NumberOfProductionCycles     25000
+
+UseMaxStep  no
+MaxStepPerCycle 1
+
+RestartFile no
+RandomSeed  0
+
+NumberOfTrialPositions 10
+NumberOfTrialOrientations 10
+NumberOfBlocks 1
+AdsorbateAllocateSpace 10240
+NumberOfSimulations 2
+SingleSimulation no
+
+DifferentFrameworks yes
+InputFileType cif
+FrameworkName Empty-Box Empty-Box
+UnitCells 0 39 39 39
+UnitCells 1 71 71 71
+
+ChargeMethod Ewald
+Temperature 240
+Pressure    1245000
+
+PrintEvery 10
+MoviesEvery 10
+
+OverlapCriteria 1e5
+CutOffVDW 15.0
+CutOffCoulomb 15.0
+EwaldPrecision 1e-6
+
+StructureFactor_Multiplier 8
+
+NPTVolumeChangeProbability 0.1
+
+SaveOutputToFile yes
+
+Component 0 MoleculeName             CO2
+            IdealGasRosenbluthWeight 1.0
+            FugacityCoefficient      1.0
+            TranslationProbability   1.0
+            RotationProbability      1.0
+            ReinsertionProbability   1.0
+            GibbsParticleXferProbability     1.0
+            CreateNumberOfMolecules  650 251

Examples/NPTMC/AllData/System_0/Component_0.data

@@ -0,0 +1 @@
+x y z charge scale scaleCoul Type