Merge branch 'adjustments'

modules/DL_MESO_DPD/dipole_dlmeso_dpd/CONTROL-3

+DL_MESO charged harmonic dimers with dpd repulsion
+
+volume 64.0
+temperature 1.0
+cutoff 1.0
+
+timestep 0.01
+steps 70000
+equilibration steps 20000
+traj 20000 100
+stats every 100
+stack size 100
+print every 100
+job time 7200.0
+close time 100.0
+
+ensemble nvt mdvv
+
+ewald sum 1.0 5 5 5
+bjerrum 42.0
+smear gauss equal
+
+finish

modules/DL_MESO_DPD/dipole_dlmeso_dpd/FIELD-3

+DL_MESO charged harmonic dimers with dpd repulsion
+
+SPECIES 2
+solp  1.0   0.46  0
+solm  1.0  -0.46  0
+
+MOLECULES 1
+DIMER
+nummols 96
+beads 2
+solp  0.0 0.0 0.0
+solm  0.1 0.0 0.0
+bonds 1
+harm 1 2 5.0 0.0
+
+finish
+
+INTERACTIONS 3
+solp  solp  dpd 25.0 1.0 4.5
+solm  solm  dpd 25.0 1.0 4.5
+solp  solm  dpd 25.0 1.0 4.5
+
+CLOSE

modules/DL_MESO_DPD/dipole_dlmeso_dpd/gen_dipole.f90

+PROGRAM gen_dipole
 !***********************************************************************************
 ! module to analyze charge dipole moments in DL_MESO
 !
 ! authors: m. a. seaton and s. chiacchiera, February 2017
 !**********************************************************************************            
-PROGRAM gen_dipole
-IMPLICIT none
+      IMPLICIT none
       INTEGER, PARAMETER :: dp = SELECTED_REAL_KIND (15, 307)
       INTEGER, PARAMETER :: ntraj=10
       REAL(KIND=dp), PARAMETER :: pi=3.141592653589793_dp
@@ -500,6 +500,11 @@ IMPLICIT none
     CONTAINS
 
       SUBROUTINE check_molecules
+!*************************************************************************************
+! subroutine to check molecular content and labelling
+!
+! authors: s. chiacchiera, February 2017 
+!************************************************************************************* 
         IMPLICIT NONE
         INTEGER i, j, k, tm, tp, imol, im, ibd
         INTEGER mxmolsize
@@ -546,10 +551,16 @@ IMPLICIT none
       END SUBROUTINE check_molecules
 
 SUBROUTINE compute_charge_dipoles (dipx_box, dipy_box, dipz_box, dip2_box)
-        !input: xxx, yyy, zzz (at a given time step) and chg 
-        !input: visit and from (obtained using connect) 
-        !output: the x,y,z components of the total dipole, sum p_i^2/N_mol
-        !for each molecule type (at a given time step)
+!*************************************************************************************
+! subroutine to compute charge dipole moments
+!
+! authors: m. a. seaton and s. chiacchiera, February 2017 
+!
+! input: xxx, yyy, zzz (at a given time step) and chg 
+! input: visit and from (obtained using connect) 
+! output: the x,y,z components of the total dipole, sum p_i^2/N_mol for each molecule
+!         type (at a given time step)
+!*************************************************************************************
         IMPLICIT NONE
         INTEGER i, j, k, tm, tp, imol, im, ibd, count, ipr
         REAL(KIND=dp), DIMENSION(nmoldef) :: dipx_box, dipy_box, dipz_box
@@ -644,8 +655,9 @@ SUBROUTINE compute_charge_dipoles (dipx_box, dipy_box, dipz_box, dip2_box)
       END SUBROUTINE compute_charge_dipoles
       
 End PROGRAM gen_dipole
+SUBROUTINE connect (nbeads, nbonds, bndtbl, visit, from)
 !**********************************************************************
-!  Analyze all the bonds (bndtbl) to obtain a schedule (visit, from) 
+!  Analyzes all the bonds (bndtbl) to obtain a schedule (visit, from) 
 !  to visit the beads so that each cluster is visited along a connected
 !  path. "visit" gives the order to include beads, "from" gives the bead 
 !  to attach them to.
@@ -654,8 +666,7 @@ End PROGRAM gen_dipole
 !
 !  author: s. chiacchiera, February 2017 
 !**********************************************************************
-SUBROUTINE connect (nbeads, nbonds, bndtbl, visit, from)
-  IMPLICIT none
+      IMPLICIT none
       INTEGER, INTENT (IN) :: bndtbl (nbonds,2)
       INTEGER, INTENT (IN) :: nbeads, nbonds
       INTEGER :: ic, i, j, k, nn, nclu, nper, lab, ref, count
@@ -757,6 +768,7 @@ SUBROUTINE connect (nbeads, nbonds, bndtbl, visit, from)
       !-----------------------------------------------------------------------
       CONTAINS
       !-----------------------------------------------------------------------
+      SUBROUTINE organize (N, NL, labnn, firstnn, lastnn, deg)
         !**********************************************************************
         ! Analyzes the bonds (bndtbl) to obtain the degree (=number of bonds)
         ! of each bead, and the nearest neighbours list.
@@ -764,8 +776,7 @@ SUBROUTINE connect (nbeads, nbonds, bndtbl, visit, from)
         !
         ! author: s. chiacchiera, February 2017 
         !**********************************************************************
-        SUBROUTINE organize (N, NL, labnn, firstnn, lastnn, deg)
-      IMPLICIT none
+        IMPLICIT none
       INTEGER, INTENT(IN) :: N, NL
       INTEGER :: i,l,count_lab, i1,i2
       INTEGER, DIMENSION (N), INTENT(OUT) :: deg

modules/DL_MESO_DPD/dipole_dlmeso_dpd/out-3

+ Number of nodes used in calculations ?
+ nchist:            0          96           0           0           0           0           0           0           0           0
+ Charges for SPECIES type solp     :
+ Charges for SPECIES type solm     :
+chg=       0.4600      -0.4600
+ Number of snapshots:          501
+ <P_x>, <P_y>, <P_z>:
+-3.627184E-02   -1.790324E-01    5.466988E-02
+ error:
+ 9.792086E-02    1.066997E-01    9.685359E-02
+ <P^2>/V:
+ 2.381825E-01
+ error:
+ 8.641061E-03
+ <p^2>:
+ 1.419998E-01
+ error:
+ 4.556992E-04
+ kirkwood factor:
+ 1.118229E+00
+ error:
+ 4.415698E-02
+ Bjerrum length?
+ epsilon_r:
+ 4.290325E+01
+ error:
+ 1.520215E+00

modules/DL_MESO_DPD/dipole_dlmeso_dpd/readme.rst

@@ -90,7 +90,15 @@ analyzed. The user is asked to provide the number of nodes used to run the
 simulation, the electric charges for all the types of beads
 and the Bjerrum length.
 
-As a test, we suggest two examples involving two (toy) molecular species: a
+To input the user-defined parameters one can enter them from the keyboard or write them into a text file (say, input.txt), one per line
+(in the right order) and run the program in this way:
+
+``gen_dipoleaf.exe < input.txt``
+
+We propose two tests to familiarize with the utility and a third one on a
+physically relevant system.
+
+The first two tests involve two (toy) molecular species: a
 branched one (four beads, T-shaped) and a simple dimer. All the beads carry charges.
 In the first case 10 molecules of each type are present and are followed for a few time steps.
 In the second case it is suggested to analyze a single snapshot with just two
@@ -177,6 +185,45 @@ and the `dipole_BRANCH` one is
 		    
 The results of this test do not depend on the number of nodes used to run the simulation.
 		    
+**Third test: water in oil**
+
+Here we suggest to consider a fluid made of harmonically bonded dimers
+:math:`(+q,-q)`. Fixing appropriately the partial charge :math:`q`
+and the Bjerrum length :math:`l_B` this system
+mimics water in an oil background, as long as the dielectric properties
+are concerned. For more details about this model, please see the page :ref:`dimers`.
+
+Run DL_MESO_DPD using for the CONTROL file
+
+.. literalinclude:: ./CONTROL-3
+
+and for the FIELD file
+
+.. literalinclude:: ./FIELD-3
+
+Analyzing the HISTORY file with `gen_dipole.exe`, this output is printed on
+the standard output
+
+.. literalinclude:: ./out-3
+
+In particular, we see that:
+
+- :math:`\vec{P}=(0.0 \pm 0.1, 0.2 \pm 0.1, 0.1 \pm 0.1)`
+- :math:`\epsilon_r= 43 \pm 2`
+- :math:`g_k = 1.12 \pm 0.04`
+
+Please notice that the error estimates are done assuming all the samples are
+independent. From the results obtained in the testing case of the
+module `gen_dipoleaf.f90`, one sees that the auto-correlation time of
+:math:`\vec{P}` in this system is about 1-2 DPD time units, so the sampling choice
+done here (trajectories are written every 100 time steps, i.e., every 1 DPD
+time units) seems reasonable, even if a bit optimistic.
+To confirm the reliability of the error estimate one can do
+another run with a different random number sequence (see the directive `seed` of
+DL_MESO) and see if the two results are compatible within error bars.
+
+  
+
 Source Code
 ___________
 .. literalinclude:: ./gen_dipole.f90
@@ -184,7 +231,7 @@ ___________
    :linenos:
 
 .. Here are the URL references used
-.. _DL_MESO: http://www.scd.stfc.ac.uk/SCD/support/40694.aspx
+.. _DL_MESO: http://www.ccp5.ac.uk/DL_MESO
 .. _ReST: http://docutils.sourceforge.net/docs/user/rst/quickref.html
 .. [1] Disambiguation on the concept of molecule. In DL\_MESO a *defined molecule*
          is a set of beads, which can be bonded or not.
@@ -193,5 +240,3 @@ ___________
 	 In fact, this, together with the reasonable assumption that each stretching
 	 bond cannot be stretched to more than half the system linear size, allows
 	 to univocally define the charge dipole moment of each molecule.
-
-.. www.ccp5.ac.uk/DL_MESO

modules/DL_MESO_DPD/format_dlmeso_dpd/readme.rst

@@ -32,7 +32,7 @@ utility for DL_MESO_DPD, the Dissipative Particle Dynamics (DPD) code from the D
 
 It converts the trajectory (HISTORY) files from *unformatted* to a
 human readable form, (optionally) including explicative comments about all the
-quantities. This module is mainly for learning/checking purpouses.
+quantities. This module is mainly for learning/checking purposes.
 The first aim is to help the user to check that the
 system was prepared as intended (e.g., showing all the bead properties and
 initial positions, all the bonds etc).
@@ -89,6 +89,6 @@ ___________
    :linenos:
 		    
 .. Here are the URL references used
-.. _DL_MESO: http://www.scd.stfc.ac.uk/SCD/support/40694.aspx
+.. _DL_MESO: http://www.ccp5.ac.uk/DL_MESO
 .. _ReST: http://docutils.sourceforge.net/docs/user/rst/quickref.html
-.. www.ccp5.ac.uk/DL_MESO
+