Merge pull request #1 from akohlmey/angle-mwlc

Small updates to PR #4433

doc/src/angle_mwlc.rst

@@ -21,9 +21,13 @@ Examples
 Description
 """""""""""
 
-The *mwlc* angle style models a meltable wormlike chain and can be used to model non-linear bending elasticity of polymers, e.g. DNA.
-*mwlc* uses a potential that is a canonical-ensemble superposition of a non-melted and a melted state :ref:`(Farrell) <Farrell>`.
-The potential is
+.. versionadded:: TBD
+
+The *mwlc* angle style models a meltable wormlike chain and can be used
+to model non-linear bending elasticity of polymers, e.g. DNA.  *mwlc*
+uses a potential that is a canonical-ensemble superposition of a
+non-melted and a melted state :ref:`(Farrell) <Farrell>`.  The potential
+is
 
 .. math::
 
@@ -58,6 +62,7 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`k_2` (energy)
 * :math:`\mu` (energy)
 * :math:`T` (temperature)
+
 ----------
 
 
@@ -65,8 +70,8 @@ Restrictions
 """"""""""""
 
 This angle style can only be used if LAMMPS was built with the
-EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>` doc page
-for more info.
+EXTRA-MOLECULE package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
 
 Related commands
 """"""""""""""""

doc/utils/sphinx-config/false_positives.txt

@@ -712,7 +712,6 @@ Dasgupta
 dashpot
 dat
 datafile
-dataset
 datatype
 datums
 Davidchack

src/EXTRA-MOLECULE/angle_mwlc.cpp

@@ -79,7 +79,7 @@ void AngleMWLC::compute(int eflag, int vflag)
     i2 = anglelist[n][1];
     i3 = anglelist[n][2];
     type = anglelist[n][3];
-    kbt = temp[type]*force->boltz;
+    kbt = temp[type] * force->boltz;
     v_min = -kbt * log(1 + exp(-mu[type] / kbt));
 
     // 1st bond
@@ -113,7 +113,7 @@ void AngleMWLC::compute(int eflag, int vflag)
     qm = exp((-k2[type] * (1.0 + c) - mu[type]) / kbt);
     Q = q + qm;
 
-    if (eflag) eangle = -kbt*log(Q) - v_min;
+    if (eflag) eangle = -kbt * log(Q) - v_min;
 
     a = (k1[type] * q + k2[type] * qm) / Q;
     a11 = a * c / rsq1;
@@ -245,7 +245,8 @@ void AngleMWLC::read_restart(FILE *fp)
 
 void AngleMWLC::write_data(FILE *fp)
 {
-  for (int i = 1; i <= atom->nangletypes; i++) fprintf(fp, "%d %g %g %g %g\n", i, k1[i], k2[i], mu[i], temp[i]);
+  for (int i = 1; i <= atom->nangletypes; i++)
+    fprintf(fp, "%d %g %g %g %g\n", i, k1[i], k2[i], mu[i], temp[i]);
 }
 
 /* ---------------------------------------------------------------------- */
@@ -254,7 +255,7 @@ double AngleMWLC::single(int type, int i1, int i2, int i3)
 {
   double **x = atom->x;
 
-  double kbt = temp[type]*force->boltz;
+  double kbt = temp[type] * force->boltz;
   double v_min = -kbt * log(1 + exp(-mu[type] / kbt));
   double delx1 = x[i1][0] - x[i2][0];
   double dely1 = x[i1][1] - x[i2][1];
@@ -283,7 +284,7 @@ double AngleMWLC::single(int type, int i1, int i2, int i3)
 void AngleMWLC::born_matrix(int type, int i1, int i2, int i3, double &du, double &du2)
 {
   double **x = atom->x;
-  double kbt = temp[type]*force->boltz;
+  double kbt = temp[type] * force->boltz;
 
   double delx1 = x[i1][0] - x[i2][0];
   double dely1 = x[i1][1] - x[i2][1];

src/EXTRA-MOLECULE/angle_mwlc.h

@@ -24,28 +24,28 @@ AngleStyle(mwlc,AngleMWLC);
 
 namespace LAMMPS_NS {
 
-    class AngleMWLC : public Angle {
-    public:
-        AngleMWLC(class LAMMPS *);
-        ~AngleMWLC() override;
-        void compute(int, int) override;
-        void coeff(int, char **) override;
-        double equilibrium_angle(int) override;
-        void write_restart(FILE *) override;
-        void read_restart(FILE *) override;
-        void write_data(FILE *) override;
-        double single(int, int, int, int) override;
-        void born_matrix(int type, int i1, int i2, int i3, double &du, double &du2) override;
-        void *extract(const char *, int &) override;
+class AngleMWLC : public Angle {
+ public:
+  AngleMWLC(class LAMMPS *);
+  ~AngleMWLC() override;
+  void compute(int, int) override;
+  void coeff(int, char **) override;
+  double equilibrium_angle(int) override;
+  void write_restart(FILE *) override;
+  void read_restart(FILE *) override;
+  void write_data(FILE *) override;
+  double single(int, int, int, int) override;
+  void born_matrix(int type, int i1, int i2, int i3, double &du, double &du2) override;
+  void *extract(const char *, int &) override;
 
-    protected:
-        double *k1;
-        double *k2;
-        double *mu;
-        double *temp;
+ protected:
+  double *k1;
+  double *k2;
+  double *mu;
+  double *temp;
 
-        virtual void allocate();
-    };
+  virtual void allocate();
+};
 
 }    // namespace LAMMPS_NS