Refactoring of Ewald summation policies and Energy class

docs/_docs/energy.md

@@ -242,7 +242,7 @@ self energies are automatically added to the Hamiltonian, activating additional
 --------------------- | ---------------------------------------------------------------------
 `kcutoff`             | Reciprocal-space cutoff
 `epss=0`              | Dielectric constant of surroundings, $\varepsilon_{surf}$ (0=tinfoil)
-`ipbc=false`          | Use isotropic periodic boundary conditions, [IPBC](http://doi.org/css8). Holds also for Yukawa-type interactions.
+`ewaldscheme=PBC`     | Periodic (`PBC`) or isotropic periodic ([`IPBC`](http://doi.org/css8)) boundary conditions
 `spherical_sum=true`  | Spherical/ellipsoidal summation in reciprocal space; cubic if `false`.
 `debyelength=`$\infty$| Debye length (Å)
 
@@ -266,12 +266,12 @@ $$
 $$
 
 $$
-A_k = \frac{e^{-( k^2 + \kappa^2 )/4\alpha^2}}{k^2}
+A\_k = \frac{e^{-( k^2 + \kappa^2 )/4\alpha^2}}{k^2}
 \quad \quad Q^{q\mu} = Q^{q} + Q^{\mu}
 $$
 
 $$
-Q^{q} = \sum_{j}q_je^{i({\bf k}\cdot {\bf r}_j)} \quad Q^{\mu} = \sum_{j}i({\boldsymbol{\mu}}_j\cdot {\bf k})  e^{i({\bf k}\cdot {\bf r}_j)}
+Q^{q} = \sum_{j}q\_je^{i({\bf k}\cdot {\bf r}\_j)} \quad Q^{\mu} = \sum_{j}i({\boldsymbol{\mu}}\_j\cdot {\bf k})  e^{i({\bf k}\cdot {\bf r}\_j)}
 $$
 
 $$

docs/schema.yml

@@ -221,6 +221,7 @@ properties:
                           alpha: {type: number}
                           kcutoff: {type: number}
                           ipbc: {type: boolean, default: false}
+                          ewaldscheme: {type: string, enum: [PBC, PBCEigen, IPBC], default: PBCEigen}
                       required: [cutoff, epss, alpha, kcutoff]
 
         mixing_rule:

examples/water/ewald.yml

@@ -0,0 +1,40 @@
+#!/usr/bin/env yason.py
+temperature: 300
+random: {seed: fixed}
+geometry: {type: cuboid, length: 18.6}
+mcloop: {macro: 5, micro: 50}
+
+atomlist:
+    - OW: {q: -0.8476, sigma: 3.166, eps: 0.650, mw: 15.999}
+    - HW: {q: 0.4238,  sigma: 2, eps: 0, mw: 1.007}
+
+moleculelist:
+    - water:
+        structure:
+            - OW: [2.30, 6.28, 1.13]
+            - HW: [ 1.37,6.26, 1.50]
+            - HW: [2.31, 5.89, 0.21]
+
+insertmolecules:
+    - water: {N: 256}
+
+energy:
+    - isobaric: {P/atm: 1}
+    - nonbonded_coulomblj:
+        lennardjones: {mixing: LB}
+        coulomb: {type: ewald, epsr: 1, cutoff: 9, kcutoff: 7.3, epss: 0, alpha: 0.2, ewaldscheme: PBCEigen}
+        cutoff_g2g: 10
+
+moves:
+    - moltransrot: {molecule: water, dp: 0.4, dprot: 0.4, repeat: N}
+    - volume: {dV: 0.03, method: isotropic}
+
+analysis:
+    - sanity: {nstep: 100}
+    - savestate: {file: confout.pqr}
+    - savestate: {file: state.ubj}
+      #- atomrdf: {file: rdf.dat, nstep: 10, dr: 0.15, name1: OW, name2: OW}
+      #- systemenergy: {file: energy.dat, nstep: 50}
+      #- xtcfile: {file: traj.xtc, nstep: 10}
+      #- density: {nstep: 50}
+

src/CMakeLists.txt

@@ -257,6 +257,11 @@ add_test(
     && ${PYTHON_EXECUTABLE} ${JSON_COMPARE} speciation.out.json out.json --tol 0.02"
     WORKING_DIRECTORY ${EXAMPLES_DIR}/speciation)
 
+add_test(
+    NAME water-ewald-NOCHECKS
+    COMMAND sh -c "${PYTHON_EXECUTABLE} ${YASON} ewald.yml | $<TARGET_FILE:faunus>"
+    WORKING_DIRECTORY ${EXAMPLES_DIR}/water)
+
 add_test(
     NAME phosphate
     COMMAND sh -c "${PYTHON_EXECUTABLE} ${YASON} phosphate.yml\