core: Add initial_pos_offset to Oscillatory LEbc

espressomd · Apr 5, 2022 · cd6765a · cd6765a
1 parent 833131d
commit cd6765a
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Showing 5 changed files with 26 additions and 12 deletions.
diff --git a/src/core/lees_edwards/protocols.hpp b/src/core/lees_edwards/protocols.hpp
@@ -37,7 +37,8 @@ struct Off {
 
 /** Lees-Edwards protocol for linear shearing */
 struct LinearShear {
-  LinearShear() : m_initial_pos_offset{0}, m_shear_velocity{0}, m_time_0{0} {}
+  LinearShear()
+      : m_initial_pos_offset{0.}, m_shear_velocity{0.}, m_time_0{0.} {}
   LinearShear(double initial_offset, double shear_velocity, double time_0)
       : m_initial_pos_offset{initial_offset},
         m_shear_velocity{shear_velocity}, m_time_0{time_0} {}
@@ -52,15 +53,20 @@ struct LinearShear {
 
 /** Lees-Edwards protocol for oscillatory shearing */
 struct OscillatoryShear {
-  OscillatoryShear() : m_amplitude{0}, m_omega{0}, m_time_0{0} {}
-  OscillatoryShear(double amplitude, double omega, double time_0)
-      : m_amplitude{amplitude}, m_omega{omega}, m_time_0{time_0} {}
+  OscillatoryShear()
+      : m_initial_pos_offset{0.}, m_amplitude{0.}, m_omega{0.}, m_time_0{0.} {}
+  OscillatoryShear(double initial_offset, double amplitude, double omega,
+                   double time_0)
+      : m_initial_pos_offset{initial_offset},
+        m_amplitude{amplitude}, m_omega{omega}, m_time_0{time_0} {}
   double pos_offset(double time) const {
-    return m_amplitude * std::sin(m_omega * (time - m_time_0));
+    return m_initial_pos_offset +
+           m_amplitude * std::sin(m_omega * (time - m_time_0));
   }
   double shear_velocity(double time) const {
     return m_omega * m_amplitude * std::cos(m_omega * (time - m_time_0));
   }
+  double m_initial_pos_offset;
   double m_amplitude;
   double m_omega;
   double m_time_0;

diff --git a/src/core/unit_tests/lees_edwards_test.cpp b/src/core/unit_tests/lees_edwards_test.cpp
@@ -132,10 +132,12 @@ BOOST_AUTO_TEST_CASE(protocol_lin) {
 
 BOOST_AUTO_TEST_CASE(protocol_osc) {
   auto const t0 = 1.2;
+  auto const x0 = 0.1;
   auto const a = 3.1;
   auto const o = 2.1;
-  auto osc = OscillatoryShear(a, o, t0);
-  BOOST_CHECK_CLOSE(get_pos_offset(3.3, osc), a * sin(o * (3.3 - t0)), tol);
+  auto osc = OscillatoryShear(x0, a, o, t0);
+  BOOST_CHECK_CLOSE(get_pos_offset(3.3, osc), x0 + a * sin(o * (3.3 - t0)),
+                    tol);
   BOOST_CHECK_CLOSE(get_shear_velocity(3.3, osc), a * o * cos(o * (3.3 - t0)),
                     tol);
 }
diff --git a/src/python/espressomd/lees_edwards.py b/src/python/espressomd/lees_edwards.py
@@ -75,6 +75,8 @@ class OscillatoryShear(ScriptInterfaceHelper):
 
     Parameters
     ----------
+    initial_pos_offset : :obj:`float`
+       Positional offset at the Lees--Edwards boundary at t=0.
     amplitude : :obj:`float`
        Maximum amplitude of the positional offset at the Lees--Edwards boundary.
     omega : :obj:`float`

diff --git a/src/script_interface/lees_edwards/OscillatoryShear.hpp b/src/script_interface/lees_edwards/OscillatoryShear.hpp
@@ -37,7 +37,10 @@ class OscillatoryShear : public Protocol {
       : m_protocol{std::make_shared<::LeesEdwards::ActiveProtocol>(
             ::LeesEdwards::OscillatoryShear())} {
     add_parameters(
-        {{"amplitude",
+        {{"initial_pos_offset",
+          boost::get<::LeesEdwards::OscillatoryShear>(*m_protocol)
+              .m_initial_pos_offset},
+         {"amplitude",
           boost::get<::LeesEdwards::OscillatoryShear>(*m_protocol).m_amplitude},
          {"omega",
           boost::get<::LeesEdwards::OscillatoryShear>(*m_protocol).m_omega},

diff --git a/testsuite/python/lees_edwards.py b/testsuite/python/lees_edwards.py
@@ -30,8 +30,9 @@
 
 
 np.random.seed(42)
-params_lin = {'shear_velocity': 1.2, 'initial_pos_offset': 0.1, 'time_0': 0.1}
-params_osc = {'amplitude': 2.3, 'omega': 2.51, 'time_0': -2.1}
+params_lin = {'initial_pos_offset': 0.1, 'time_0': 0.1, 'shear_velocity': 1.2}
+params_osc = {'initial_pos_offset': 0.1, 'time_0': -2.1, 'amplitude': 2.3,
+              'omega': 2.51}
 lin_protocol = espressomd.lees_edwards.LinearShear(**params_lin)
 osc_protocol = espressomd.lees_edwards.OscillatoryShear(**params_osc)
 off_protocol = espressomd.lees_edwards.Off()
@@ -113,7 +114,7 @@ def test_protocols(self):
         # check that LE offsets are recalculated on simulation time change
         for time in [0., 2.3]:
             system.time = time
-            expected_pos = params_osc['amplitude'] * \
+            expected_pos = params_osc['initial_pos_offset'] + params_osc['amplitude'] * \
                 np.sin(params_osc['omega'] * (time - params_osc['time_0']))
             expected_vel = params_osc['amplitude'] * params_osc['omega'] * \
                 np.cos(params_osc['omega'] * (time - params_osc['time_0']))
@@ -124,7 +125,7 @@ def test_protocols(self):
         # Check that time change during integration updates offsets
         system.integrator.run(1)
         time = system.time
-        expected_pos = params_osc['amplitude'] * \
+        expected_pos = params_osc['initial_pos_offset'] + params_osc['amplitude'] * \
             np.sin(params_osc['omega'] * (time - params_osc['time_0']))
         expected_vel = params_osc['amplitude'] * params_osc['omega'] * \
             np.cos(params_osc['omega'] * (time - params_osc['time_0']))