Update adding CPR to JJ model. Code cleanup

JoeyDelp · Aug 4, 2022 · 1894f6e · 1894f6e
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,6 +1,6 @@
 cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
 
-project(JoSIM VERSION 2.6.3)
+project(JoSIM VERSION 2.6.4)
 
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)

diff --git a/docs/index.md b/docs/index.md
@@ -1,12 +1,12 @@
 # JoSIM - Superconducting Circuit Simulator
 
-Developers Manual for v2.5.1
+Developers Manual for v2.6.4
 
 ## Project Status
 
-### Testing: v2.6 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoSIM-CI-Devel?branchName=testing)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=1&branchName=testing)
+### Testing: v2.6.4 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoSIM-CI-Devel?branchName=testing)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=1&branchName=testing)
 
-### Stable: v2.6 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoeyDelp.JoSIM?branchName=master)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=3&branchName=master)
+### Stable: v2.6.4 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoeyDelp.JoSIM?branchName=master)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=3&branchName=master)
 
 ## Introduction
 

diff --git a/docs/jp/index_jp.md b/docs/jp/index_jp.md
@@ -1,12 +1,12 @@
 # JoSIM - 超伝導回路シミュレータ
 
-Developers Manual for v2.5.1
+Developers Manual for v2.6.4
 
 ## プロジェクトの状況
 
-### Testing: v2.6 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoSIM-CI-Devel?branchName=testing)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=1&branchName=testing)
+### Testing: v2.6.4 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoSIM-CI-Devel?branchName=testing)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=1&branchName=testing)
 
-### Stable: v2.6 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoeyDelp.JoSIM?branchName=master)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=3&branchName=master)
+### Stable: v2.6.4 - Status: [![Build Status](https://joeydelp.visualstudio.com/JoSIM/_apis/build/status/JoeyDelp.JoSIM?branchName=master)](https://joeydelp.visualstudio.com/JoSIM/_build/latest?definitionId=3&branchName=master)
 
 ## はじめに
 

diff --git a/docs/jp/syntax_jp.md b/docs/jp/syntax_jp.md
@@ -106,13 +106,16 @@ JoSIMで現在サポートしている接合モデルはRCSJモデルだけで
 | D               | 0.0, 1              | 0.0             | 電流位相関係に影響する接点の透過率 |
 | ICFCT or ICFACT | 0, 1                | $\frac{\pi}{4}$ | 臨界電流の準粒子ステップ高さに対する比       |
 | PHI             | 0, $2\pi$           | 0               | $\pi$-junctionのようなphi-junctionを実現可能にする   |
+| CPR | 0,$\infty$ | 1 | 電流の位相関係定数を設定します。 |
 
 *.model* の行はサブサーキット固有であるため同じ名前の異なるモデルを分離されたサブサーキット下にそれぞれ置くことができます。サブサーキット下にモデルが見つからなかった場合グローバルなものを探すことになり、それでも見つからない場合はデフォルトの値（デフォルトのモデル）が使用されます。
 
 **AREA**と**IC**パラメータはモデルパラメータの修飾子としてはたらきます。**IC**が指定されると**AREA**の値は$AREA=\frac{IC_{jj}}{IC_{model}}$によって置き換えられる、臨界電流でかけられた値となります。
 
 モデルの**PHI**パラメータを設定することで、JJ電流の$\sin(\phi)$部分の中にある位相($\phi$)から常に引いたものが位相の値になります。これによって$\pi$-junctionのような素子をモデル化可能です。
 
+***CPR***を設定すると、超電流位相関係の係数が変更されます。デフォルトは$I_S=I_C\sin(\phi)$に関連する1です。これを2に設定すると、この関係が$I_S = I_C\sin(2\phi)$に変更され、超電流の2次高調波のみを有効にして、最初の高調波を抑制することにより、$\pi$-junctionを使用できるようになります。[^1][^2]
+
 
 ### Transmission Line {#transmission-line}
 
@@ -461,3 +464,5 @@ JoSIMはビルトインの定数セットを持っており、展開された時
 | EPS0      | $\epsilon_{0}$                               | 8.854187817E-12         |
 | SIGMA     | $\sigma$ (short for $\frac{\Phi_{0}}{2\pi}$) | 3.291059757E-16         |
 
+[^1]:I. Salameh, E. G. Friedman and S. Kvatinsky, "Superconductive Logic Using 2ϕ—Josephson Junctions With Half Flux Quantum Pulses," in *IEEE Transactions on Circuits and Systems II: Express Briefs*, vol. 69, no. 5, pp. 2533-2537, May 2022, doi: 10.1109/TCSII.2022.3162723.
+[^2]:S. V. Bakurskiy et al., "Current-phase relations in SIsFS junctions in the vicinity of 0-$\pi$ Transition", *Phys. Rev. B Condens. Matter*, vol. 95, pp. 94522-94528, Mar. 2017.
diff --git a/docs/refer.bib b/docs/refer.bib
@@ -78,4 +78,29 @@ @article{haberkorn
 	pages={K161--K164},
 	year={1978},
 	publisher={Wiley Online Library}
-}
+}
+
+@ARTICLE{ebyCPR,
+  author={Salameh, Issa and Friedman, Eby G. and Kvatinsky, Shahar},
+  journal={IEEE Transactions on Circuits and Systems II: Express Briefs}, 
+  title={Superconductive Logic Using 2&#x03D5;&#x2014;Josephson Junctions With Half Flux Quantum Pulses}, 
+  year={2022},
+  volume={69},
+  number={5},
+  pages={2533-2537},
+  doi={10.1109/TCSII.2022.3162723}}
+  
+@article{bakyrskiyCPR,
+  title = {Current-phase relations in SIsFS junctions in the vicinity of 0-$\ensuremath{\pi}$ transition},
+  author = {Bakurskiy, S. V. and Filippov, V. I. and Ruzhickiy, V. I. and Klenov, N. V. and Soloviev, I. I. and Kupriyanov, M. Yu. and Golubov, A. A.},
+  journal = {Phys. Rev. B},
+  volume = {95},
+  issue = {9},
+  pages = {094522},
+  numpages = {11},
+  year = {2017},
+  month = {Mar},
+  publisher = {American Physical Society},
+  doi = {10.1103/PhysRevB.95.094522},
+  url = {https://link.aps.org/doi/10.1103/PhysRevB.95.094522}
+}
diff --git a/docs/syntax.md b/docs/syntax.md
@@ -99,13 +99,16 @@ The only junction model currently supported by JoSIM is the RCSJ model and thus
 | D               | 0.0, 1              | 0.0             | Point of contact transparency affecting current phase relationship |
 | ICFCT or ICFACT | 0, 1                | $\frac{\pi}{4}$ | Ratio of critical current to quasiparticle step height       |
 | PHI             | 0, $2\pi$           | 0               | Allows phi-junction capability such as the $\pi$-junction.   |
+| CPR             | 0, $\infty$         | 1               | Sets the Current Phase Relationship constant.                |
 
 The *.model* line is unique to the subcircuit it falls under and can thus allow different models with the same name under separate subcircuits. If the model is not found under the subcircuit it will be searched for globally and if not found default values (default model) will be used instead.
 
 The **AREA** and **IC** parameters act as modifiers to the model parameters. **AREA** is a critical current multiplier, where if **IC** is specified it replaces the **AREA** value by $AREA=\frac{IC_{jj}}{IC_{model}}$. 
 
 By setting the **PHI** parameter of the model, the phase value is persistantly subtracted from the phase ($\phi$) in the $\sin(\phi)$ part of the JJ current. This allows elements such as the $\pi$-junction to be modeled. 
 
+Setting **CPR** changes the coefficient of the supercurrent phase relationship. Default is 1 relating to $I_S=I_C\sin(\phi)$. Setting this to 2 would change this relationship to $I_S=I_C\sin(2\phi)$ which allows the use of $\pi$-junctions by enabling only the second harmonic of the supercurrent and suppressing the first.[^1][^2]
+
 ### Transmission Line
 
 **T**Label&emsp;$N^{+}_{1}$&emsp;$N^{-}_{1}$&emsp;$N^{+}_{2}$&emsp;$N^{-}_{2}$&emsp;**TD=VALUE**&emsp;**Z0=VALUE**
@@ -434,3 +437,5 @@ JoSIM has a set of built in constants that when used expand to the corresponding
 | EPS0      | $\epsilon_{0}$                               | 8.854187817E-12         |
 | SIGMA     | $\sigma$ (short for $\frac{\Phi_{0}}{2\pi}$) | 3.291059757E-16         |
 
+[^1]: I. Salameh, E. G. Friedman and S. Kvatinsky, "Superconductive Logic Using 2ϕ—Josephson Junctions With Half Flux Quantum Pulses," in *IEEE Transactions on Circuits and Systems II: Express Briefs*, vol. 69, no. 5, pp. 2533-2537, May 2022, doi: 10.1109/TCSII.2022.3162723.
+[^2]:S. V. Bakurskiy et al., "Current-phase relations in SIsFS junctions in the vicinity of 0-$\pi$ Transition", *Phys. Rev. B Condens. Matter*, vol. 95, pp. 94522-94528, Mar. 2017.
diff --git a/include/JoSIM/AnalysisType.hpp b/include/JoSIM/AnalysisType.hpp
@@ -7,21 +7,19 @@
 
 namespace JoSIM {
 
-  enum class AnalysisType : int64_t {
-    Voltage = 0, Phase = 1
-  };
+enum class AnalysisType : int64_t { Voltage = 0, Phase = 1 };
 
-  constexpr AnalysisType analysis_type_from_int(AnalysisType type) {
-    switch (type) {
+constexpr AnalysisType analysis_type_from_int(AnalysisType type) {
+  switch (type) {
     case AnalysisType::Voltage:
       return AnalysisType::Voltage;
     case AnalysisType::Phase:
       return AnalysisType::Phase;
     default:
       throw std::runtime_error("Invalid analysis type");
-    }
   }
+}
 
-} // namespace JoSIM
+}  // namespace JoSIM
 
-#endif // JOSIM_ANALYSISTYPE_HPP
+#endif  // JOSIM_ANALYSISTYPE_HPP
diff --git a/include/JoSIM/BasicComponent.hpp b/include/JoSIM/BasicComponent.hpp
@@ -3,75 +3,72 @@
 #ifndef JOSIM_BASICCOMPONENT_H
 #define JOSIM_BASICCOMPONENT_H
 
-#include "JoSIM/TypeDefines.hpp"
-#include "JoSIM/Errors.hpp"
-
-#include <vector>
-#include <unordered_map>
 #include <cmath>
+#include <unordered_map>
+#include <vector>
+
+#include "JoSIM/Errors.hpp"
+#include "JoSIM/TypeDefines.hpp"
 
 namespace JoSIM {
-  enum class NodeConfig {
-    GND = 0, POSGND = 1, GNDNEG = 2, POSNEG = 3
-  };
-
-  using nodemap = std::unordered_map<std::string, int64_t>;
-  using nodeconnections = std::vector<std::vector<std::pair<double, int64_t>>>;
-
-  class NetlistInfo {
-    public:
-    std::string label_;
-    double value_ = 0.0;
-  };
-
-  class IndexInfo {
-    public:
-    int_o posIndex_, negIndex_, currentIndex_;
-    NodeConfig nodeConfig_  = NodeConfig::GND;
-  };
-
-  class MatrixInfo {
-    public:
-    std::vector<double> nonZeros_;
-    std::vector<int64_t> columnIndex_;
-    std::vector<int64_t> rowPointer_;
-  };
-
-  class BasicComponent {
-    public:
-    NetlistInfo netlistInfo;
-    IndexInfo indexInfo;
-    MatrixInfo matrixInfo;
-
-
-    void set_node_indices(
-      const tokens_t& t, const nodemap& nm, nodeconnections& nc) {
-      switch (indexInfo.nodeConfig_) {
+enum class NodeConfig { GND = 0, POSGND = 1, GNDNEG = 2, POSNEG = 3 };
+
+using nodemap = std::unordered_map<std::string, int64_t>;
+using nodeconnections = std::vector<std::vector<std::pair<double, int64_t>>>;
+
+class NetlistInfo {
+ public:
+  std::string label_;
+  double value_ = 0.0;
+};
+
+class IndexInfo {
+ public:
+  int_o posIndex_, negIndex_, currentIndex_;
+  NodeConfig nodeConfig_ = NodeConfig::GND;
+};
+
+class MatrixInfo {
+ public:
+  std::vector<double> nonZeros_;
+  std::vector<int64_t> columnIndex_;
+  std::vector<int64_t> rowPointer_;
+};
+
+class BasicComponent {
+ public:
+  NetlistInfo netlistInfo;
+  IndexInfo indexInfo;
+  MatrixInfo matrixInfo;
+
+  void set_node_indices(const tokens_t& t, const nodemap& nm,
+                        nodeconnections& nc) {
+    switch (indexInfo.nodeConfig_) {
       case NodeConfig::POSGND:
         indexInfo.posIndex_ = nm.at(t.at(0));
-        nc.at(nm.at(t.at(0))).emplace_back(
-          std::make_pair(1, indexInfo.currentIndex_.value()));
+        nc.at(nm.at(t.at(0)))
+            .emplace_back(std::make_pair(1, indexInfo.currentIndex_.value()));
         break;
       case NodeConfig::GNDNEG:
         indexInfo.negIndex_ = nm.at(t.at(1));
-        nc.at(nm.at(t.at(1))).emplace_back(
-          std::make_pair(-1, indexInfo.currentIndex_.value()));
+        nc.at(nm.at(t.at(1)))
+            .emplace_back(std::make_pair(-1, indexInfo.currentIndex_.value()));
         break;
       case NodeConfig::POSNEG:
         indexInfo.posIndex_ = nm.at(t.at(0));
         indexInfo.negIndex_ = nm.at(t.at(1));
-        nc.at(nm.at(t.at(0))).emplace_back(
-          std::make_pair(1, indexInfo.currentIndex_.value()));
-        nc.at(nm.at(t.at(1))).emplace_back(
-          std::make_pair(-1, indexInfo.currentIndex_.value()));
+        nc.at(nm.at(t.at(0)))
+            .emplace_back(std::make_pair(1, indexInfo.currentIndex_.value()));
+        nc.at(nm.at(t.at(1)))
+            .emplace_back(std::make_pair(-1, indexInfo.currentIndex_.value()));
         break;
       case NodeConfig::GND:
         break;
-      }
     }
+  }
 
-    void set_matrix_info() {
-      switch (indexInfo.nodeConfig_) {
+  void set_matrix_info() {
+    switch (indexInfo.nodeConfig_) {
       case NodeConfig::POSGND:
         matrixInfo.nonZeros_.emplace_back(1);
         matrixInfo.columnIndex_.emplace_back(indexInfo.posIndex_.value());
@@ -92,27 +89,26 @@ namespace JoSIM {
       case NodeConfig::GND:
         matrixInfo.rowPointer_.emplace_back(1);
         break;
-      }
-      matrixInfo.columnIndex_.emplace_back(indexInfo.currentIndex_.value());
-      sanity_check();
     }
-
-    void sanity_check() {
-      for (auto& i : matrixInfo.nonZeros_) {
-        if (i == 0 || std::isinf(i) || std::isnan(i)) {
-          Errors::matrix_errors(
-            MatrixErrors::SANITY_ERROR, netlistInfo.label_);
-        }
+    matrixInfo.columnIndex_.emplace_back(indexInfo.currentIndex_.value());
+    sanity_check();
+  }
+
+  void sanity_check() {
+    for (auto& i : matrixInfo.nonZeros_) {
+      if (i == 0 || std::isinf(i) || std::isnan(i)) {
+        Errors::matrix_errors(MatrixErrors::SANITY_ERROR, netlistInfo.label_);
       }
     }
+  }
 
-    virtual void update_timestep(const double& factor) {};
+  virtual void update_timestep(const double& factor){};
 
-    virtual void step_back() {};
+  virtual void step_back(){};
 
-    virtual ~BasicComponent() {}
+  virtual ~BasicComponent() {}
 
-  }; // class BasicComponent
+};  // class BasicComponent
 
-} // namespace JoSIM
+}  // namespace JoSIM
 #endif
diff --git a/include/JoSIM/CCCS.hpp b/include/JoSIM/CCCS.hpp
@@ -3,45 +3,44 @@
 #ifndef JOSIM_CCCS_HPP
 #define JOSIM_CCCS_HPP
 
+#include <optional>
+#include <unordered_map>
+#include <unordered_set>
+#include <vector>
+
+#include "JoSIM/AnalysisType.hpp"
 #include "JoSIM/BasicComponent.hpp"
 #include "JoSIM/ParameterName.hpp"
 #include "JoSIM/Parameters.hpp"
-#include "JoSIM/AnalysisType.hpp"
-
-#include <vector>
-#include <unordered_map>
-#include <unordered_set>
-#include <optional>
 
 namespace JoSIM {
 
-  /*
-   Flabel Vo⁺ Vo⁻ Vc⁺ Vc⁻ G
+/*
+ Flabel Vo⁺ Vo⁻ Vc⁺ Vc⁻ G
 
-   Io = GIc
+ Io = GIc
 
-   ⎡ 0  0  0  0    1⎤ ⎡Vo⁺⎤   ⎡ 0⎤
-   ⎜ 0  0  0  0   -1⎟ ⎜Vo⁻⎟   ⎜ 0⎟
-   ⎜ 0  0  0  0  1/G⎟ ⎜Vc⁺⎟ = ⎜ 0⎟
-   ⎜ 0  0  0  0 -1/G⎟ ⎜Vc⁻⎟   ⎜ 0⎟
-   ⎣ 0  0  1 -1    0⎦ ⎣Io ⎦   ⎣ 0⎦
-  */
+ ⎡ 0  0  0  0    1⎤ ⎡Vo⁺⎤   ⎡ 0⎤
+ ⎜ 0  0  0  0   -1⎟ ⎜Vo⁻⎟   ⎜ 0⎟
+ ⎜ 0  0  0  0  1/G⎟ ⎜Vc⁺⎟ = ⎜ 0⎟
+ ⎜ 0  0  0  0 -1/G⎟ ⎜Vc⁻⎟   ⎜ 0⎟
+ ⎣ 0  0  1 -1    0⎦ ⎣Io ⎦   ⎣ 0⎦
+*/
 
-  class CCCS : public BasicComponent {
-    public:
-    NodeConfig nodeConfig2_;
-    int_o posIndex2_, negIndex2_;
+class CCCS : public BasicComponent {
+ public:
+  NodeConfig nodeConfig2_;
+  int_o posIndex2_, negIndex2_;
 
-    CCCS(
-      const std::pair<tokens_t, string_o>& s, const NodeConfig& ncon,
-      const std::optional<NodeConfig>& ncon2, const nodemap& nm,
-      std::unordered_set<std::string>& lm, nodeconnections& nc,
-      const param_map& pm, int64_t& bi);
+  CCCS(const std::pair<tokens_t, string_o>& s, const NodeConfig& ncon,
+       const std::optional<NodeConfig>& ncon2, const nodemap& nm,
+       std::unordered_set<std::string>& lm, nodeconnections& nc,
+       const param_map& pm, int64_t& bi);
 
-    void set_node_indices(
-      const tokens_t& t, const nodemap& nm, nodeconnections& nc);
-    void set_matrix_info();
-  }; // class CCCS
+  void set_node_indices(const tokens_t& t, const nodemap& nm,
+                        nodeconnections& nc);
+  void set_matrix_info();
+};  // class CCCS
 
-} // namespace JoSIM
+}  // namespace JoSIM
 #endif