From 3bd1f02e078153a44e9925a0487872e34bcffb57 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 12:10:40 +0100
Subject: [PATCH 01/11] add hybrid scaled method fo liquid

---
 calphy/integrators.py |  12 +--
 calphy/liquid.py      | 165 +++++++++++++++++++++++++++---------------
 2 files changed, 111 insertions(+), 66 deletions(-)

diff --git a/calphy/integrators.py b/calphy/integrators.py
index 66782b9..7982d6a 100644
--- a/calphy/integrators.py
+++ b/calphy/integrators.py
@@ -229,12 +229,12 @@ def integrate_path(fwdfilename, bkdfilename, nelements=1, concentration=[1,], us
             # - Liquid : UFM system energy is not scaled with fix:adapt (this is actually wrong, but works for us)
             # - Liquid : So we only unscale the system of interest in liquid
             # - Alchemy : Both system energies are scaled with fix:adapt, so we need to unscale both
-            for i in range(len(fdui)):
-                if flambda[i] !=0:
-                    fdui[i] = fdui[i]/flambda[i]
-            for i in range(len(bdui)):
-                if blambda[i] !=0:
-                    bdui[i] = bdui[i]/blambda[i]
+            #for i in range(len(fdui)):
+            #    if flambda[i] !=0:
+            #        fdui[i] = fdui[i]/flambda[i]
+            #for i in range(len(bdui)):
+            #    if blambda[i] !=0:
+            #        bdui[i] = bdui[i]/blambda[i]
 
             if alchemy:
                 """
diff --git a/calphy/liquid.py b/calphy/liquid.py
index eed1825..0e78218 100644
--- a/calphy/liquid.py
+++ b/calphy/liquid.py
@@ -228,76 +228,121 @@ def run_integration(self, iteration=1):
         lmp = ph.read_dump(lmp, conf, species=self.options["nelements"])
 
         #set hybrid ufm and normal potential
-        lmp = ph.set_hybrid_potential(lmp, self.options, self.eps)
+        #lmp = ph.set_hybrid_potential(lmp, self.options, self.eps)
 
         #remap the box to get the correct pressure
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
 
-        #apply the necessary thermostat
-        lmp.command("fix             f1 all nve")                              
-        lmp.command("fix             f2 all langevin %f %f %f %d"%(self.t, self.t, self.options["md"]["tdamp"],
-            np.random.randint(0, 10000)))
+        lmp = ph.set_potential(lmp, self.options)
 
-        # Compute the potential energy of each pair style.
-        lmp.command("compute         c1 all pair %s"%self.options["md"]["pair_style"])
-        lmp.command("compute         c2 all pair ufm")
+        
+        lmp.command("fix              f1 all nve")
+        lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], 
+                                        np.random.randint(0, 10000)))
+        lmp.command("run               %d"%self.options["md"]["te"])
 
-        # Output variables.
-        lmp.command("variable        step equal step")
-        lmp.command("variable        dU1 equal c_c1/atoms")             # Driving-force obtained from NEHI procedure.
-        lmp.command("variable        dU2 equal c_c2/atoms")
+        lmp.command("unfix            f1")
+        lmp.command("unfix            f2")
 
-        #force thermo to evaluate variables
-        lmp.command("thermo_style    custom step v_dU1 v_dU2")
-        lmp.command("thermo          1000")
+        #---------------------------------------------------------------
+        # FWD cycle
+        #---------------------------------------------------------------
 
-        #switching completely to potential of interest
-        lmp.command("variable        zero equal 0")
-        lmp.command("fix             f0 all adapt 0 pair ufm scale * * v_zero")
-        lmp.command("run             0")
-        lmp.command("unfix           f0")
+        lmp.command("variable         flambda equal ramp(${li},${lf})")
+        lmp.command("variable         blambda equal 1.0-v_flambda")
 
-        #Equilibrate system
-        lmp.command("run             %d"%self.options["md"]["te"])
+        lmp.command("pair_style       hybrid/scaled v_flambda %s v_blambda ufm 7.5"%options["md"]["pair_style"])
 
-        #print header
-        lmp.command("print           \"${dU1} ${dU2} ${li}\" file forward_%d.dat"%iteration)
-        
-        #set up scaling variables
-        lmp.command("variable        lambda_p1 equal ramp(${li},${lf})")
-        lmp.command("variable        lambda_p2 equal ramp(${lf},${li})")
-
-        #Forward switching run
-        lmp.command("fix             f3 all adapt 1 pair %s scale * * v_lambda_p1"%self.options["md"]["pair_style"])
-        lmp.command("fix             f4 all adapt 1 pair ufm scale * * v_lambda_p2")
-        lmp.command("fix             f5 all print 1 \"${dU1} ${dU2} ${lambda_p1}\" screen no append forward_%d.dat"%iteration)
-        lmp.command("run             %d"%self.options["md"]["ts"])
-
-        #unfix things
-        lmp.command("unfix           f3")
-        lmp.command("unfix           f4")
-        lmp.command("unfix           f5")
-
-        #Equilibriate at UFM potential
-        lmp.command("run             %d"%self.options["md"]["te"])
-
-        #print file header
-        lmp.command("print           \"${dU1} ${dU2} ${lf}\" file backward_%d.dat"%iteration)
-        
-        #set up scaling variables
-        lmp.command("variable        lambda_p1 equal ramp(${lf},${li})")
-        lmp.command("variable        lambda_p2 equal ramp(${li},${lf})")
-
-        #Reverse switching run
-        lmp.command("fix             f3 all adapt 1 pair %s scale * * v_lambda_p1"%self.options["md"]["pair_style"])
-        lmp.command("fix             f4 all adapt 1 pair ufm scale * * v_lambda_p2")
-        lmp.command("fix             f5 all print 1 \"${dU1} ${dU2} ${lambda_p1}\" screen no append backward_%d.dat"%iteration)
-        lmp.command("run             %d"%self.options["md"]["ts"])
-
-        #unfix things
-        lmp.command("unfix           f3")
-        lmp.command("unfix           f4")
-        lmp.command("unfix           f5")
+        pc =  self.options["md"]["pair_coeff"]
+        pcraw = pc.split()
+        pcnew = " ".join([*pcraw[:2], *[self.options["md"]["pair_style"],], *pcraw[2:]])
+
+        lmp.command("pair_coeff       * * %s"%pcnew)
+        lmp.command("pair_coeff       * * ufm %f 1.5"%self.eps)
+
+        lmp.command("compute          c1 all pair %s"%options["md"]["pair_style"])
+        lmp.command("compute          c2 all pair ufm")
+
+        lmp.command("variable         step equal step")
+        lmp.command("variable         dU1 equal c_c1/atoms")
+        lmp.command("variable         dU2 equal c_c2/atoms")
+
+        lmp.command("thermo_style     custom step v_dU1 v_dU2")
+        lmp.command("thermo           1000")
+
+
+        lmp.command("velocity         all create %f %d mom yes rot yes dist gaussian"%(self.t, np.random.randint(0, 10000)))
+
+        lmp.command("fix              f1 all nve")
+        lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], 
+                                        np.random.randint(0, 10000)))
+        lmp.command("compute          Tcm all temp/com")
+        lmp.command("fix_modify       f2 temp Tcm")
+
+        lmp.command("fix              f3 all print 1 \"${dU1} ${dU2} ${flambda}\" screen no file forward_%d.dat"%iteration)
+        lmp.command("run               %d"%self.options["md"]["ts"])
+
+        lmp.command("unfix            f1")
+        lmp.command("unfix            f2")
+        lmp.command("unfix            f3")
+        lmp.command("uncompute        c1")
+        lmp.command("uncompute        c2")
+
+        #---------------------------------------------------------------
+        # EQBRM cycle
+        #---------------------------------------------------------------
+
+        lmp.command("pair_style       ufm 7.5")
+        lmp.command("pair_coeff       * * %f 1.5"%self.eps)
+
+        lmp.command("thermo_style     custom step pe")
+        lmp.command("thermo           1000")
+
+        lmp.command("fix              f1 all nve")
+        lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], 
+                                        np.random.randint(0, 10000)))
+        lmp.command("fix_modify       f2 temp Tcm")
+
+        lmp.command("run               %d"%self.options["md"]["te"])
+
+        lmp.command("unfix            f1")
+        lmp.command("unfix            f2")
+
+        #---------------------------------------------------------------
+        # BKD cycle
+        #---------------------------------------------------------------
+
+        lmp.command("variable         flambda equal ramp(${lf},${li})")
+        lmp.command("variable         blambda equal 1.0-v_flambda")
+
+        lmp.command("pair_style       hybrid/scaled v_flambda %s v_blambda ufm 7.5"%options["md"]["pair_style"])
+
+        lmp.command("pair_coeff       * * %s"%pcnew)
+        lmp.command("pair_coeff       * * ufm %f 1.5"%self.eps)
+
+        lmp.command("compute          c1 all pair %s"%options["md"]["pair_style"])
+        lmp.command("compute          c2 all pair ufm")
+
+        lmp.command("variable         step equal step")
+        lmp.command("variable         dU1 equal c_c1/atoms")
+        lmp.command("variable         dU2 equal c_c2/atoms")
+
+        lmp.command("thermo_style     custom step v_dU1 v_dU2")
+        lmp.command("thermo           1000")
+
+        lmp.command("fix              f1 all nve")
+        lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], 
+                                        np.random.randint(0, 10000)))
+        lmp.command("fix_modify       f2 temp Tcm")
+
+        lmp.command("fix              f3 all print 1 \"${dU1} ${dU2} ${flambda}\" screen no file backward_%d.dat"%iteration)
+        lmp.command("run               %d"%self.options["md"]["ts"])
+
+        lmp.command("unfix            f1")
+        lmp.command("unfix            f2")
+        lmp.command("unfix            f3")
+        lmp.command("uncompute        c1")
+        lmp.command("uncompute        c2")
         
         #close object
         lmp.close()

From 8dcde7c2e3a69caaf6dee6f85bbd92ea3ba742c5 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 13:07:04 +0100
Subject: [PATCH 02/11] update liquid code

---
 calphy/liquid.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/calphy/liquid.py b/calphy/liquid.py
index 0e78218..4c0ecae 100644
--- a/calphy/liquid.py
+++ b/calphy/liquid.py
@@ -229,12 +229,11 @@ def run_integration(self, iteration=1):
 
         #set hybrid ufm and normal potential
         #lmp = ph.set_hybrid_potential(lmp, self.options, self.eps)
+        lmp = ph.set_potential(lmp, self.options)
 
         #remap the box to get the correct pressure
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
 
-        lmp = ph.set_potential(lmp, self.options)
-
         
         lmp.command("fix              f1 all nve")
         lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], 
@@ -251,7 +250,7 @@ def run_integration(self, iteration=1):
         lmp.command("variable         flambda equal ramp(${li},${lf})")
         lmp.command("variable         blambda equal 1.0-v_flambda")
 
-        lmp.command("pair_style       hybrid/scaled v_flambda %s v_blambda ufm 7.5"%options["md"]["pair_style"])
+        lmp.command("pair_style       hybrid/scaled v_flambda %s v_blambda ufm 7.5"%self.options["md"]["pair_style"])
 
         pc =  self.options["md"]["pair_coeff"]
         pcraw = pc.split()
@@ -260,7 +259,7 @@ def run_integration(self, iteration=1):
         lmp.command("pair_coeff       * * %s"%pcnew)
         lmp.command("pair_coeff       * * ufm %f 1.5"%self.eps)
 
-        lmp.command("compute          c1 all pair %s"%options["md"]["pair_style"])
+        lmp.command("compute          c1 all pair %s"%self.options["md"]["pair_style"])
         lmp.command("compute          c2 all pair ufm")
 
         lmp.command("variable         step equal step")
@@ -315,12 +314,12 @@ def run_integration(self, iteration=1):
         lmp.command("variable         flambda equal ramp(${lf},${li})")
         lmp.command("variable         blambda equal 1.0-v_flambda")
 
-        lmp.command("pair_style       hybrid/scaled v_flambda %s v_blambda ufm 7.5"%options["md"]["pair_style"])
+        lmp.command("pair_style       hybrid/scaled v_flambda %s v_blambda ufm 7.5"%self.options["md"]["pair_style"])
 
         lmp.command("pair_coeff       * * %s"%pcnew)
         lmp.command("pair_coeff       * * ufm %f 1.5"%self.eps)
 
-        lmp.command("compute          c1 all pair %s"%options["md"]["pair_style"])
+        lmp.command("compute          c1 all pair %s"%self.options["md"]["pair_style"])
         lmp.command("compute          c2 all pair ufm")
 
         lmp.command("variable         step equal step")

From cbbca54c4aefd7f2738aa6a7f3deb6e479a9a62a Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 13:09:33 +0100
Subject: [PATCH 03/11] fix pair hybrid for liquid

---
 calphy/liquid.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/calphy/liquid.py b/calphy/liquid.py
index 4c0ecae..4e19163 100644
--- a/calphy/liquid.py
+++ b/calphy/liquid.py
@@ -256,7 +256,7 @@ def run_integration(self, iteration=1):
         pcraw = pc.split()
         pcnew = " ".join([*pcraw[:2], *[self.options["md"]["pair_style"],], *pcraw[2:]])
 
-        lmp.command("pair_coeff       * * %s"%pcnew)
+        lmp.command("pair_coeff       %s"%pcnew)
         lmp.command("pair_coeff       * * ufm %f 1.5"%self.eps)
 
         lmp.command("compute          c1 all pair %s"%self.options["md"]["pair_style"])
@@ -316,7 +316,7 @@ def run_integration(self, iteration=1):
 
         lmp.command("pair_style       hybrid/scaled v_flambda %s v_blambda ufm 7.5"%self.options["md"]["pair_style"])
 
-        lmp.command("pair_coeff       * * %s"%pcnew)
+        lmp.command("pair_coeff       %s"%pcnew)
         lmp.command("pair_coeff       * * ufm %f 1.5"%self.eps)
 
         lmp.command("compute          c1 all pair %s"%self.options["md"]["pair_style"])

From 36953b2fe52841d69620ca549a4d258b825b0cd7 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 15:58:11 +0100
Subject: [PATCH 04/11] add new rs method in phase

---
 calphy/phase.py | 134 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 134 insertions(+)

diff --git a/calphy/phase.py b/calphy/phase.py
index 8a348e7..27f953c 100644
--- a/calphy/phase.py
+++ b/calphy/phase.py
@@ -249,6 +249,140 @@ def submit_report(self):
         elif self.calc["mode"] == "mts":
             self.logger.info("- 10.1063/1.1420486") 
 
+
+    def reversible_scaling(self, iteration=1):
+        """
+        Perform reversible scaling calculation in NPT
+
+        Parameters
+        ----------
+        iteration : int, optional
+            iteration of the calculation. Default 1
+
+        Returns
+        -------
+        None
+        """
+        t0 = self.t
+        tf = self.tend
+        li = 1
+        lf = t0/tf
+        pi = self.p
+        pf = lf*pi
+
+        #create lammps object
+        lmp = ph.create_object(self.cores, self.simfolder, self.options["md"]["timestep"])
+
+        lmp.command("echo              log")
+        lmp.command("variable          li equal %f"%li)
+        lmp.command("variable          lf equal %f"%lf)
+
+        #read in conf file
+        conf = os.path.join(self.simfolder, "conf.dump")
+        lmp = ph.read_dump(lmp, conf, species=self.options["nelements"])
+
+        #set up potential
+        lmp = ph.set_potential(lmp, self.options)
+
+        #remap the box to get the correct pressure
+        lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
+
+        #set thermostat and run equilibrium
+        lmp.command("fix               f1 all nph iso %f %f %f"%(self.p, self.p, self.options["md"]["pdamp"]))
+        lmp.command("fix               f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
+        lmp.command("run               %d"%self.options["md"]["te"])
+        lmp.command("unfix             f1")
+        lmp.command("unfix             f2")
+
+        #now fix com
+        lmp.command("variable         xcm equal xcm(all,x)")
+        lmp.command("variable         ycm equal xcm(all,y)")
+        lmp.command("variable         zcm equal xcm(all,z)")
+        
+        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.p, self.p, self.options["md"]["pdamp"]))
+        lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(t0, t0, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
+        
+        #compute com and modify fix
+        lmp.command("compute           tcm all temp/com")
+        lmp.command("fix_modify        f1 temp tcm")
+        lmp.command("fix_modify        f2 temp tcm")
+
+        lmp.command("variable          step    equal step")
+        lmp.command("variable          dU      equal c_thermo_pe/atoms")        
+        lmp.command("thermo_style      custom step pe c_tcm press vol")
+        lmp.command("thermo            10000")
+
+        #create velocity and equilibriate
+        lmp.command("velocity          all create %f %d mom yes rot yes dist gaussian"%(t0, np.random.randint(0, 10000)))   
+        lmp.command("run               %d"%self.options["md"]["te"])
+        
+        #unfix nph
+        lmp.command("unfix             f1")
+
+
+        lmp.command("variable         flambda equal ramp(${li},${lf})")
+        lmp.command("variable         blambda equal ramp(${lf},${li})")
+        lmp.command("variable         fscale equal v_flambda-1.0")
+        lmp.command("variable         bscale equal v_blambda-1.0")
+        lmp.command("variable         one equal 1.0")
+
+        #set up potential
+        pc =  self.options["md"]["pair_coeff"]
+        pcraw = pc.split()
+        pcnew1 = " ".join([*pcraw1[:2], *[pair_style[0],], "1", *pcraw1[2:]])
+        pcnew2 = " ".join([*pcraw2[:2], *[pair_style[1],], "2", *pcraw2[2:]])
+
+        lmp.command("pair_style       hybrid/scaled v_one %s v_fscale %s"%(self.options["md"]["pair_style"], self.options["md"]["pair_style"]))
+        lmp.command("pair_coeff       %s"%pcnew1)
+        lmp.command("pair_coeff       %s"%pcnew2)
+
+        #start scaling over switching time
+        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pi, 
+            pf, self.options["md"]["pdamp"]))
+        lmp.command("fix_modify        f1 temp tcm")
+        lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file forward_%d.dat"%iteration)
+        lmp.command("run               %d"%self.options["md"]["ts"])
+
+        #unfix
+        lmp.command("unfix             f3")
+        lmp.command("unfix             f1")
+
+
+        #switch potential
+        lmp = ph.set_potential(lmp, self.options)
+
+        #equilibriate scaled hamiltonian
+        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pf, 
+            pf, self.options["md"]["pdamp"]))
+        lmp.command("fix_modify        f1 temp tcm")        
+        lmp.command("run               %d"%self.options["md"]["te"])
+        lmp.command("unfix             f1")
+
+
+        #reverse scaling
+        lmp.command("variable         flambda equal ramp(${li},${lf})")
+        lmp.command("variable         blambda equal ramp(${lf},${li})")
+        lmp.command("variable         fscale equal v_flambda-1.0")
+        lmp.command("variable         bscale equal v_blambda-1.0")
+        lmp.command("variable         one equal 1.0")
+
+        lmp.command("pair_style       hybrid/scaled v_one %s v_bscale %s"%(self.options["md"]["pair_style"], self.options["md"]["pair_style"]))
+        lmp.command("pair_coeff       %s"%pcnew1)
+        lmp.command("pair_coeff       %s"%pcnew2)
+
+        #apply fix and perform switching        
+        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pf, 
+            pi, self.options["md"]["pdamp"]))
+        lmp.command("fix_modify        f1 temp tcm")
+        lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file backward_%d.dat"%iteration)
+        lmp.command("run               %d"%self.options["md"]["ts"])
+        
+        lmp.command("unfix             f3")
+        lmp.command("unfix             f1")
+        
+        #close the object
+        lmp.close()
+
     def integrate_reversible_scaling(self, scale_energy=False, return_values=False):
         """
         Perform integration after reversible scaling

From c8dc6632f5f6ba0fe53c7d9bfefcf0b1fe82039d Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 20:26:36 +0100
Subject: [PATCH 05/11] generalise reversible scaling function

---
 calphy/liquid.py | 110 -----------------------------------------
 calphy/phase.py  |  10 +++-
 calphy/solid.py  | 124 -----------------------------------------------
 3 files changed, 9 insertions(+), 235 deletions(-)

diff --git a/calphy/liquid.py b/calphy/liquid.py
index 4e19163..9056b1a 100644
--- a/calphy/liquid.py
+++ b/calphy/liquid.py
@@ -391,113 +391,3 @@ def thermodynamic_integration(self):
         self.fe = self.fideal + self.fref - self.w + self.pv
 
 
-
-    def reversible_scaling(self, iteration=1):
-        """
-        Perform reversible scaling calculation in NPT
-
-        Parameters
-        ----------
-        iteration : int, optional
-            iteration of the calculation. Default 1
-
-        Returns
-        -------
-        None
-        """
-        t0 = self.t
-        tf = self.tend
-        li = 1
-        lf = t0/tf
-        pi = self.p
-        pf = lf*pi
-
-        #create lammps object
-        lmp = ph.create_object(self.cores, self.simfolder, self.options["md"]["timestep"])
-
-        lmp.command("echo              log")
-        lmp.command("variable          li equal %f"%li)
-        lmp.command("variable          lf equal %f"%lf)
-
-        #read in conf file
-        conf = os.path.join(self.simfolder, "conf.dump")
-        lmp = ph.read_dump(lmp, conf, species=self.options["nelements"])
-
-        #set up potential
-        lmp = ph.set_potential(lmp, self.options)
-
-        #remap the box to get the correct pressure
-        lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
-
-        #set thermostat and run equilibrium
-        lmp.command("fix               f1 all nph iso %f %f %f"%(self.p, self.p, self.options["md"]["pdamp"]))
-        lmp.command("fix               f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
-        lmp.command("run               %d"%self.options["md"]["te"])
-        lmp.command("unfix             f1")
-        lmp.command("unfix             f2")
-
-        #now fix com
-        lmp.command("variable         xcm equal xcm(all,x)")
-        lmp.command("variable         ycm equal xcm(all,y)")
-        lmp.command("variable         zcm equal xcm(all,z)")
-        
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.p, self.p, self.options["md"]["pdamp"]))
-        lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(t0, t0, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
-        
-        #compute com and modify fix
-        lmp.command("compute           tcm all temp/com")
-        lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix_modify        f2 temp tcm")
-
-        lmp.command("variable          step    equal step")
-        lmp.command("variable          dU      equal c_thermo_pe/atoms")        
-        lmp.command("thermo_style      custom step pe c_tcm press vol")
-        lmp.command("thermo            10000")
-
-        #create velocity and equilibriate
-        lmp.command("velocity          all create %f %d mom yes rot yes dist gaussian"%(t0, np.random.randint(0, 10000)))   
-        lmp.command("run               %d"%self.options["md"]["te"])
-        
-        #unfix nph
-        lmp.command("unfix             f1")
-
-        #define ramp
-        lmp.command("variable          lambda equal ramp(${li},${lf})")
-
-        #start scaling over switching time
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pi, 
-            pf, self.options["md"]["pdamp"]))
-        lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix               f3 all adapt 1 pair %s scale * * v_lambda"%self.options["md"]["pair_style"])
-        lmp.command("fix               f4 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file forward_%d.dat"%iteration)
-        lmp.command("run               %d"%self.options["md"]["ts"])
-
-        #unfix
-        lmp.command("unfix             f3")
-        lmp.command("unfix             f4")
-        lmp.command("unfix             f1")
-
-         #equilibriate scaled hamiltonian
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pf, 
-            pf, self.options["md"]["pdamp"]))
-        lmp.command("fix_modify        f1 temp tcm")        
-        lmp.command("run               %d"%self.options["md"]["te"])
-        lmp.command("unfix             f1")
-
-        #reverse lambda ramp
-        lmp.command("variable          lambda equal ramp(${lf},${li})")
-
-        #apply fix and perform switching        
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pf, 
-            pi, self.options["md"]["pdamp"]))
-        lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix               f3 all adapt 1 pair %s scale * * v_lambda"%self.options["md"]["pair_style"])
-        lmp.command("fix               f4 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file backward_%d.dat"%iteration)
-        lmp.command("run               %d"%self.options["md"]["ts"])
-        lmp.command("unfix             f3")
-        lmp.command("unfix             f4")
-        lmp.command("unfix             f1")
-        
-        #close the object
-        lmp.close()
-
diff --git a/calphy/phase.py b/calphy/phase.py
index 27f953c..6d04f4d 100644
--- a/calphy/phase.py
+++ b/calphy/phase.py
@@ -250,7 +250,7 @@ def submit_report(self):
             self.logger.info("- 10.1063/1.1420486") 
 
 
-    def reversible_scaling(self, iteration=1):
+    def reversible_scaling(self, iteration=1, solid=False):
         """
         Perform reversible scaling calculation in NPT
 
@@ -359,6 +359,14 @@ def reversible_scaling(self, iteration=1):
         lmp.command("unfix             f1")
 
 
+        if solid:
+            solids = ph.find_solid_fraction(os.path.join(self.simfolder, "traj.dat"))
+            if (solids/lmp.natoms < self.options["conv"]["solid_frac"]):
+                lmp.close()
+                raise RuntimeError("System melted, increase size or reduce scaling!")
+            
+
+
         #reverse scaling
         lmp.command("variable         flambda equal ramp(${li},${lf})")
         lmp.command("variable         blambda equal ramp(${lf},${li})")
diff --git a/calphy/solid.py b/calphy/solid.py
index 76eaa71..58468fd 100644
--- a/calphy/solid.py
+++ b/calphy/solid.py
@@ -446,128 +446,4 @@ def thermodynamic_integration(self):
         #calculate final free energy
         self.fe = self.fref + self.w + self.pv
 
-
-
-
-    def reversible_scaling(self, iteration=1):
-        """
-        Perform reversible scaling calculation in NPT
-
-        Parameters
-        ----------
-        iteration : int, optional
-            iteration of the calculation. Default 1
-
-        Returns
-        -------
-        None
-        """
-        
-        t0 = self.t
-        tf = self.tend
-        li = 1
-        lf = t0/tf
-        pi = self.p
-        pf = lf*pi
-
-        #create lammps object
-        lmp = ph.create_object(self.cores, self.simfolder, self.options["md"]["timestep"])
-
-        lmp.command("echo              log")
-        lmp.command("variable          li equal %f"%li)
-        lmp.command("variable          lf equal %f"%lf)
-
-        #read in conf
-        conf = os.path.join(self.simfolder, "conf.dump")
-        lmp = ph.read_dump(lmp, conf, species=self.options["nelements"])
-
-        #set up potential
-        lmp = ph.set_potential(lmp, self.options)
-
-        #remap the box to get the correct pressure
-        lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
-
-        #set up thermostat and barostat and run equilibrium
-        lmp.command("fix               f1 all nph %s %f %f %f"%(self.iso, self.p, self.p, self.options["md"]["pdamp"]))
-        lmp.command("fix               f2 all langevin %f %f %f %d zero yes"%(t0, t0, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
-        lmp.command("run               %d"%self.options["md"]["te"])
-        lmp.command("unfix             f1")
-        lmp.command("unfix             f2")
-
-        #now fix com
-        lmp.command("variable         xcm equal xcm(all,x)")
-        lmp.command("variable         ycm equal xcm(all,y)")
-        lmp.command("variable         zcm equal xcm(all,z)")
-        
-        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, self.p, self.p, self.options["md"]["pdamp"]))
-        lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(t0, t0, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
-        
-        #compute com and modify fix
-        lmp.command("compute           tcm all temp/com")
-        lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix_modify        f2 temp tcm")
-
-        #get output variables
-        lmp.command("variable          step    equal step")
-        lmp.command("variable          dU      equal c_thermo_pe/atoms")        
-        lmp.command("thermo_style      custom step pe c_tcm press vol")
-        lmp.command("thermo            10000")
-
-        #create velocity and equilibriate
-        lmp.command("velocity          all create %f %d mom yes rot yes dist gaussian"%(t0, np.random.randint(0, 10000)))   
-        lmp.command("run               %d"%self.options["md"]["te"])
-
-        #unfix nph
-        lmp.command("unfix             f1")
-
-        #define ramp
-        lmp.command("variable          lambda equal ramp(${li},${lf})")
-
-        #start scaling over switching time
-        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, pi, 
-            pf, self.options["md"]["pdamp"]))
-        lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix               f3 all adapt 1 pair %s scale * * v_lambda"%self.options["md"]["pair_style"])
-        lmp.command("fix               f4 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file forward_%d.dat"%iteration)
-        lmp.command("run               %d"%self.options["md"]["ts"])
-
-        #unfix
-        lmp.command("unfix             f3")
-        lmp.command("unfix             f4")
-        lmp.command("unfix             f1")
-
-        #check for melting
-        lmp.command("dump              2 all custom 1 traj.dat id type mass x y z vx vy vz")
-        lmp.command("run               0")
-        lmp.command("undump            2")
-        
-        solids = ph.find_solid_fraction(os.path.join(self.simfolder, "traj.dat"))
-        if (solids/lmp.natoms < self.options["conv"]["solid_frac"]):
-            lmp.close()
-            raise RuntimeError("System melted, increase size or reduce scaling!")
-        
-        #equilibriate scaled hamiltonian
-        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%( self.iso, pf, 
-            pf, self.options["md"]["pdamp"]))
-        lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("run               %d"%self.options["md"]["te"])
-        lmp.command("unfix             f1")
-
-        #reverse lambda ramp
-        lmp.command("variable          lambda equal ramp(${lf},${li})")
-        
-        #apply fix and perform switching
-        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, pf, 
-            pi, self.options["md"]["pdamp"]))
-        lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix               f3 all adapt 1 pair %s scale * * v_lambda"%self.options["md"]["pair_style"])
-        lmp.command("fix               f4 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file backward_%d.dat"%iteration)
-        lmp.command("run               %d"%self.options["md"]["ts"])
-        lmp.command("unfix             f3")
-        lmp.command("unfix             f4")
-        lmp.command("unfix             f1")
-        
-        #close the object
-        lmp.close()
-
         
\ No newline at end of file

From 6e2f604c8f8d4c3b6f9e2e6d9366a3d1ac08df67 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 20:29:33 +0100
Subject: [PATCH 06/11] update iso selection in rs routine

---
 calphy/phase.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/calphy/phase.py b/calphy/phase.py
index 6d04f4d..fdb5d79 100644
--- a/calphy/phase.py
+++ b/calphy/phase.py
@@ -288,7 +288,7 @@ def reversible_scaling(self, iteration=1, solid=False):
         lmp = ph.remap_box(lmp, self.lx, self.ly, self.lz)
 
         #set thermostat and run equilibrium
-        lmp.command("fix               f1 all nph iso %f %f %f"%(self.p, self.p, self.options["md"]["pdamp"]))
+        lmp.command("fix               f1 all nph %s %f %f %f"%(self.iso, self.p, self.p, self.options["md"]["pdamp"]))
         lmp.command("fix               f2 all langevin %f %f %f %d zero yes"%(self.t, self.t, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
         lmp.command("run               %d"%self.options["md"]["te"])
         lmp.command("unfix             f1")
@@ -299,7 +299,7 @@ def reversible_scaling(self, iteration=1, solid=False):
         lmp.command("variable         ycm equal xcm(all,y)")
         lmp.command("variable         zcm equal xcm(all,z)")
         
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.p, self.p, self.options["md"]["pdamp"]))
+        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, self.p, self.p, self.options["md"]["pdamp"]))
         lmp.command("fix              f2 all langevin %f %f %f %d zero yes"%(t0, t0, self.options["md"]["tdamp"], np.random.randint(0, 10000)))
         
         #compute com and modify fix
@@ -337,7 +337,7 @@ def reversible_scaling(self, iteration=1, solid=False):
         lmp.command("pair_coeff       %s"%pcnew2)
 
         #start scaling over switching time
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pi, 
+        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, pi, 
             pf, self.options["md"]["pdamp"]))
         lmp.command("fix_modify        f1 temp tcm")
         lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file forward_%d.dat"%iteration)
@@ -352,7 +352,7 @@ def reversible_scaling(self, iteration=1, solid=False):
         lmp = ph.set_potential(lmp, self.options)
 
         #equilibriate scaled hamiltonian
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pf, 
+        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, pf, 
             pf, self.options["md"]["pdamp"]))
         lmp.command("fix_modify        f1 temp tcm")        
         lmp.command("run               %d"%self.options["md"]["te"])
@@ -364,7 +364,7 @@ def reversible_scaling(self, iteration=1, solid=False):
             if (solids/lmp.natoms < self.options["conv"]["solid_frac"]):
                 lmp.close()
                 raise RuntimeError("System melted, increase size or reduce scaling!")
-            
+
 
 
         #reverse scaling
@@ -379,7 +379,7 @@ def reversible_scaling(self, iteration=1, solid=False):
         lmp.command("pair_coeff       %s"%pcnew2)
 
         #apply fix and perform switching        
-        lmp.command("fix              f1 all nph iso %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(pf, 
+        lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, pf, 
             pi, self.options["md"]["pdamp"]))
         lmp.command("fix_modify        f1 temp tcm")
         lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file backward_%d.dat"%iteration)

From 15dd4aabc2df8beddd5e615c685d679324b45302 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 20:38:02 +0100
Subject: [PATCH 07/11] bug fixes in rs methid

---
 calphy/phase.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/calphy/phase.py b/calphy/phase.py
index fdb5d79..ca0cea0 100644
--- a/calphy/phase.py
+++ b/calphy/phase.py
@@ -329,8 +329,8 @@ def reversible_scaling(self, iteration=1, solid=False):
         #set up potential
         pc =  self.options["md"]["pair_coeff"]
         pcraw = pc.split()
-        pcnew1 = " ".join([*pcraw1[:2], *[pair_style[0],], "1", *pcraw1[2:]])
-        pcnew2 = " ".join([*pcraw2[:2], *[pair_style[1],], "2", *pcraw2[2:]])
+        pcnew1 = " ".join([*pcraw[:2], *[self.options["md"]["pair_style"],], "1", *pcraw[2:]])
+        pcnew2 = " ".join([*pcraw[:2], *[self.options["md"]["pair_style"],], "2", *pcraw[2:]])
 
         lmp.command("pair_style       hybrid/scaled v_one %s v_fscale %s"%(self.options["md"]["pair_style"], self.options["md"]["pair_style"]))
         lmp.command("pair_coeff       %s"%pcnew1)
@@ -340,7 +340,7 @@ def reversible_scaling(self, iteration=1, solid=False):
         lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, pi, 
             pf, self.options["md"]["pdamp"]))
         lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file forward_%d.dat"%iteration)
+        lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${flambda}\" screen no file forward_%d.dat"%iteration)
         lmp.command("run               %d"%self.options["md"]["ts"])
 
         #unfix
@@ -382,7 +382,7 @@ def reversible_scaling(self, iteration=1, solid=False):
         lmp.command("fix              f1 all nph %s %f %f %f fixedpoint ${xcm} ${ycm} ${zcm}"%(self.iso, pf, 
             pi, self.options["md"]["pdamp"]))
         lmp.command("fix_modify        f1 temp tcm")
-        lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${lambda}\" screen no file backward_%d.dat"%iteration)
+        lmp.command("fix               f3 all print 1 \"${dU} $(press) $(vol) ${blambda}\" screen no file backward_%d.dat"%iteration)
         lmp.command("run               %d"%self.options["md"]["ts"])
         
         lmp.command("unfix             f3")

From fdf400cd1b7a74f5ec5177a3c54f240cbcc9dca3 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Tue, 2 Nov 2021 21:09:37 +0100
Subject: [PATCH 08/11] minor update to docs

---
 docs/source/gettingstarted.md | 186 +++++-----------------------------
 docs/source/index.rst         |   3 +
 2 files changed, 26 insertions(+), 163 deletions(-)

diff --git a/docs/source/gettingstarted.md b/docs/source/gettingstarted.md
index 54bed92..6474d35 100644
--- a/docs/source/gettingstarted.md
+++ b/docs/source/gettingstarted.md
@@ -4,41 +4,42 @@ Python library and command line tool for calculation of free energies.
 
 ## Installation
 
-In this section, the installation method for `calphy` is explained. Depending on which potential is used, a different version of LAMMPS might be required, leading to a different installation method. The table below lists the pair styles, and the corresponding installation methods.
+### Supported operating systems
 
+`calphy` can be installed on Linux and Mac OS based systems. On Windows systems, it is recommended to use  [Windows subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install).
 
+### Installation using [Conda](https://anaconda.org/)
+
+calphy can be installed directly using [Conda](https://docs.conda.io/en/latest/) from the [conda-forge channel](https://conda-forge.org/) by the following statement:
+
+```
+conda install -c conda-forge calphy
+```
 
-| pair style                                              	| installation 	|
-|---------------------------------------------------------	|--------------	|
-| eam, eam/fs, eam/alloy                                  	| [method 1](#id1)     	|
-| pace                                                    	| [method 2](#id2)     	|
-| adp, snap, sw, tersoff, tersoff/mod, tersoff/modc, meam 	| [method 3](#id3)     	|
 
 ### Dependencies
 
-- lammps              2021.05.27  
-- mendeleev           0.7.0       `pip install mendeleev`
-- pylammpsmpi         0.0.8       `pip install pylammpsmpi`
-- pyscal              2.10.14     `pip install git+https://github.com/srmnitc/pyscal`
-- pyyaml              5.4.1       `pip install pyyaml`
-- scipy               1.7.0       `pip install scipy`
-- tqdm                4.61.2      `pip install tqdm`
+- lammps                            `conda install -c conda-forge lammps`
+- mendeleev           >=0.7.0       `pip install mendeleev`
+- pylammpsmpi         >=0.0.8       `pip install pylammpsmpi`
+- pyscal              >=2.10.14     `pip install git+https://github.com/srmnitc/pyscal`
+- pyyaml              >=5.4.1       `pip install pyyaml`
+- scipy               >=1.7.0       `pip install scipy`
+- tqdm                >=4.61.2      `pip install tqdm`
 
 #### Optional
 
-- matplotlib          3.4.2       `pip install matplotlib`
-- pytest              6.2.4       `pip install pytest`
-
-### Method 1 
+- matplotlib          >=3.4.2       `pip install matplotlib`
+- pytest              >=6.2.4       `pip install pytest`
 
-> This method only supports the `eam`, `eam/fs` and `eam/alloy` pair styles. However, direct free energy calculations for solid state can be carried out for any pair style using this installation.
+### Using a conda environment
 
 It is **strongly** recommended to install and use `calphy` within a conda environment. To see how you can install conda see [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).
 
 Once a conda distribution is available, the following steps will help set up an environment to use `calphy`. First step is to clone the repository.
 
 ```
-git clone https://git.noc.ruhr-uni-bochum.de/atomicclusterexpansion/calphy.git
+git clone https://github.com/ICAMS/calphy.git
 ```
 
 After cloning, an environment can be created from the included file-
@@ -48,6 +49,7 @@ cd calphy
 conda env create -f environment.yml
 ```
 
+Note that the conda-forge distribution of LAMMPS will be automatically installed. Alternatively, you can use an existing version of LAMMPS (compiled as library). If a LAMMPS distribution need not be installed, use the  `calphy/environment-nolammps.yml` file instead to create the environment.
 This will install the necessary packages and create an environment called calphy. It can be activated by,
 
 ```
@@ -57,150 +59,8 @@ conda activate calphy
 then, install `calphy` using,
 
 ```
-python setup.py install --user
+python setup.py install
 ```
 The environment is now set up to run calphy.
 
-### Method 2
-
-> This method supports `pace` pair style [1]. Additionally it can also be used if a custom version of LAMMPS is required. Drect free energy calculations for solid state can be carried out for any pair style using this installation.
-
-> **NOTE**: 08 July 2021: The upcoming release of [LAMMPS](https://github.com/lammps/lammps/releases) will significantly change the compilation procedure and render the below information outdated.
-
-
-For using with pair style PACE, the LAMMPS distribution has to be compiled manually:
-
-```
-git clone https://github.com/ICAMS/calphy.git
-conda env create -f calphy/environment-nolammps.yml
-```
-
-Now proceed with LAMMPS installation
-
-```
-wget https://github.com/lammps/lammps/archive/refs/tags/patch_27May2021.tar.gz
-tar -xvf patch_27May2021.tar.gz
-cd lammps-patch_27May2021
-mkdir build_lib
-cd build_lib
-cmake -D BUILD_LIB=ON -D BUILD_SHARED_LIBS=ON -D BUILD_MPI=ON -D PKG_MANYBODY=ON -D PKG_USER-MISC=ON -D PKG_USER-PACE=ON ../cmake
-make 
-cp liblammps${SHLIB_EXT}* ../src
-```
-
-Now the python wrapper can be installed:
-
-```
-cd ../src
-make install-python 
-```
-
-In the case of a conda environment, the following commands can be used to copy the compiled libraries to an accessible path:
-
-```
-mkdir -p $CONDA_PREFIX/include/lammps
-cp library.h $CONDA_PREFIX/include/lammps
-cp liblammps${SHLIB_EXT}* $CONDA_PREFIX/lib/
-```
-
-The combined libraries **should be available** on the system or the environment paths. Please see [here](https://lammps.sandia.gov/doc/Python_install.html) for more details. 
-
-Once LAMMPS is compiled and the libraries are available in an accessible location, the following commands can be used within python to test the installation:
-
-```
-from lammps import lammps
-lmp = lammps()
-```
-
-Now, we install `pylammpsmpi` using,
-
-```
-pip install pylammpsmpi
-```
-
-and finally `calphy`:
-
-```
-cd calphy
-python setup.py install --user
-```
-
-### Method 3
-
-> This method supports adp, meam, snap, sw, tersoff, tersoff/mod and tersoff/modc pair styles. Additionally it can also be used if a custom version of LAMMPS is required. Drect free energy calculations for solid state can be carried out for any pair style using this installation.
-
-> **NOTE**: 08 July 2021: The upcoming release of [LAMMPS](https://github.com/lammps/lammps/releases) will significantly change the compilation procedure and render the below information outdated.
-
-```
-git clone https://github.com/ICAMS/calphy.git
-conda env create -f calphy/environment-nolammps.yml
-```
-
-Now download LAMMPS,
-
-```
-wget https://github.com/lammps/lammps/archive/refs/tags/patch_27May2021.tar.gz
-tar -xvf patch_27May2021.tar.gz
-```
-
-Get the modified pair styles
-
-```
-git clone https://github.com/srmnitc/lammps-calphy.git
-```
-
-The cloned repository contains the necessary files for pair styles. For example, to use sw pair style, replace the original LAMMPS files with the modified ones:
-
-```
-cp lammps-calphy/src/MANYBODY/pair_sw.* lammps-patch_27May2021/src/MANYBODY/
-```
-
-After copying the necessary files, LAMMPS can be installed:
-
-```
-cd lammps-patch_27May2021
-mkdir build_lib
-cd build_lib
-cmake -D BUILD_LIB=ON -D BUILD_SHARED_LIBS=ON -D BUILD_MPI=ON -D PKG_MANYBODY=ON -D PKG_USER-MISC=ON ../cmake
-make
-cp liblammps${SHLIB_EXT}* ../src
-```
-
-Now the python wrapper can be installed:
-
-```
-cd ../src
-make install-python 
-```
-
-In the case of a conda environment, the following commands can be used to copy the compiled libraries to an accessible path:
-
-```
-mkdir -p $CONDA_PREFIX/include/lammps
-cp library.h $CONDA_PREFIX/include/lammps
-cp liblammps${SHLIB_EXT}* $CONDA_PREFIX/lib/
-```
-
-The combined libraries **should be available** on the system or the environment paths. Please see [here](https://lammps.sandia.gov/doc/Python_install.html) for more details. 
-
-Once LAMMPS is compiled and the libraries are available in an accessible location, the following commands can be used within python to test the installation:
-
-```
-from lammps import lammps
-lmp = lammps()
-```
-
-Now, we install `pylammpsmpi` using,
-
-```
-pip install pylammpsmpi
-```
-
-and finally `calphy`:
-
-```
-cd calphy
-python setup.py install --user
-```
-
-[1]  Lysogorskiy, Yury, Cas van der Oord, Anton Bochkarev, Sarath Menon, Matteo Rinaldi, Thomas Hammerschmidt, Matous Mrovec, et al. “Performant Implementation of the Atomic Cluster Expansion (PACE) and Application to Copper and Silicon.” Npj Computational Materials 7, no. 1 (December 2021): 97. https://doi.org/10.1038/s41524-021-00559-9.
+### 
\ No newline at end of file
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 0c5723e..fc5f638 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -6,6 +6,9 @@
 calphy
 ======
 
+calphy is a Python library and command line application which can be used for automated calculation of free energies through molecular dynamics calculations.
+
+
 .. toctree::
    gettingstarted	
 

From 775fb769e442f815664f9e38e88e4f0ab93a6be5 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Wed, 3 Nov 2021 10:53:06 +0100
Subject: [PATCH 09/11] update docs

---
 docs/source/gettingstarted.md | 124 ++++++++++++++++++++++++++++++----
 1 file changed, 110 insertions(+), 14 deletions(-)

diff --git a/docs/source/gettingstarted.md b/docs/source/gettingstarted.md
index 6474d35..27f96a7 100644
--- a/docs/source/gettingstarted.md
+++ b/docs/source/gettingstarted.md
@@ -1,6 +1,17 @@
 # calphy
 
-Python library and command line tool for calculation of free energies.
+`calphy`(pronounced _cal-phee_) is a Python library and command line tool for calculation of free energies. It uses [LAMMPS](https://www.lammps.org/) as the molecular dynamics driver to enable calculation of free energies using thermodynamic integration in a completely automated and efficient manner. The various methods that calphy can perform are:
+
+- $F(V_i,T_i)$ and $G(P_i,T_i)$ for both solid and liquid phases at the given thermodynamic conditions using [non-equilibrium Hamiltonian interpolation](https://linkinghub.elsevier.com/retrieve/pii/S0927025615007089).
+- $F(T_i \to T_f)$ and $G(T_i \to T_f)$, temperature dependence of Gibbs and Helmholtz free energies using the [reversible scaling](https://link.aps.org/doi/10.1103/PhysRevLett.83.3973) approach.
+- Calculation of solid-solid or solid-liquid phase transition temperatures.
+- Calculation of coexistence lines using [dynamic Clausius-Clapeyron integration](http://aip.scitation.org/doi/10.1063/1.1420486).
+- Calculation of specific heat $c_P(T)$ as a function of temperature.
+- Calculation of $F(x, T)$ and $G(x, T)$ for multicomponent systems using [alchemical transformations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
+- [Upsampling calculations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
+
+Calphy works with all [interatomic potentials implemented in LAMMPS](https://docs.lammps.org/pairs.html) and can obtain reliable results with low error bars in as low as 50 ps of simulation time with less than 3000 atoms. More information about the methods in calphy can be found in the [associated publication](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
+
 
 ## Installation
 
@@ -16,21 +27,17 @@ calphy can be installed directly using [Conda](https://docs.conda.io/en/latest/)
 conda install -c conda-forge calphy
 ```
 
+### Installation from the repository
 
-### Dependencies
+calphy can be built from the repository by-
 
-- lammps                            `conda install -c conda-forge lammps`
-- mendeleev           >=0.7.0       `pip install mendeleev`
-- pylammpsmpi         >=0.0.8       `pip install pylammpsmpi`
-- pyscal              >=2.10.14     `pip install git+https://github.com/srmnitc/pyscal`
-- pyyaml              >=5.4.1       `pip install pyyaml`
-- scipy               >=1.7.0       `pip install scipy`
-- tqdm                >=4.61.2      `pip install tqdm`
-
-#### Optional
+```
+git clone https://github.com/ICAMS/calphy.git
+cd calphy
+python setup.py install --user
+```
 
-- matplotlib          >=3.4.2       `pip install matplotlib`
-- pytest              >=6.2.4       `pip install pytest`
+Please note that the list of dependencies mentioned below has to installed manually by the user.
 
 ### Using a conda environment
 
@@ -63,4 +70,93 @@ python setup.py install
 ```
 The environment is now set up to run calphy.
 
-### 
\ No newline at end of file
+### Dependencies
+
+- lammps                            `conda install -c conda-forge lammps`
+- mendeleev           >=0.7.0       `pip install mendeleev`
+- pylammpsmpi         >=0.0.8       `pip install pylammpsmpi`
+- pyscal              >=2.10.14     `pip install git+https://github.com/srmnitc/pyscal`
+- pyyaml              >=5.4.1       `pip install pyyaml`
+- scipy               >=1.7.0       `pip install scipy`
+- tqdm                >=4.61.2      `pip install tqdm`
+
+#### Optional
+
+- matplotlib          >=3.4.2       `pip install matplotlib`
+- pytest              >=6.2.4       `pip install pytest`
+
+## About [LAMMPS](https://www.lammps.org/) for `calphy`
+
+calphy uses LAMMPS as the driver for molecular dynamics simulations. For calphy to work, LAMMPS needs to be compiled as a library along with the Python interface. The easiest way to do this is to install LAMMPS through the conda-forge channel using:
+
+```
+conda install -c conda-forge lammps
+```
+
+Alternatively, when interatomic potentials with special compilation needs are to be used, LAMMPS (Stable release 29 Sept 2021 and above) can be compiled manually using the following set of instructions:
+
+First step is to obtain the stable version from [here](https://github.com/lammps/lammps/archive/refs/tags/stable_29Sep2021.tar.gz) and extract the archive. From the extracted archive, the following steps, used in the [conda-forge recipe](https://github.com/conda-forge/lammps-feedstock/blob/master/recipe/build.sh) can be run:
+
+```
+mkdir build_lib
+cd build_lib
+cmake -D BUILD_LIB=ON -D BUILD_SHARED_LIBS=ON -D BUILD_MPI=ON -D PKG_MPIIO=ON -D LAMMPS_EXCEPTIONS=yes -D PKG_MANYBODY=ON -D PKG_MISC=ON -D PKG_MISC=ON -D PKG_EXTRA-COMPUTE=ON -D PKG_EXTRA-DUMP=ON -D PKG_EXTRA-FIX=ON -D PKG_EXTRA-PAIR=ON ../cmake
+make
+cp liblammps${SHLIB_EXT}* ../src 
+cd ../src
+make install-python 
+mkdir -p $PREFIX/include/lammps
+cp library.h $PREFIX/include/lammps
+cp liblammps${SHLIB_EXT}* "${PREFIX}"/lib/
+cd ..
+```
+
+The above commands only builds the [MANYBODY](https://docs.lammps.org/Packages_details.html#pkg-manybody) package. To use some of the other potentials, the following commands could be added to the `cmake` call.
+
+- `-D PKG_ML-PACE` for performant [Atomic Cluster Expansion](https://docs.lammps.org/Packages_details.html#pkg-ml-pace) potential.
+- `-D PKG_ML-SNAP=ON`for [SNAP potential](https://docs.lammps.org/Packages_details.html#pkg-ml-snap).
+- `-D PKG_MEAM=ON` for [MEAM potential](https://docs.lammps.org/Packages_details.html#meam-package).
+- `-D PKG_KIM=ON` for [KIM support](https://docs.lammps.org/Packages_details.html#pkg-kim).
+
+Now the python wrapper can be installed:
+
+```
+cd ../src
+make install-python
+```
+In the case of a conda environment, the following commands can be used to copy the compiled libraries to an accessible path:
+
+```
+mkdir -p $CONDA_PREFIX/include/lammps
+cp library.h $CONDA_PREFIX/include/lammps
+cp liblammps${SHLIB_EXT}* $CONDA_PREFIX/lib/
+```
+
+The combined libraries **should be available** on the system or the environment paths. Please see here for more details.
+
+Once LAMMPS is compiled and the libraries are available in an accessible location, the following commands can be used within python to test the installation:
+
+```
+from lammps import lammps
+lmp = lammps()
+```
+Now, we install pylammpsmpi using,
+
+```
+pip install pylammpsmpi
+```
+and finally calphy:
+
+```
+cd calphy
+python setup.py install --user
+```
+
+
+
+
+
+
+
+
+

From b7343511ad752d2e347fe4829884e878d8020240 Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Wed, 3 Nov 2021 10:54:08 +0100
Subject: [PATCH 10/11] update README

---
 README.md | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 86e02d9..48caed0 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,16 @@
 # calphy
 
-Python library and command line tool for calculation of free energies.
+`calphy`(pronounced _cal-phee_) is a Python library and command line tool for calculation of free energies. It uses [LAMMPS](https://www.lammps.org/) as the molecular dynamics driver to enable calculation of free energies using thermodynamic integration in a completely automated and efficient manner. The various methods that calphy can perform are:
+
+- $F(V_i,T_i)$ and $G(P_i,T_i)$ for both solid and liquid phases at the given thermodynamic conditions using [non-equilibrium Hamiltonian interpolation](https://linkinghub.elsevier.com/retrieve/pii/S0927025615007089).
+- $F(T_i \to T_f)$ and $G(T_i \to T_f)$, temperature dependence of Gibbs and Helmholtz free energies using the [reversible scaling](https://link.aps.org/doi/10.1103/PhysRevLett.83.3973) approach.
+- Calculation of solid-solid or solid-liquid phase transition temperatures.
+- Calculation of coexistence lines using [dynamic Clausius-Clapeyron integration](http://aip.scitation.org/doi/10.1063/1.1420486).
+- Calculation of specific heat $c_P(T)$ as a function of temperature.
+- Calculation of $F(x, T)$ and $G(x, T)$ for multicomponent systems using [alchemical transformations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
+- [Upsampling calculations](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
+
+Calphy works with all [interatomic potentials implemented in LAMMPS](https://docs.lammps.org/pairs.html) and can obtain reliable results with low error bars in as low as 50 ps of simulation time with less than 3000 atoms. More information about the methods in calphy can be found in the [associated publication](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801).
 
 ## Installation, examples and documentation
 
@@ -13,7 +23,7 @@ Python library and command line tool for calculation of free energies.
 ## Citing calphy
 
 If you find calphy useful, please consider citing:  
-Menon, Sarath, Yury Lysogorskiy, Jutta Rogal, and Ralf Drautz. 
+Menon, Sarath, Yury Lysogorskiy, Jutta Rogal, and Ralf Drautz.   
 [“Automated Free Energy Calculation from Atomistic Simulations.”](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.5.103801) 
 Physical Review Materials 5(10), 2021  
 DOI: 10.1103/PhysRevMaterials.5.103801  

From 9f1dba43d6c8d241d02e52c6d0ebe9f39eb9854c Mon Sep 17 00:00:00 2001
From: srmnitc <sarath.r.menon@gmail.com>
Date: Wed, 3 Nov 2021 10:54:43 +0100
Subject: [PATCH 11/11] =?UTF-8?q?Bump=20version:=200.5.8=20=E2=86=92=200.6?=
 =?UTF-8?q?.0?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 .bumpversion.cfg | 2 +-
 setup.py         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.bumpversion.cfg b/.bumpversion.cfg
index 8f60cdd..5f5fe49 100644
--- a/.bumpversion.cfg
+++ b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.8
+current_version = 0.6.0
 commit = True
 tag = True
 
diff --git a/setup.py b/setup.py
index a3f93c8..4e09f77 100644
--- a/setup.py
+++ b/setup.py
@@ -64,7 +64,7 @@
     test_suite='tests',
     tests_require=test_requirements,
     url='https://git.noc.ruhr-uni-bochum.de/atomicclusterexpansion/calphy',
-    version='0.5.8',
+    version='0.6.0',
     zip_safe=False,
     entry_points={
         'console_scripts': [